Nature , IF:49.962 , 2022 Jun doi: 10.1038/s41586-022-04883-y
Structures and mechanism of the plant PIN-FORMED auxin transporter.
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.; Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.; Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY, USA.; Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany. ulrich.hammes@tum.de.; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark. bpp@mbg.au.dk.
Auxins are hormones that have central roles and control nearly all aspects of growth and development in plants(1-3). The proteins in the PIN-FORMED (PIN) family (also known as the auxin efflux carrier family) are key participants in this process and control auxin export from the cytosol to the extracellular space(4-9). Owing to a lack of structural and biochemical data, the molecular mechanism of PIN-mediated auxin transport is not understood. Here we present biophysical analysis together with three structures of Arabidopsis thaliana PIN8: two outward-facing conformations with and without auxin, and one inward-facing conformation bound to the herbicide naphthylphthalamic acid. The structure forms a homodimer, with each monomer divided into a transport and scaffold domain with a clearly defined auxin binding site. Next to the binding site, a proline-proline crossover is a pivot point for structural changes associated with transport, which we show to be independent of proton and ion gradients and probably driven by the negative charge of the auxin. The structures and biochemical data reveal an elevator-type transport mechanism reminiscent of bile acid/sodium symporters, bicarbonate/sodium symporters and sodium/proton antiporters. Our results provide a comprehensive molecular model for auxin recognition and transport by PINs, link and expand on a well-known conceptual framework for transport, and explain a central mechanism of polar auxin transport, a core feature of plant physiology, growth and development.
PMID: 35768502
Trends Biotechnol , IF:19.536 , 2022 Jun doi: 10.1016/j.tibtech.2022.06.005
Dynamically regulating metabolic fluxes with synthetic metabolons.
Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany. Electronic address: YOZhang@mpimp-golm.mpg.de.; Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany. Electronic address: fernie@mpimp-golm.mpg.de.
Enzyme-enzyme assemblies commonly occur naturally, yet the factors that lead to their transient nature are not fully understood. Mitkas et al. have shown how clustered regularly interspaced short palindromic repeats (CRISPR) enzymes and RNA scaffolds allow synthetic enzyme complexes to be formed and disassembled as needed, providing powerful new tools for metabolic engineering.
PMID: 35753889
Trends Plant Sci , IF:18.313 , 2022 Jul doi: 10.1016/j.tplants.2022.06.002
Towards a hierarchical gene regulatory network underlying somatic embryogenesis.
National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; University of Chinese Academy of Sciences (UCAS), Shanghai 200032, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; ShanghaiTech University, Shanghai 200031, PR China. Electronic address: jwwang@sippe.ac.cn.
Genome-editing technologies have advanced in recent years but designing future crops remains limited by current methods of improving somatic embryogenesis (SE) capacity. In this Opinion, we provide an update on the molecular event by which the phytohormone auxin promotes the acquisition of plant cell totipotency through evoking massive changes in transcriptome and chromatin accessibility. We propose that the chromatin states and individual totipotency-related transcription factors (TFs) from disparate gene families organize into a hierarchical gene regulatory network underlying SE. We conclude with a discussion of the practical paths to probe the cellular origin of the somatic embryo and the epigenetic landscape of the totipotent cell state in the era of single-cell genomics.
PMID: 35810071
Nat Commun , IF:14.919 , 2022 Jul , V13 (1) : P4015 doi: 10.1038/s41467-022-31628-2
Regulation of AUXIN RESPONSE FACTOR condensation and nucleo-cytoplasmic partitioning.
Department of Biology, Duke University, Durham, NC, 27008, USA.; Center for Engineering MechanoBiology, Washington University, St. Louis, MO, 63130, USA.; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO, 63130, USA.; Department of Biology, Washington University, St. Louis, MO, 63130, USA.; Department of Biology, Duke University, Durham, NC, 27008, USA. lucia.strader@duke.edu.; Center for Engineering MechanoBiology, Washington University, St. Louis, MO, 63130, USA. lucia.strader@duke.edu.; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO, 63130, USA. lucia.strader@duke.edu.
Auxin critically regulates plant growth and development. Auxin-driven transcriptional responses are mediated through the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. ARF protein condensation attenuates ARF activity, resulting in dramatic shifts in the auxin transcriptional landscape. Here, we perform a forward genetics screen for ARF hypercondensation, identifying an F-box protein, which we named AUXIN RESPONSE FACTOR F-BOX1 (AFF1). Functional characterization of SCF(AFF1) revealed that this E3 ubiquitin ligase directly interacts with ARF19 and ARF7 to regulate their accumulation, condensation, and nucleo-cytoplasmic partitioning. Mutants defective in AFF1 display attenuated auxin responsiveness, and developmental defects, suggesting that SCF(AFF1) -mediated regulation of ARF protein drives aspects of auxin response and plant development.
PMID: 35817767
Nat Commun , IF:14.919 , 2022 Jul , V13 (1) : P3985 doi: 10.1038/s41467-022-31656-y
Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA. zliu@umd.edu.
The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is the induction of auxin synthesis in the endosperm, and the mobile auxin subsequently stimulates seedcoat and fruit development. However, the regulatory mechanism of auxin synthesis in the endosperm remains unknown. Here, we show that a type I MADS box gene AGL62 is required for the activation of auxin synthesis in the endosperm in both Fragaria vesca, a diploid strawberry, and in Arabidopsis. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis. In this work, we identify a key mechanism for auxin induction to mediate fertilization success, a finding broadly relevant to flowering plants.
PMID: 35810202
Sci Adv , IF:14.136 , 2022 Jun , V8 (25) : Peabm8791 doi: 10.1126/sciadv.abm8791
Phased small RNA-mediated systemic signaling in plants.
Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA.; College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.; Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA.
Systemic acquired resistance (SAR) involves the generation of systemically transported signal that arms distal plant parts against secondary infections. We show that two phased 21-nucleotide (nt) trans-acting small interfering RNA3a RNAs (tasi-RNA) derived from TAS3a and synthesized within 3 hours of pathogen infection are the early mobile signal in SAR. TAS3a undergoes alternate polyadenylation, resulting in the generation of 555- and 367-nt transcripts. The 555-nt transcripts likely serves as the sole precursor for tasi-RNAs D7 and D8, which cleave Auxin response factors (ARF) 2, 3, and 4 to induce SAR. Conversely, increased expression of ARF3 represses SAR. Knockout mutations in TAS3a or RNA silencing components required for tasi-RNA biogenesis compromise SAR without altering levels of known SAR-inducing chemicals. Both tasi-ARFs and the 367-nt transcripts are mobile and transported via plasmodesmata. Together, we show that tasi-ARFs are the early mobile signal in SAR.
PMID: 35749505
Sci Adv , IF:14.136 , 2022 Jun , V8 (23) : Peabn0368 doi: 10.1126/sciadv.abn0368
Coactivation of antagonistic genes stabilizes polarity patterning during shoot organogenesis.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.; Beijing International Center for Mathematical Research, Center for Quantitative Biology, Peking University, Beijing 100871, China.; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Center for Quantitative Biology, Peking University, Beijing 100871, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
Spatiotemporal patterns of gene expression are instrumental to morphogenesis. A stable pattern interface, often between reciprocal-inhibiting morphogens, must be robustly maintained after initial patterning cues diminish, organ growth, or organ geometry changes. In plants, floral and leaf primordia obtain the adaxial-abaxial pattern at the shoot apical meristem periphery. However, it is unknown how the pattern is maintained after primordia have left the shoot apex. Here, through a combination of computational simulations, time-lapse imaging, and genetic analysis, we propose a model in which auxin simultaneously promotes both adaxial and abaxial domains of expression. Furthermore, we identified multilevel feedback regulation of auxin signaling to refine the spatiotemporal patterns. Our results demonstrate that coactivation by auxin determines and stabilizes antagonistic adaxial-abaxial patterning during aerial organ formation.
PMID: 35675392
Trends Biochem Sci , IF:13.807 , 2022 Jul doi: 10.1016/j.tibs.2022.06.004
Intrinsic and extrinsic regulators of Aux/IAA protein degradation dynamics.
Department of Biology, Duke University, Durham, NC, USA.; Department of Biology, Duke University, Durham, NC, USA. Electronic address: lucia.strader@duke.edu.
The plant hormone auxin acts through regulated degradation of Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins to regulate transcriptional events. In this review, we examine the composition and function of each Aux/IAA structural motif. We then focus on recent characterization of Aux/IAA N-terminal disordered regions, formation of secondary structure within these disordered regions, and post-translational modifications (PTMs) that affect Aux/IAA function and stability. We propose how structural variations between Aux/IAA family members may be tuned for differential transcriptional repression and degradation dynamics.
PMID: 35817652
Mol Plant , IF:13.164 , 2022 Jun , V15 (6) : P973-990 doi: 10.1016/j.molp.2022.04.009
Coordination of plant growth and abiotic stress responses by tryptophan synthase beta subunit 1 through modulation of tryptophan and ABA homeostasis in Arabidopsis.
State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.; State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.; State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China. Electronic address: yingtlu@whu.edu.cn.
To adapt to changing environments, plants have evolved elaborate regulatory mechanisms balancing their growth with stress responses. It is currently unclear whether and how the tryptophan (Trp), the growth-related hormone auxin, and the stress hormone abscisic acid (ABA) are coordinated in this trade-off. Here, we show that tryptophan synthase beta subunit 1 (TSB1) is involved in the coordination of Trp and ABA, thereby affecting plant growth and abiotic stress responses. Plants experiencing high salinity or drought display reduced TSB1 expression, resulting in decreased Trp and auxin accumulation and thus reduced growth. In comparison with the wild type, amiR-TSB1 lines and TSB1 mutants exhibited repressed growth under non-stress conditions but had enhanced ABA accumulation and stress tolerance when subjected to salt or drought stress. Furthermore, we found that TSB1 interacts with and inhibits beta-glucosidase 1 (BG1), which hydrolyses glucose-conjugated ABA into active ABA. Mutation of BG1 in the amiR-TSB1 lines compromised their increased ABA accumulation and enhanced stress tolerance. Moreover, stress-induced H2O2 disrupted the interaction between TSB1 and BG1 by sulfenylating cysteine-308 of TSB1, relieving the TSB1-mediated inhibition of BG1 activity. Taken together, we revealed that TSB1 serves as a key coordinator of plant growth and stress responses by balancing Trp and ABA homeostasis.
PMID: 35488429
Plant Cell , IF:11.277 , 2022 Jun doi: 10.1093/plcell/koac175
From the archives: Polar auxin transport in nodule development, DNA replication timing, and developmentally light-regulated genes.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.; Center for Plant Systems Biology, VIB, Belgium.
PMID: 35770820
Plant Cell , IF:11.277 , 2022 Jun doi: 10.1093/plcell/koac193
Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors.
Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.; Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China.; Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China.; State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
Moso bamboo (Phyllostachys edulis) shows remarkably rapid growth (114.5 cm/d), but the underlying biological mechanisms remain unclear. After examining >12,750 internodes from >510 culms from 17 Moso populations, we identified internode 18 as a representative internode for rapid growth. This internode includes a 2-cm cell division zone, a cell elongation zone up to 12-cm, and a secondary cell wall (SCW) thickening zone. These zones elongated 11.8 cm, produced approximately 570,000,000 cells, and deposited approximately 28 mg g-1 dry weight (DW) lignin and approximately 44 mg g-1 DW cellulose daily, far exceeding vegetative growth observed in other plants. We used anatomical, mathematical, physiological, and genomic data to characterize development and transcriptional networks during rapid growth in internode 18. Our results suggest that 1) gibberellin may directly trigger the rapid growth of Moso shoots, 2) decreased cytokinin and increased auxin accumulation may trigger cell division zone elongation, and 3) abscisic acid and mechanical pressure may stimulate rapid SCW thickening via MYB83L. We conclude that internode length involves a possible trade-off mediated by mechanical pressure caused by rapid growth, possibly influenced by environmental temperature and regulated by genes related to cell division and elongation. Our results provide insight into the rapid growth of Moso bamboo.
PMID: 35766883
Plant Cell , IF:11.277 , 2022 Jun doi: 10.1093/plcell/koac179
On the trail of auxin: reporters and sensors.
CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
The phytohormone auxin is a master regulator of plant growth and development in response to many endogenous and environmental signals. The underlying coordination of growth is mediated by the formation of auxin maxima and concentration gradients. The visualization of auxin dynamics and distribution can therefore provide essential information to increase our understanding of the mechanisms by which auxin orchestrates these growth and developmental processes. Several auxin reporters have been developed to better perceive the auxin distribution and signaling machinery in vivo. This review focuses on different types of auxin reporters and biosensors used to monitor auxin distribution and its dynamics, as well as auxin signaling, at the cellular and tissue levels in different plant species. We provide a brief history of each reporter and biosensor group and explain their principles and utilities.
PMID: 35708654
Plant Cell , IF:11.277 , 2022 Jun doi: 10.1093/plcell/koac177
The retrograde signalling regulator ANAC017 recruits the MKK9-MPK3/6, ethylene, and auxin signalling pathways to balance mitochondrial dysfunction with growth.
Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria 3086, Australia.; ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia.
In plant cells, mitochondria are ideally positioned to sense and balance changes in energy metabolism in response to changing environmental conditions. Retrograde signalling from mitochondria to the nucleus is crucial for adjusting the required transcriptional responses. We show that ANAC017, the master regulator of mitochondrial stress, directly recruits a signalling cascade involving the plant hormones ethylene and auxin as well as the MAP KINASE KINASE (MKK) 9 - MAP KINASE (MPK) 3/6 pathway in Arabidopsis thaliana. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and overexpression demonstrated that ANAC017 directly regulates several genes of the ethylene and auxin pathways, including MKK9, 1-AMINO-CYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2 and YUCCA 5, in addition to genes encoding transcription factors regulating plant growth and stress responses such as BASIC REGION/LEUCINE ZIPPER MOTIF (bZIP) 60, bZIP53, ANAC081/ATAF2 and RADICAL-INDUCED CELL DEATH1. A time-resolved RNA-seq experiment established that ethylene signalling precedes the stimulation of auxin signalling in the mitochondrial stress response, with a large part of the transcriptional regulation dependent on ETHYLENE INSENSITIVE 3. These results were confirmed by mutant analyses. Our findings identify the molecular components controlled by ANAC017, which integrates the primary stress responses to mitochondrial dysfunction with whole plant growth via the activation of regulatory and partly antagonistic feedback loops.
PMID: 35708648
Plant Cell , IF:11.277 , 2022 Jul , V34 (7) : P2688-2707 doi: 10.1093/plcell/koac107
AUXIN RESPONSE FACTOR7 integrates gibberellin and auxin signaling via interactions between DELLA and AUX/IAA proteins to regulate cambial activity in poplar.
Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China.; School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia.; Department of Land, Air and Water Resources, University of California at Davis, Davis, California 95616, USA.; Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China.
Cambial development in the stems of perennial woody species is rigorously regulated by phytohormones. Auxin and gibberellin (GA) play crucial roles in stimulating cambial activity in poplar (Populus spp.). In this study, we show that the DELLA protein REPRESSOR of ga1-3 Like 1 (RGL1), AUXIN RESPONSE FACTOR 7 (ARF7), and Aux/INDOLE-3-ACETIC ACID 9 (IAA9) form a ternary complex that mediates crosstalk between the auxin and GA signaling pathways in poplar stems during cambial development. Biochemical analysis revealed that ARF7 physically interacts with RGL1 and IAA9 through distinct domains. The arf7 loss-of-function mutant showed markedly attenuated responses to auxin and GA, whereas transgenic poplar plants overexpressing ARF7 displayed strongly improved cambial activity. ARF7 directly binds to the promoter region of the cambial stem cell regulator WOX4 to modulate its expression, thus integrating auxin and GA signaling to regulate cambial activity. Furthermore, the direct activation of PIN-FORMED 1 expression by ARF7 in the RGL1-ARF7-IAA9 module increased GA-dependent cambial activity via polar auxin transport. Collectively, these findings reveal that the crosstalk between auxin and GA signaling mediated by the RGL1-ARF7-IAA9 module is crucial for the precise regulation of cambial development in poplar.
PMID: 35435234
Plant Cell , IF:11.277 , 2022 Jul , V34 (7) : P2518-2533 doi: 10.1093/plcell/koac080
Genetic control of branching patterns in grass inflorescences.
Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA.
Inflorescence branching in the grasses controls the number of florets and hence the number of seeds. Recent data on the underlying genetics come primarily from rice and maize, although new data are accumulating in other systems as well. This review focuses on a window in developmental time from the production of primary branches by the inflorescence meristem through to the production of glumes, which indicate the transition to producing a spikelet. Several major developmental regulatory modules appear to be conserved among most or all grasses. Placement and development of primary branches are controlled by conserved auxin regulatory genes. Subtending bracts are repressed by a network including TASSELSHEATH4, and axillary branch meristems are regulated largely by signaling centers that are adjacent to but not within the meristems themselves. Gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators extend along the inflorescence axis and the branches, governing the transition from production of branches to production of spikelets. The relative speed of this transition determines the extent of secondary and higher order branching. This inflorescence regulatory network is modified within individual species, particularly as regards formation of secondary branches. Differences between species are caused both by modifications of gene expression and regulators and by presence or absence of critical genes. The unified networks described here may provide tools for investigating orphan crops and grasses other than the well-studied maize and rice.
PMID: 35258600
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Aug , V119 (31) : Pe2122460119 doi: 10.1073/pnas.2122460119
Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses.
Institute of Science and Technology Austria, Klosterneuburg, 3400 Austria.; Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany, The Czech Academy of Sciences, Olomouc, 78371,Czech Republic.; Institute for Plant Sciences of Montpellier (IPSiM), CNRS, National Research Institute for Agriculture, Food and the Environment (INRAE), Institut Agro, Universite Montpellier, Montpellier, 34060, France.; Institut Jean-Pierre Bourgin, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Universite Paris-Saclay, Versailles, 78000, France.
Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.
PMID: 35878040
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Aug , V119 (31) : Pe2121058119 doi: 10.1073/pnas.2121058119
RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis.
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, 100193 Beijing, China.; Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.; Department of Biotechnology, College of Science, Taif University, 21944 Taif, Saudi Arabia.; Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences, 78371 Olomouc, Czech Republic.
Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379-402 (2020); Blackburn et al., Plant Physiol. 182, 1657-1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H(+) influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term.
PMID: 35878023
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Jul , V119 (30) : Pe2201072119 doi: 10.1073/pnas.2201072119
Ethylene inhibits rice root elongation in compacted soil via ABA- and auxin-mediated mechanisms.
Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.; Future Food Beacon and School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom.; Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacky University, CZ-78371 Olomouc, Czech Republic.; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.; Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, The Netherlands.; Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom.; Division of Plant Science and Technology and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211.; School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia.
Soil compaction represents a major agronomic challenge, inhibiting root elongation and impacting crop yields. Roots use ethylene to sense soil compaction as the restricted air space causes this gaseous signal to accumulate around root tips. Ethylene inhibits root elongation and promotes radial expansion in compacted soil, but its mechanistic basis remains unclear. Here, we report that ethylene promotes abscisic acid (ABA) biosynthesis and cortical cell radial expansion. Rice mutants of ABA biosynthetic genes had attenuated cortical cell radial expansion in compacted soil, leading to better penetration. Soil compaction-induced ethylene also up-regulates the auxin biosynthesis gene OsYUC8. Mutants lacking OsYUC8 are better able to penetrate compacted soil. The auxin influx transporter OsAUX1 is also required to mobilize auxin from the root tip to the elongation zone during a root compaction response. Moreover, osaux1 mutants penetrate compacted soil better than the wild-type roots and do not exhibit cortical cell radial expansion. We conclude that ethylene uses auxin and ABA as downstream signals to modify rice root cell elongation and radial expansion, causing root tips to swell and reducing their ability to penetrate compacted soil.
PMID: 35858424
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Jul , V119 (27) : Pe2202669119 doi: 10.1073/pnas.2202669119
The calcium signaling module CaM-IQM destabilizes IAA-ARF interaction to regulate callus and lateral root formation.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; National Center for Plant Gene Research, Beijing 100093, China.
Induction of a pluripotent cell mass, called callus, from detached organs is an initial step in in vitro plant regeneration, during which phytohormone auxin-induced ectopic activation of a root developmental program has been shown to be required for subsequent de novo regeneration of shoots and roots. However, whether other signals are involved in governing callus formation, and thus plant regeneration capability, remains largely unclear. Here, we report that the Arabidopsis calcium (Ca(2+)) signaling module CALMODULIN IQ-MOTIF CONTAINING PROTEIN (CaM-IQM) interacts with auxin signaling to regulate callus and lateral root formation. We show that disruption of IQMs or CaMs retards auxin-induced callus and lateral root formation by dampening auxin responsiveness, and that CaM-IQM complexes physically interact with the auxin signaling repressors INDOLE-3-ACETIC ACID INDUCIBLE (IAA) proteins in a Ca(2+)-dependent manner. We further provide evidence that the physical interaction of CaM6 with IAA19 destabilizes the repressive interaction of IAA19 with AUXIN RESPONSE FACTOR 7 (ARF7), and thus regulates auxin-induced callus formation. These findings not only define a critical role of CaM-IQM-mediated Ca(2+) signaling in callus and lateral root formation, but also provide insight into the interplay of Ca(2+) signaling and auxin actions during plant regeneration and development.
PMID: 35763576
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Jun , V119 (25) : Pe2203633119 doi: 10.1073/pnas.2203633119
Indole-3-pyruvic acid regulates TAA1 activity, which plays a key role in coordinating the two steps of auxin biosynthesis.
Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa 244-0813, Japan.; Western Region Agricultural Research Center (WARC), National Agriculture and Food Research Organization (NARO), Kagawa 765-8508, Japan.
Auxin biosynthesis involves two types of enzymes: the Trp aminotransferases (TAA/TARs) and the flavin monooxygenases (YUCCAs). This two-step pathway is highly conserved throughout the plant kingdom and is essential for almost all of the major developmental processes. Despite their importance, it is unclear how these enzymes are regulated and how their activities are coordinated. Here, we show that TAA1/TARs are regulated by their product indole-3-pyruvic acid (IPyA) (or its mimic KOK2099) via negative feedback regulation in Arabidopsis thaliana. This regulatory system also functions in rice and tomato. This negative feedback regulation appears to be achieved by both the reversibility of Trp aminotransferase activity and the competitive inhibition of TAA1 activity by IPyA. The Km value of IPyA is 0.7 microM, and that of Trp is 43.6 microM; this allows IPyA to be maintained at low levels and prevents unfavorable nonenzymatic indole-3-acetic acid (IAA) formation from IPyA in vivo. Thus, IPyA levels are maintained by the push (by TAA1/TARs) and pull (by YUCCAs) of the two biosynthetic enzymes, in which TAA1 plays a key role in preventing the over- or under-accumulation of IPyA. TAA1 prefer Ala among various amino acid substrates in the reverse reaction of auxin biosynthesis, allowing TAA1 to show specificity for converting Trp and pyruvate to IPyA and Ala, and the reverse reaction.
PMID: 35696560
Curr Biol , IF:10.834 , 2022 Jul doi: 10.1016/j.cub.2022.06.064
Apical dominance control by TAR-YUC-mediated auxin biosynthesis is a deep homology of land plants.
Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, 750 07 Uppsala, Sweden.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon 69007, France; Experimental Biology Research Group, Institute of Biology, Faculty of Sciences, University of Neuchatel, 2000 Neuchatel, Switzerland.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon 69007, France; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Universite Paris-Saclay, 78000 Versailles, France.; Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.; Universite Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; Universite de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon 69007, France. Electronic address: yoan.coudert@cnrs.fr.
A key aim in biology is to identify which genetic changes contributed to the evolution of form through time. Apical dominance, the inhibitory effect exerted by shoot apices on the initiation or outgrowth of distant lateral buds, is a major regulatory mechanism of plant form.(1) Nearly a century of studies in the sporophyte of flowering plants have established the phytohormone auxin as a front-runner in the search for key factors controlling apical dominance,(2)(,)(3) identifying critical roles for long-range polar auxin transport and local auxin biosynthesis in modulating shoot branching.(4-10) A capacity for lateral branching evolved by convergence in the gametophytic shoot of mosses and primed its diversification;(11) however, polar auxin transport is relatively unimportant in this developmental process,(12) the contribution of auxin biosynthesis genes has not been assessed, and more generally, the extent of conservation in apical dominance regulation within the land plants remains largely unknown. To fill this knowledge gap, we sought to identify genetic determinants of apical dominance in the moss Physcomitrium patens. Here, we show that leafy shoot apex decapitation releases apical dominance through massive and rapid transcriptional reprogramming of auxin-responsive genes and altering auxin biosynthesis gene activity. We pinpoint a subset of P. patens TRYPTOPHAN AMINO-TRANSFERASE (TAR) and YUCCA FLAVIN MONOOXYGENASE-LIKE (YUC) auxin biosynthesis genes expressed in the main and lateral shoot apices and show that they are essential for coordinating branch initiation and outgrowth. Our results demonstrate that local auxin biosynthesis acts as a pivotal regulator of apical dominance in moss and constitutes a shared mechanism underpinning shoot architecture control in land plants.
PMID: 35841890
J Hazard Mater , IF:10.588 , 2022 Jul , V433 : P128769 doi: 10.1016/j.jhazmat.2022.128769
LncRNA PMAT-PtoMYB46 module represses PtoMATE and PtoARF2 promoting Pb(2+) uptake and plant growth in poplar.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China; School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, PR China.; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China.; Linnean Center for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Box 7080, SE-750 07 Uppsala, Sweden.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umea, Sweden.; Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China; School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, PR China. Electronic address: DeqiangZhang@bjfu.edu.cn.
Lead (Pb(2+)) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb(2+) uptake in woody plants remains unclear. Here, we identified 226 Pb(2+)-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb(2+)-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb(2+) uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT-PtoMYB46-PtoMATE-PtoARF2 regulatory module control Pb(2+) tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb(2+) in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.
PMID: 35364535
New Phytol , IF:10.151 , 2022 Jul doi: 10.1111/nph.18381
The Arabidopsis IDD14 transcription factor interacts with bZIP-type ABFs/AREBs and cooperatively regulates ABA-mediated drought tolerance.
School of Life Sciences, Qilu Normal University, Jinan, 250200, China.; School of Life Sciences, Shandong Normal University, Jinan, 250014, China.; State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai, 200438, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
The IDD transcription factors mediate various aspects of plant growth and development. We previously reported that an Arabidopsis IDD subfamily regulates spatial auxin accumulation and thus organ morphogenesis and gravitropic responses. However, its functions in stress responses are not well defined. Here, we use a combination of physiological, biochemical, molecular, and genetic approaches to provide evidence that the IDD14 cooperates with bZIP-type binding factors/AREB-binding proteins (ABFs/AREBs) in ABA-mediated drought tolerance. idd14-1D, a gain-of-function mutant of IDD14, exhibits decreased leaf water loss and improved drought tolerance, whereas inactivation of IDD14 in idd14-1 results in increased transpiration and reduced drought tolerance. Altered IDD14 expression affects ABA sensitivity and ABA-mediated stomatal closure. IDD14 can physically interact with ABF1-4 and subsequently promote their transcriptional activities. Moreover, ectopic expression and mutation of ABFs could suppress and enhance plant sensitivity to drought stress in the idd14-1 mutant, respectively. Our results demonstrate that IDD14 forms a functional complex with ABFs and positively regulates drought-stress responses, thus revealing a previously unidentified role of IDD14 in ABA signaling and drought responses.
PMID: 35842794
New Phytol , IF:10.151 , 2022 Jun doi: 10.1111/nph.18317
miR169o and ZmNF-YA13 act in concert to coordinate the expression of ZmYUC1 that determines seed size and weight in maize kernels.
Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China.; National Nanfan Research Institute (Sanya), 572022, Sanya, Hainan, China.; National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, 100039, Beijing, China.
MicroRNAs (miRNAs) play key regulatory roles in seed development and emerge as new key targets for engineering grain size and yield. The Zma-miRNA169 family is highly expressed during maize seed development, but its functional roles in seed development remain elusive. Here, we generated zma-miR169o and ZmNF-YA13 transgenic plants. Phenotypic and genetic analyses were performed on these lines. Seed development and auxins contents were investigated. Overexpression of maize miRNA zma-miR169o increases seed size and weight, whereas the opposite is true when its expression is suppressed. Further studies revealed that zma-miR169 acts by negatively regulating its target gene, a transcription factor ZmNF-YA13 that also plays a key role in determining seed size. We demonstrate that ZmNF-YA13 regulates the expression of the auxin biosynthetic gene ZmYUC1, which modulates auxin levels in the early developing seeds and determines the number of endosperm cells, thereby governing maize seed size and ultimately yield. Overall, our present study has identified zma-miR169o and ZmNF-YA13 that form a functional module regulating auxin accumulation in maize seeds and playing an important role in determining maize seed size and yield, providing a set of novel molecular tools for yield improvement in molecular breeding and genetic engineering.
PMID: 35713356
New Phytol , IF:10.151 , 2022 Jul , V235 (2) : P402-419 doi: 10.1111/nph.18159
Auxin response factors are keys to the many auxin doors.
Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France.; Laboratoire de Reproduction et Developpement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Univ. Lyon, Lyon, France.
In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.
PMID: 35434800
New Phytol , IF:10.151 , 2022 Jul , V235 (1) : P292-305 doi: 10.1111/nph.18128
Arbuscular mycorrhizal symbiosis enhances tomato lateral root formation by modulating CEP2 peptide expression.
Institute of Plant Biology, Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
Plant lateral root (LR) growth usually is stimulated by arbuscular mycorrhizal (AM) symbiosis. However, the molecular mechanism is still unclear. We used gene expression analysis, peptide treatment and virus-induced gene alteration assays to demonstrate that C-terminally encoded peptide (CEP2) expression in tomato was downregulated during AM symbiosis to mitigate its negative effect on LR formation through an auxin-related pathway. We showed that enhanced LR density and downregulated CEP2 expression were observed during mycorrhizal symbiosis. Synthetic CEP2 peptide treatment reduced LR density and impaired the expression of genes involved in indole-3-butyric acid (IBA, the precursor of IAA) to IAA conversion, auxin polar transport and the LR-related signaling pathway; however, application of IBA or synthetic auxin 1-naphthaleneacetic acid (NAA) to the roots may rescue both defective LR formation and reduced gene expression. CEP receptor 1 (CEPR1) might be the receptor of CEP2 because its knockdown plants did not respond to CEP2 treatment. Most importantly, the LR density of CEP2 overexpression or knockdown plants could not be further increased by AM inoculation, suggesting that CEP2 was critical for AM-induced LR formation. These results indicated that AM symbiosis may regulate root development by modulating CEP2, which affects the auxin-related pathway.
PMID: 35358343
New Phytol , IF:10.151 , 2022 Jul , V235 (1) : P263-275 doi: 10.1111/nph.18114
Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit.
Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, 901 83, Umea, Sweden.; Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 27, Olomouc, Czech Republic.; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.
PMID: 35322877
New Phytol , IF:10.151 , 2022 Jul , V235 (1) : P356-371 doi: 10.1111/nph.18111
MicroRNA172 controls inflorescence meristem size through regulation of APETALA2 in Arabidopsis.
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany.; Institute of Systems, Integrative, and Molecular Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
The APETALA2 (AP2) transcription factor regulates flower development, floral transition and shoot apical meristem (SAM) maintenance in Arabidopsis. AP2 is also regulated at the post-transcriptional level by microRNA172 (miR172), but the contribution of this to SAM maintenance is poorly understood. We generated transgenic plants carrying a form of AP2 that is resistant to miR172 (rAP2) or carrying a wild-type AP2 susceptible to miR172. Phenotypic and genetic analyses were performed on these lines and mir172 mutants to study the role of AP2 regulation by miR172 on meristem size and the rate of flower production. We found that rAP2 enlarges the inflorescence meristem by increasing cell size and cell number. Misexpression of rAP2 from heterologous promoters showed that AP2 acts in the central zone (CZ) and organizing center (OC) to increase SAM size. Furthermore, we found that AP2 is negatively regulated by AUXIN RESPONSE FACTOR 3 (ARF3). However, genetic analyses indicated that ARF3 also influences SAM size and flower production rate independently of AP2. The study identifies miR172/AP2 as a regulatory module controlling inflorescence meristem size and suggests that transcriptional regulation of AP2 by ARF3 fine-tunes SAM size determination.
PMID: 35318684
New Phytol , IF:10.151 , 2022 Jul , V235 (1) : P126-140 doi: 10.1111/nph.18110
KAI2 regulates seedling development by mediating light-induced remodelling of auxin transport.
School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.; Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umea, Sweden.; Sainsbury Laboratory Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK.; Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354, Freising, Germany.; Genetics, Faculty of Biology, LMU Munich, Grosshaderner St. 4, 82152, Martinsried, Germany.
Photomorphogenic remodelling of seedling growth is a key developmental transition in the plant life cycle. The alpha/beta-hydrolase signalling protein KARRIKIN-INSENSITIVE2 (KAI2), a close homologue of the strigolactone receptor DWARF14 (D14), is involved in this process, but it is unclear how the effects of KAI2 on development are mediated. Here, using a combination of physiological, pharmacological, genetic and imaging approaches in Arabidopsis thaliana (Heynh.) we show that kai2 phenotypes arise because of a failure to downregulate auxin transport from the seedling shoot apex towards the root system, rather than a failure to respond to light per se. We demonstrate that KAI2 controls the light-induced remodelling of the PIN-mediated auxin transport system in seedlings, promoting a reduction in PIN7 abundance in older tissues, and an increase of PIN1/PIN2 abundance in the root meristem. We show that removing PIN3, PIN4 and PIN7 from kai2 mutants, or pharmacological inhibition of auxin transport and synthesis, is sufficient to suppress most kai2 seedling phenotypes. We conclude that KAI2 regulates seedling morphogenesis by its effects on the auxin transport system. We propose that KAI2 is not required for the light-mediated changes in PIN gene expression but is required for the appropriate changes in PIN protein abundance within cells.
PMID: 35313031
Plant Physiol , IF:8.34 , 2022 Jul doi: 10.1093/plphys/kiac332
Class I TCP transcription factor AtTCP8 modulates key brassinosteroid-responsive genes.
Department of Biological Sciences, Butler University, Indianapolis, Indiana, United States of America.; Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America.; Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America.; Department of Biology, Marian University, Indianapolis, Indiana, United States of America.
The plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor family is most closely associated with regulating plant developmental programs. Recently, TCPs were also shown to mediate host immune signaling, both as targets of pathogen virulence factors and as regulators of plant defense genes. However, comprehensive characterization of TCP gene targets is still lacking. Loss of function of the class I TCP gene AtTCP8 attenuates early immune signaling and, when combined with mutations in AtTCP14 and AtTCP15, additional layers of defense signaling in Arabidopsis (Arabidopsis thaliana). Here, we focus on TCP8, the most poorly characterized of the three to date. We used chromatin immunoprecipitation and RNA-sequencing to identify TCP8-bound gene promoters and differentially regulated genes in the tcp8 mutant; these data sets were heavily enriched in signaling components for multiple phytohormone pathways, including brassinosteroids (BRs), auxin, and jasmonic acid. Using BR signaling as a representative example, we showed that TCP8 directly binds and activates the promoters of the key BR transcriptional regulatory genes BRASSINAZOLE-RESISTANT1 (BZR1) and BRASSINAZOLE-RESISTANT2 (BZR2/BES1). Furthermore, tcp8 mutant seedlings exhibited altered BR-responsive growth patterns and complementary reductions in BZR2 transcript levels, while TCP8 protein demonstrated BR-responsive changes in subnuclear localization and transcriptional activity. We conclude that one explanation for the substantial targeting of TCP8 alongside other TCP family members by pathogen effectors may lie in its role as a modulator of BR and other plant hormone signaling pathways.
PMID: 35866682
Plant Physiol , IF:8.34 , 2022 Jun doi: 10.1093/plphys/kiac288
Initiation of aboveground organ primordia depends on combined action of auxin, ERECTA family genes, and PINOID.
Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.; UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee, USA.
Leaves and flowers are produced by the shoot apical meristem (SAM) at a certain distance from its center, a process that requires the hormone auxin. The amount of auxin and the pattern of its distribution in the initiation zone determine the size and spatial arrangement of organ primordia. Auxin gradients in the SAM are formed by PIN-FORMED (PIN) auxin efflux carriers whose polar localization in the plasma membrane depends on the protein kinase PINOID (PID). Previous work determined that ERECTA (ER) family genes (ERfs) control initiation of leaves. ERfs are plasma membrane receptors that enable cell-to-cell communication by sensing extracellular small proteins from the EPIDERMAL PATTERNING FACTOR/EPF-LIKE (EPF/EPFL) family. Here, we investigated whether ERfs regulate initiation of organs by altering auxin distribution or signaling in Arabidopsis (Arabidopsis thaliana). Genetic and pharmacological data suggested that ERfs do not regulate organogenesis through PINs while transcriptomics data showed ERfs do not alter primary transcriptional responses to auxin. Our results indicated that in the absence of ERf signaling the peripheral zone cells inefficiently initiate leaves in response to auxin signals and that increased accumulation of auxin in the er erecta-like1 (erl1) erl2 SAM can partially rescue organ initiation defects. We propose that both auxin and ERfs are essential for leaf initiation and that they have common downstream targets. Genetic data also indicated that the role of PID in initiation of cotyledons and leaves cannot be attributed solely to regulation of PIN polarity, and PID is likely to have other functions in addition to regulation of auxin distribution.
PMID: 35703946
Plant Physiol , IF:8.34 , 2022 Jun doi: 10.1093/plphys/kiac266
The Brassicaceae Genome Resource (TBGR): a comprehensive genome platform for Brassicaceae plants.
School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China.; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.; Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
The Brassicaceae is an important plant family. We built a user-friendly, web-based, comparative, and functional genomic database, The Brassicaceae Genome Resource (TBGR, http://www.tbgr.org.cn), based on 82 released genomes from 27 Brassicaceae species. The TBGR database contains a large number of important functional genes, including 4,096 glucosinolate genes, 6,625 auxin genes, 13,805 flowering genes, 36,632 resistance genes, 1,939 anthocyanin genes, and 1,231 m6A genes. A total of 1,174,049 specific guide sequences for CRISPR and 5,856,479 transposable elements were detected in Brassicaceae. TBGR also provides information on synteny, duplication, and orthologs for 27 Brassicaceae species. The TBGR database contains 1,183,851 gene annotations obtained using the TrEMBL, Swiss-Prot, Nr, GO, and Pfam databases. The BLAST, Synteny, Primer Design, Seq_fetch, and JBrowse tools are provided to help users perform comparative genomic analyses. All the genome assemblies, gene models, annotations, and bioinformatics results can be easily downloaded from the TBGR database. We plan to improve and continuously update the database with newly assembled genomes and comparative genomic studies. We expect the TBGR database to become a key resource for the study of the Brassicaceae.
PMID: 35670735
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1553-1569 doi: 10.1093/plphys/kiac158
SPATULA and ALCATRAZ confer female sterility and fruit cavity via mediating pistil development in cucumber.
Department of Vegetable Sciences, State Key Laboratories of Agrobiotechnology, Joint International Research Laboratory of Crop Molecular Breeding, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.; College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.
Fruits and seeds play essential roles in plant sexual reproduction and the human diet. Successful fertilization involves delivery of sperm in the pollen tube to the egg cell within the ovary along the transmitting tract (TT). Fruit cavity is an undesirable trait directly affecting cucumber (Cucumis sativus) commercial value. However, the regulatory genes underlying fruit cavity formation and female fertility determination remain unknown in crops. Here, we characterized a basic Helix-Loop-Helix (bHLH) gene C. sativus SPATULA (CsSPT) and its redundant and divergent function with ALCATRAZ (CsALC) in cucumber. CsSPT transcripts were enriched in reproductive organs. Mutation of CsSPT resulted in 60% reduction in female fertility, with seed produced only in the upper portion of fruits. Csspt Csalc mutants displayed complete loss of female fertility and fruit cavity due to carpel separation. Further examination showed that stigmas in the double mutant turned outward with defective papillae identity, and extracellular matrix contents in the abnormal TT were dramatically reduced, which resulted in no path for pollen tube extension and no ovules fertilized. Biochemical and transcriptome analysis showed that CsSPT and CsALC act in homodimers and heterodimers to confer fruit cavity and female sterility by mediating genes involved in TT development, auxin-mediated signaling, and cell wall organization in cucumber.
PMID: 35389464
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1757-1773 doi: 10.1093/plphys/kiac157
The interplay of auxin and brassinosteroid signaling tunes root growth under low and different nitrogen forms.
National Institute of Plant Genome Research, New Delhi, 110067, India.
The coordinated signaling activity of auxin and brassinosteroids (BRs) is critical for optimal plant growth and development. Nutrient-derived signals regulate root growth by modulating the levels and spatial distribution of growth hormones to optimize nutrient uptake and assimilation. However, the effect of the interaction of these two hormones and their signaling on root plasticity during low and differential availability of nitrogen (N) forms (NH4+/NO3-) remains elusive. We demonstrate that root elongation under low N (LN) is an outcome of the interdependent activity of auxin and BR signaling pathways in Arabidopsis (Arabidopsis thaliana). LN promotes root elongation by increasing BR-induced auxin transport activity in the roots. Increased nuclear auxin signaling and its transport efficiency have a distinct impact on root elongation under LN conditions. High auxin levels reversibly inhibit BR signaling via BRI1 KINASE INHIBITOR1. Using the tissue-specific approach, we show that BR signaling from root vasculature (stele) tissues is sufficient to promote cell elongation and, hence, root growth under LN condition. Further, we show that N form-defined root growth attenuation or enhancement depends on the fine balance of BR and auxin signaling activity. NH4+ as a sole N source represses BR signaling and response, which in turn inhibits auxin response and transport, whereas NO3- promotes root elongation in a BR signaling-dependent manner. In this study, we demonstrate the interplay of auxin and BR-derived signals, which are critical for root growth in a heterogeneous N environment and appear essential for root N foraging response and adaptation.
PMID: 35377445
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1728-1740 doi: 10.1093/plphys/kiac150
APYRASE1/2 mediate red light-induced de-etiolation growth in Arabidopsis seedlings.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
In etiolated seedlings, red light (R) activates phytochrome and initiates signals that generate major changes at molecular and physiological levels. These changes include inhibition of hypocotyl growth and promotion of the growth of primary roots, apical hooks, and cotyledons. An earlier report showed that the sharp decrease in hypocotyl growth rapidly induced by R was accompanied by an equally rapid decrease in the transcript and protein levels of two closely related apyrases (APYs; nucleoside triphosphate-diphosphohydrolases) in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, enzymes whose expression alters auxin transport and growth in seedlings. Here, we report that single knockouts of either APY inhibit R-induced promotion of the growth of primary roots, apical hooks, and cotyledons, and RNAi-induced suppression of APY1 expression in the background of apy2 inhibits R-induced apical hook opening. When R-irradiated primary roots and apical hook-cotyledons began to show a gradual increase in their growth relative to dark controls, they concurrently showed increased levels of APY protein, but in hook-cotyledon tissue, this occurred without parallel increases in their transcripts. In wild-type seedlings whose root growth is suppressed by the photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, the R-induced increased APY expression in roots was also inhibited. In unirradiated plants, the constitutive expression of APY2 promoted both hook opening and changes in the transcript abundance of Small Auxin Upregulated RNA (SAUR), SAUR17 and SAUR50 that help mediate de-etiolation. These results provide evidence that the expression of APY1/APY2 is regulated by R and that APY1/APY2 participate in the signaling pathway by which phytochrome induces differential growth changes in different tissues of etiolated seedlings.
PMID: 35357495
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1397-1415 doi: 10.1093/plphys/kiac138
MicroRNA858a, its encoded peptide, and phytosulfokine regulate Arabidopsis growth and development.
CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Lucknow 226001, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India.
Small molecules, such as peptides and miRNAs, are crucial regulators of plant growth. Here, we show the importance of cross-talk between miPEP858a (microRNA858a-encoded peptide)/miR858a and phytosulfokine (PSK4) in regulating plant growth and development in Arabidopsis (Arabidopsis thaliana). Genome-wide expression analysis suggested modulated expression of PSK4 in miR858a mutants and miR858a-overexpressing (miR858aOX) plants. The silencing of PSK4 in miR858aOX plants compromised growth, whereas overexpression of PSK4 in the miR858a mutant rescued the developmental defects. The exogenous application of synthetic PSK4 further complemented the plant development in mutant plants. Exogenous treatment of synthetic miPEP858a in the PSK4 mutant led to clathrin-mediated internalization of the peptide; however, it did not enhance growth as is the case in wild-type plants. We also demonstrated that MYB3 is an important molecular component participating in the miPEP858a/miR858a-PSK4 module. Finally, our work highlights the signaling between miR858a/miPEP858a-MYB3-PSK4 in modulating the expression of key elements involved in auxin responses, leading to the regulation of growth.
PMID: 35325214
Sci Total Environ , IF:7.963 , 2022 Oct , V841 : P156486 doi: 10.1016/j.scitotenv.2022.156486
Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India.
Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.; Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India. Electronic address: psar@bt.iitkgp.ac.in.
Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 x 10(7) gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO4(3-), SO4(2-) and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO4(2-) and NO3(-) reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO4(3-) and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO3(-) reduction to ammonium), and S (assimilatory SO4(2-) reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.
PMID: 35667424
Curr Opin Plant Biol , IF:7.834 , 2022 Jul , V68 : P102258 doi: 10.1016/j.pbi.2022.102258
Inter-organismal phytohormone networks in plant-microbe interactions.
State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.; State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China. Electronic address: tsuda@mail.hzau.edu.cn.
Phytohormones are produced by plants and play central roles in interactions with pathogenic and beneficial microbes as well as plant growth and development. Each phytohormone pathway consists of its biosynthesis, transport, perception, and signaling and is intertwined with each other at various levels to form phytohormone networks in plants. Different kinds of microbes also produce phytohormones that exert physiological roles within microbes and manipulate phytohormone networks in plants by using phytohormones, their mimics, and proteinaceous effectors. In turn, plant-derived phytohormones can directly or indirectly through plant signaling networks affect microbial metabolism and community assembly. Therefore, phytohormone networks in plants and microbes are connected through plant and microbial phytohormones and other molecules to form inter-organismal phytohormone networks. In this review, we summarize recent progress on molecular mechanisms of inter-organismal phytohormone networks and discuss future steps necessary for advancing our understanding of phytohormone networks.
PMID: 35820321
Plant Cell Environ , IF:7.228 , 2022 Aug , V45 (8) : P2508-2519 doi: 10.1111/pce.14366
The co-chaperone HOP participates in TIR1 stabilisation and in auxin response in plants.
Centro de Biotecnologia y Genomica de Plantas. Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcon, Madrid, Spain.; Departamento de Botanica, Ecologia y Fisiologia Vegetal, Universidad de Cordoba, Campus de Rabanales, Cordoba, Spain.; Fundacion Instituto Leloir and Instituto de Investigaciones Bioquimicas de Buenos Aires (IIBA, CONICET), Buenos Aires, Argentina.
HOP (HSP70-HSP90 organising protein) is a conserved family of co-chaperones well known in mammals for its role in the folding of signalling proteins associated with development. In plants, HOP proteins have been involved in the response to multiple stresses, but their role in plant development remains elusive. Herein, we describe that the members of the HOP family participate in different aspects of plant development as well as in the response to warm temperatures through the regulation of auxin signalling. Arabidopsis hop1 hop2 hop3 triple mutant shows different auxin-related phenotypes and a reduced auxin sensitivity. HOP interacts with TIR1 auxin coreceptor in vivo. Furthermore, TIR1 accumulation and auxin transcriptional response are reduced in the hop1 hop2 hop3 triple mutant, suggesting that HOP's function in auxin signalling is related, at least, to TIR1 interaction and stabilisation. Interestingly, HOP proteins form part of the same complexes as SGT1b (a different HSP90 co-chaperone) and these co-chaperones synergistically cooperate in auxin signalling. This study provides relevant data about the role of HOP in auxin regulation in plants and uncovers that both co-chaperones, SGT1b and HOP, cooperate in the stabilisation of common targets involved in plant development.
PMID: 35610185
Microbiol Spectr , IF:7.171 , 2022 Jul : Pe0081022 doi: 10.1128/spectrum.00810-22
Impact of Phyllosphere Methylobacterium on Host Rice Landraces.
National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
The genus Methylobacterium includes widespread plant-associated bacteria that are abundant in the plant phyllosphere (leaf surfaces), consume plant-secreted methanol, and can produce plant growth-promoting metabolites. However, despite the potential to increase agricultural productivity, their impact on host fitness in the natural environment is relatively poorly understood. Here, we conducted field experiments with three traditionally cultivated rice landraces from northeastern India. We inoculated seedlings with native versus nonnative phyllosphere Methylobacterium strains and found significant impacts on plant growth and grain yield. However, these effects were variable. Whereas some Methylobacterium isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium on its own. Host plant benefits were not consistently associated with Methylobacterium colonization and did not have altered phyllosphere microbiome composition, changes in the early expression of plant stress response pathways, or bacterial auxin production. We provide the first demonstration of the benefits of phyllosphere Methylobacterium for rice yield under field conditions and highlight the need for further analysis to understand the mechanisms underlying these benefits. Given that the host landrace-Methylobacterium relationship was not generalizable, future agricultural applications will require careful testing to identify coevolved host-bacterium pairs that may enhance the productivity of high-value rice varieties. IMPORTANCE Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse. We tested the effects of native, leaf-inhabiting bacteria (genus Methylobacterium) on traditionally cultivated rice varieties in a crop field. We found that inoculation with some bacteria increased rice grain production substantially while a nonnative bacterium reduced plant health. Overall, the effect of bacterial inoculation varied across pairs of rice varieties and their native bacteria. Thus, knowledge of evolved associations between specific bacteria hosted by specific rice varieties is necessary to develop ways to increase the yield of traditional rice landraces and preserve these important sources of cultural and genetic diversity.
PMID: 35856668
Cell Biosci , IF:7.133 , 2022 Jul , V12 (1) : P107 doi: 10.1186/s13578-022-00840-4
Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China.; Sanya Institute, Zhengzhou University, Sanya, 572024, Hainan, China.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China. xingyadi@zzu.edu.cn.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China. aylifug@caas.cn.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. aylifug@caas.cn.
BACKGROUND: Histone deacetylation is one of the most important epigenetic modifications and plays diverse roles in plant development. However, the detailed functions and mechanisms of histone deacetylation in fiber development of cotton are still unclear. HDAC inhibitors (HDACi) have been commonly used to study the molecular mechanism underlying histone deacetylation or to facilitate disease therapy in humans through hindering the histone deacetylase catalytic activity. Trichostatin A (TSA)-the most widely used HDACi has been extensively employed to determine the role of histone deacetylation on different developmental stages of plants. RESULTS: Through in vitro culture of ovules, we observed that exogenous application of TSA was able to inhibit the fiber initiation development. Subsequently, we performed a transcriptomic analysis to reveal the underlying mechanisms. The data showed that TSA treatment resulted in 4209 differentially expressed genes, which were mostly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, and carbon metabolism pathways. The phytohormone signal transduction pathways harbor the most differentially expressed genes. Deeper studies showed that some genes promoting auxin, Gibberellic Acid (GA) signaling were down-regulated, while some genes facilitating Abscisic Acid (ABA) and inhibiting Jasmonic Acid (JA) signaling were up-regulated after the TSA treatments. Further analysis of plant hormone contents proved that TSA significantly promoted the accumulation of ABA, JA and GA3. CONCLUSIONS: Collectively, histone deacetylation can regulate some key genes involved in different phytohormone pathways, and consequently promoting the auxin, GA, and JA signaling, whereas repressing the ABA synthesis and signaling to improve the fiber cell initiation. Moreover, the genes associated with energy metabolism, phenylpropanoid, and glutathione metabolism were also regulated by histone deacetylation. The above results provided novel clues to illuminate the underlying mechanisms of epigenetic modifications as well as related different phytohormones in fiber cell differentiation, which is also very valuable for the molecular breeding of higher quality cotton.
PMID: 35831870
J Integr Plant Biol , IF:7.061 , 2022 Jul doi: 10.1111/jipb.13326
ABA-dependent PMT1 expression regulates salt tolerance by alleviating ABA-mediated ROS production in Arabidopsis.
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.; State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
Phosphocholine (PCho) is an intermediate metabolite of nonplastid plant membranes that is essential for salt tolerance. However, how PCho metabolism modulates response to salt stress remains unknown. Here, we characterize the role of phosphoethanolamine N-methyltransferase 1 (PMT1) in salt stress tolerance in Arabidopsis thaliana using a T-DNA insertional mutant, gene-editing alleles, and complemented lines. The pmt1 mutants showed a severe inhibition of root elongation when exposed to salt stress, but exogenous ChoCl or lecithin rescued this defect. pmt1 also displayed altered glycerolipid metabolism under salt stress, suggesting that glycerolipids contribute to salt tolerance. Moreover, pmt1 mutants exhibited altered reactive oxygen species (ROS) accumulation and distribution, reduced cell division activity, and disturbed auxin distribution in the primary root compared to wild-type seedlings. We show that PMT1 expression is induced by salt stress and relies on the abscisic acid (ABA) signaling pathway, as this induction was abolished in the aba2-1 and pyl112458 mutants. However, ABA aggravated the salt sensitivity of the pmt1 mutants by perturbing ROS distribution in the root tip. Taken together, we propose that PMT1 is an important phosphoethanolamine N-methyltransferase participating in root development of primary root elongation under salt stress conditions by balancing ROS production and distribution through ABA signaling. This article is protected by copyright. All rights reserved.
PMID: 35789105
J Integr Plant Biol , IF:7.061 , 2022 Jul , V64 (7) : P1325-1338 doi: 10.1111/jipb.13269
GmPIN1-mediated auxin asymmetry regulates leaf petiole angle and plant architecture in soybean.
Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Department of Horticulture, Beijing Vocational College of Agriculture, Beijing, 102442, China.; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
Crop breeding during the Green Revolution resulted in high yields largely due to the creation of plants with semi-dwarf architectures that could tolerate high-density planting. Although semi-dwarf varieties have been developed in rice, wheat and maize, none was reported in soybean (Glycine max), and few genes controlling plant architecture have been characterized in soybean. Here, we demonstrate that the auxin efflux transporter PINFORMED1 (GmPIN1), which determines polar auxin transport, regulates the leaf petiole angle in soybean. CRISPR-Cas9-induced Gmpin1abc and Gmpin1bc multiple mutants displayed a compact architecture with a smaller petiole angle than wild-type plants. GmPIN1 transcripts and auxin were distributed asymmetrically in the petiole base, with high levels of GmPIN1a/c transcript and auxin in the lower cells, which resulted in asymmetric cell expansion. By contrast, the (iso)flavonoid content was greater in the upper petiole cells than in the lower cells. Our results suggest that (iso)flavonoids inhibit GmPIN1a/c expression to regulate the petiole angle. Overall, our study demonstrates that a signal cascade that integrates (iso)flavonoid biosynthesis, GmPIN1a/c expression, auxin accumulation, and cell expansion in an asymmetric manner creates a desirable petiole curvature in soybean. This study provides a genetic resource for improving soybean plant architecture.
PMID: 35485227
J Integr Plant Biol , IF:7.061 , 2022 Jul , V64 (7) : P1339-1351 doi: 10.1111/jipb.13268
A feedback regulation between ARF7-mediated auxin signaling and auxin homeostasis involving MES17 affects plant gravitropism.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, China.; Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Gravitropism is an essential adaptive response of land plants. Asymmetric auxin gradients across plant organs, interpreted by multiple auxin signaling components including AUXIN RESPONSE FACTOR7 (ARF7), trigger differential growth and bending response. However, how this fundamental process is strictly maintained in nature remains unclear. Here, we report that gravity stimulates the transcription of METHYL ESTERASE17 (MES17) along the lower side of the hypocotyl via ARF7-dependent auxin signaling. The asymmetric distribution of MES17, a methyltransferase that converts auxin from its inactive form methyl indole-3-acetic acid ester (MeIAA) to its biologically active form free-IAA, enhanced the gradient of active auxin across the hypocotyl, which in turn reversely amplified the asymmetric auxin responses and differential growth that shape gravitropic bending. Taken together, our findings reveal the novel role of MES17-mediated auxin homeostasis in gravitropic responses and identify an ARF7-triggered feedback mechanism that reinforces the asymmetric distribution of active auxin and strictly controls gravitropism in plants.
PMID: 35475598
J Exp Bot , IF:6.992 , 2022 Jul doi: 10.1093/jxb/erac319
bZIP88 transcription factor upregulation is involved in resistance to three different herbicides in both Echinochloa crus-galli and Echinochloa glabrescens.
College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education.
The resistance of weeds to herbicides poses a huge threat to agricultural production. Non target-site resistance (NTSR) is often more detrimental as NTSR mechanisms can in some cases confer resistance to herbicides from multiple modes of action, termed here as multiple-herbicide resistance (MHR). We hypothesized that bZIP transcription factors (TFs), which regulate abiotic stress responses in many plants, play a regulatory role in NTSR. The results of whole-plant assays revealed that Echinochloa crus-galli and E. glabrescens are resistant to the herbicides penoxsulam, cyhalofop-butyl, and quintrione. The results of transcriptome sequencing identified 101 and 49 bZIP TFs with altered expression with differential expression following penoxsulam treatment in E. crus-galli and E. glabrescens, respectively. Twelve of these genes (bZIP36/37/39/4/44/45/50/52/53/79/87/88) had >60% homology with rice genes. bZIP88 expression was considerably upregulated 6 h after treatment with three different herbicides. The relative expression levels before and 12 h after herbicide treatment were not different, and the upregulation was similar between resistant and susceptible populations. We used rice (Oryza sativa L. japonica. cv. Nipponbare) as a model system for functional validation. CRISPR/Cas9 bZIP88 ortholog in rice knockouts increased sensitivity, whereas overexpression reduced. The OsbZIP88 proteins localized to the nucleus. OsbZIP88 was found, with chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq), to form a network regulatory center with other TFs such as bZIP20/52/59, that regulate genes (OsKS1, OsCOE1, OsIM1) related to auxin, abscisic acid (ABA), brassinosteroids (BR), gibberellic acid (GA). Based on these results, weestablished a database of bZIP TFs corresponding to herbicide stress, and resolved the mechanisms of the positive regulation of herbicide resistance by bZIP88, creating a new perspective for NTSR.
PMID: 35867472
J Exp Bot , IF:6.992 , 2022 Jul doi: 10.1093/jxb/erac282
TOR kinase, a GPS in the complex nutrient and hormonal signaling networks to guide plant growth and development.
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Haixia Institute of Science and Technology, Plant Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
To survive and sustain growth, sessile plants have developed sophisticated internal signalling networks that respond to various external and internal cues. Despite the central roles of nutrient and hormone signaling in plant growth and development, how hormone-driven processes coordinate with metabolic status remains largely enigmatic. Target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator that integrates energy, nutrients, growth factors, hormones and stress signals to promote growth in all eukaryotes. Inspired by recent comprehensive systems, chemical, genetic and genomic studies on plant TOR, this review discusses a potential role of TOR as the global positioning system to both temporally and spatially direct plant growth and developmental programs by integrating dynamic information in the complex nutrient and hormonal signaling networks. We further evaluate and depict the possible functional and mechanistic models for how a single protein kinase TOR is able to recognize, integrate and even distinguish a plethora of positive and negative input signals to execute appropriate and distinct downstream biological processes via multiple partners and effectors.
PMID: 35781569
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac280
Actin isovariant ACT7 controls root meristem development in Arabidopsis through modulating auxin and ethylene responses.
Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan.; The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan.; Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada.
Meristem is the most functionally dynamic part in a plant body. The shaping of the meristem requires constant cell division and cell elongation, which are influenced by hormones and cell cytoskeletal component, actin. Although the roles of hormones in modulating meristem development have been extensively studied, the role of actin in this process is still elusive. Using the single and double mutants of the vegetative class actin, we demonstrate that actin isovariant ACT7 plays an important role in root meristem development. In absence of ACT7, but not ACT8 and ACT2, depolymerization of actin was observed. Consistently, act7 mutant showed reduced cell division, cell elongation, and meristem length. Intracellular distribution and trafficking of auxin transport proteins in the actin mutants revealed that ACT7 specifically functions in root meristem to facilitate the trafficking of auxin efflux carriers PIN1 and PIN2, and consequently the transport of auxin. Compared with act7, act7act8 double mutant shows slightly enhanced phenotypic response and altered intracellular trafficking. The altered distribution of auxin in act7 and act7act8 affects the response of the roots to ethylene but not to cytokinin. Collectively, our results suggest that ACT7 dependent auxin-ethylene response plays a key role in controlling Arabidopsis root meristem development.
PMID: 35749807
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P3828-3830 doi: 10.1093/jxb/erac175
Prohibitin 3 gives birth to a new lateral root primordium.
MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
PMID: 35749693
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P3831-3835 doi: 10.1093/jxb/erac237
Auxins in the right space and time regulate pea fruit development.
Technische Universitat Dresden, Faculty of Biology, D-01062 Dresden, Germany.
PMID: 35749692
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac281
MAX2-dependent competence for callus formation and shoot regeneration from Arabidopsis thaliana root explants.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Gent, Belgium.; Center for Plant Systems Biology, VIB, Technologiepark, Gent, Belgium.; Laboratory of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, Yeonsu-Gu, Incheon, Korea.; Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, UPR2301, Universite Paris-Sud, Universite Paris-Saclay, 1 Avenue de la Terrasse, Gif-sur-Yvette, France.; Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg, Ghent, Belgium.
Although the division of the pericycle cells initiates both the lateral root development and the root-derived callus formation, these developmental processes are affected differently in the strigolactone (SL) and karrikin (KAR)/KAI2 ligand (KL) signalling mutant, more axillary growth 2 (max2). Whereas max2 produces more lateral roots than the wild type, it is defective in the regeneration of shoots from root explants. We suggest that the decreased shoot regeneration of max2 originates from a delayed callus primordium formation, yielding less callus material to regenerate shoots. Indeed, when incubated on callus-inducing medium, the pericycle cell division was reduced in max2 and the early gene expression varied when compared to the wild type, as determined by a transcriptomics analysis. Furthermore, the expression of the LATERAL ORGAN BOUNDARIES DOMAIN genes and of callus induction genes was modified in correlation with the max2 phenotype, suggesting a role for MAX2 in the regulation of the interplay between cytokinin, auxin, and light signalling in callus initiation. Additionally, we found that the in vitro shoot regeneration phenotype of max2 might be caused by a defect in KAI2, rather than D14, signalling. Nevertheless, the shoot regeneration assays revealed that also the SL biosynthesis mutants max3 and max4 play a minor role.
PMID: 35738874
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac253
Stress-induced higher vein density in C3-C4 intermediate Moricandia suffruticosa under drought and heat stress.
Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, People's Republic of China.; Hubei Hongshan Laboratory, Wuhan, China.
C4 evolution involves multiple anatomical and physiological modifications, yet our knowledge of its genetic regulation remains elusive. In this study, systematic analyses were conducted between C3-C4 intermediate Moricandia suffruticosa and its C3 relative Brassica napus. We found that M. suffruticosa leaves had significantly higher vein density than those of B. napus, and the vein density was further increased in M. suffruticosa under drought and heat stress. Moreover, the bundle sheath distance decreased and the number of centripetal chloroplasts in bundle sheath cells was found to be altered in M. suffruticosa leaves under drought and heat treatments. These results suggest that abiotic stress can induce a change in an intermediate C3-C4 anatomy towards a C4-like anatomy in land plants. By integrating drought and heat factors, co-expression network and comparative transcriptome analyses between M. suffruticosa and B. napus effectively revealed that inducible auxin signaling regulated vascular development and autophagy-related vesicle trafficking process were associated with this stress-induced anatomy change. Overexpressing three candidate genes, MsERF02, MsSCL01 and MsDOF01, increased leaf vein density and/or also enhanced photosynthetic assimilation and drought adaptability in the transgenic lines. The findings of this study may improve our understanding of the genetic regulation and evolution of C4 anatomy.
PMID: 35675763
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac251
Jasmonate action and crosstalk in flower development and fertility.
Plant Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.; Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, 100048, China.; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.; School of Life Sciences, Tsinghua University, Beijing 100084, China.
Flower development and fertility are coordinately regulated by endogenous developmental signals, including the phytohormones jasmonates (JAs), auxin, and gibberellin, and environmental cues. JAs regulate stamen development and fertility at basal conditions, affect root growth and trichome formation under stress conditions, and control defense responses against insect herbivores and pathogens. Since 1990s, an increasing number of studies have revealed the essential roles of JA biosynthesis, signaling, and crosstalk in regulation of flower development and fertility. Here, we summarize and present an updated overview of JA pathway and crosstalk in modulating flower/sexual organ development and fertility in Arabidopsis, tomato, rice, maize, and sorghum.
PMID: 35670512
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4094-4112 doi: 10.1093/jxb/erac152
Auxin receptors as integrators of developmental and hormonal signals during reproductive development in pea.
Plant BioSystems, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
Auxins regulate many aspects of plant growth and development. In pea, three of the five TIR1/AFB members (PsTIR1a, PsTIR1b, and PsAFB2) have been implicated in auxin-related responses during fruit/seed development; however, the roles of PsAFB4 and PsAFB6 in these processes are unknown. Using yeast two-hybrid assays, we found that all five pea TIR1/AFB receptor proteins interacted with the pea AUX/IAAs PsIAA6 and/or PsIAA7 in an auxin-dependent manner, a requirement for functional auxin receptors. All five auxin receptors are expressed in young ovaries (pericarps) and rapidly developing seeds, with overlapping and unique developmental and hormone-regulated gene expression patterns. Pericarp PsAFB6 expression was suppressed by seeds and increased in response to deseeding, and exogenous hormone treatments suggest that seed-derived auxin and deseeding-induced ethylene are involved in these responses, respectively. Ethylene-induced elevation of pericarp PsAFB6 expression was associated with 4-Cl-IAA-specific reduction in ethylene responsiveness. In developing seeds, expression of PsTAR2 and PsYUC10 auxin biosynthesis genes was associated with high auxin levels in seed coat and cotyledon tissues, and PsAFB2 dominated the seed tissue transcript pool. Overall, auxin receptors had overlapping and unique developmental and hormone-regulated gene expression patterns during fruit/seed development, suggesting mediation of diverse responses to auxin, with PsAFB6 linking auxin and ethylene signaling.
PMID: 35395070
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4113-4128 doi: 10.1093/jxb/erac143
Reduced auxin signalling through the cyclophilin gene DIAGEOTROPICA impacts tomato fruit development and metabolism during ripening.
Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.; Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.; Departmento de Ciencias Biologicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de Sao Paulo, Piracicaba, Brazil.; Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany.
Auxin is an important hormone playing crucial roles during fruit growth and ripening; however, the metabolic impact of changes in auxin signalling during tomato (Solanum lycopersicum L.) ripening remains unclear. Here, we investigated the significance of changes in auxin signalling during different stages of fruit development by analysing changes in tomato fruit quality and primary metabolism using mutants with either lower or higher auxin sensitivity [diageotropica (dgt) and entire mutants, respectively]. Altered auxin sensitivity modifies metabolism, through direct impacts on fruit respiration and fruit growth. We verified that the dgt mutant plants exhibit reductions in fruit set, total fruit dry weight, fruit size, number of seeds per fruit, and fresh weight loss during post-harvest. Sugar accumulation was associated with delayed fruit ripening in dgt, probably connected with reduced ethylene levels and respiration, coupled with a lower rate of starch degradation. In contrast, despite exhibiting parthenocarpy, increased auxin perception (entire) did not alter fruit ripening, leading to only minor changes in primary metabolism. By performing a comprehensive analysis, our results connect auxin signalling and metabolic changes during tomato fruit development, indicating that reduced auxin signalling led to extensive changes in sugar concentration and starch metabolism during tomato fruit ripening.
PMID: 35383842
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4147-4156 doi: 10.1093/jxb/erac119
Impaired auxin signaling increases vein and stomatal density but reduces hydraulic efficiency and ultimately net photosynthesis.
Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, MG, 36570-900, Brazil.; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
Auxins are known to regulate xylem development in plants, but their effects on water transport efficiency are poorly known. Here we used tomato plants with the diageotropica mutation (dgt), which has impaired function of a cyclophilin 1 cis-trans isomerase involved in auxin signaling, and the corresponding wild type (WT) to explore the mutation's effects on plant hydraulics and leaf gas exchange. The xylem of the dgt mutant showed a reduced hydraulically weighted vessel diameter (Dh) (24-43%) and conduit number (25-58%) in petioles and stems, resulting in lower theoretical hydraulic conductivities (Kt); on the other hand, no changes in root Dh and Kt were observed. The measured stem and leaf hydraulic conductances of the dgt mutant were lower (up to 81%), in agreement with the Kt values; however, despite dgt and WT plants showing similar root Dh and Kt, the measured root hydraulic conductance of the dgt mutant was 75% lower. The dgt mutation increased the vein and stomatal density, which could potentially increase photosynthesis. Nevertheless, even though it had the same photosynthetic capacity as WT plants, the dgt mutant showed a photosynthetic rate c. 25% lower, coupled with a stomatal conductance reduction of 52%. These results clearly demonstrate that increases in minor vein and stomatal density only result in higher leaf gas exchange when accompanied by higher hydraulic efficiency.
PMID: 35312771
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4034-4045 doi: 10.1093/jxb/erac115
PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.; College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China.; College of Agriculture Science and Technology, Shandong Agriculture and Engineering University, Jinan Shandong, China.; Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA.
We have previously shown that Arabidopsis thaliana Prohibitin 3 (PHB3) controls auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates lateral root (LR) development mainly through influencing lateral root primordia (LRP) initiation, via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 mutant was largely rescued by treatment with a NO donor. The decreased NO accumulation in phb3 caused a lower expression of GATA TRANSCRIPTION FACTOR 23 (GATA23) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) through inhibiting the degradation of INDOLE-3-ACETIC ACID INDUCIBLE 14/28 (IAA14/28). Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced density of LRP. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signalling, by modulating the degradation of IAA14/28.
PMID: 35303089
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3552-3568 doi: 10.1093/jxb/erac088
Cytokinin oxidase/dehydrogenase family genes exhibit functional divergence and overlap in rice growth and development, especially in control of tillering.
College of Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.; Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing 210095, People's Republic of China.; Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing 210095, People's Republic of China.
Cytokinins play key roles in plant growth and development, and hence their biosynthesis and degradation have been extensively studied. Cytokinin oxidase/dehydrogenases (CKXs) are a group of enzymes that regulate oxidative cleavage to maintain cytokinin homeostasis. In rice, 11 CKX genes have been identified to date; however, most of their functions remain unknown. In this study, we comprehensively examined the expression patterns and functions of the CKXs in rice by using CRISPR/Cas9 technology to construct mutants of all 11 genes. The results revealed that the ckx single-mutants and higher-order ckx4 ckx9 mutant lines showed functional overlaps and sub-functionalization. Notably, the ckx1 ckx2 and ckx4 ckx9 double-mutants displayed contrasting phenotypic changes in tiller number and panicle size compared to the wild-type. In addition, we identified several genes with significantly altered expression in both the ckx4 and ckx9 single-mutant and double-mutant plants. Many of the differentially expressed genes were found to be associated with auxin and cytokinin pathways, and cytokinins in the ckx4 ckx9 double-mutant were increased compared to the wild-type. Taken together, our findings provide new insights into the functions of CKX genes in rice growth and may provide the foundations for future studies aimed at improving rice yield.
PMID: 35247044
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3511-3530 doi: 10.1093/jxb/erac083
Nitrate-dependent regulation of miR444-OsMADS27 signalling cascade controls root development in rice.
National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India.; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Universite Paris- Saclay, Versailles, France.; SASTRA University, Thirumalaisamudram, Thanjavur, India.; Department of Biological Sciences, North Dakota State University, Fargo, ND, USA.
Nitrate is an important nutrient and a key signalling molecule for plant development. A number of transcription factors involved in the response to nitrate and their regulatory mechanisms have been identified. However, little is known about the transcription factors involved in nitrate sensing and their regulatory mechanisms among crop plants. In this study, we identified functions of a nitrate-responsive miR444:MADS-box transcription factor OsMADS27 module and its downstream targets mediating rice root growth and stress responses. Transgenic rice plants expressing miR444 target mimic improved rice root growth. Although miR444 has the potential to target multiple genes, we identified OsMADS27 as the major miR444 target that regulates the expression of nitrate transporters, as well as several key genes including expansins, and those associated with auxin signalling, to promote root growth. In agreement with this, overexpression of miRNA-resistant OsMADS27 improved root development and tolerance to abiotic stresses, while its silencing suppressed root growth. OsMADS27 mediated robust stress tolerance in plants through its ability to bind to the promoters of specific stress regulators, as observed in ChIP-seq analysis. Our results provide evidence of a nitrate-dependent miR444-OsMADS27 signalling cascade involved in the regulation of rice root growth, as well as its surprising role in stress responses.
PMID: 35243491
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3496-3510 doi: 10.1093/jxb/erac079
PUCHI represses early meristem formation in developing lateral roots of Arabidopsis thaliana.
DIADE, Univ Montpellier, IRD, Montpellier, France.; Univ Montpellier, CNRS, INSERM, Montpellier, France.; Montpellier GenomiX, France Genomique, Montpellier, France.
Lateral root organogenesis is a key process in the development of a plant's root system and its adaptation to the environment. During lateral root formation, an early phase of cell proliferation first produces a four-cell-layered primordium, and only from this stage onwards is a root meristem-like structure, expressing root stem cell niche marker genes, being established in the developing organ. Previous studies reported that the gene regulatory network controlling lateral root formation is organized into two subnetworks whose mutual inhibition may contribute to organ patterning. PUCHI encodes an AP2/ERF transcription factor expressed early during lateral root primordium development and required for correct lateral root formation. To dissect the molecular events occurring during this early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 mutants and wild types. Transcriptomic and reporter analyses revealed that meristem-related genes were expressed ectopically at early stages of lateral root formation in puchi-1 mutants. We conclude that, consistent with the inhibition of genetic modules contributing to lateral root development, PUCHI represses ectopic establishment of meristematic cell identities at early stages of organ development. These findings shed light on gene network properties that orchestrate correct timing and patterning during lateral root formation.
PMID: 35224628
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3711-3725 doi: 10.1093/jxb/erac074
Serratia marcescens PLR enhances lateral root formation through supplying PLR-derived auxin and enhancing auxin biosynthesis in Arabidopsis.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China.; Peking University Institute of Advanced Agricultural Sciences, Weifang, China.; Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
Plant growth promoting rhizobacteria (PGPR) refer to bacteria that colonize the rhizosphere and contribute to plant growth or stress tolerance. To further understand the molecular mechanism by which PGPR exhibit symbiosis with plants, we performed a high-throughput single colony screening from the rhizosphere, and uncovered a bacterium (named promoting lateral root, PLR) that significantly promotes Arabidopsis lateral root formation. By 16S rDNA sequencing, PLR was identified as a novel sub-species of Serratia marcescens. RNA-seq analysis of Arabidopsis integrated with phenotypic verification of auxin signalling mutants demonstrated that the promoting effect of PLR on lateral root formation is dependent on auxin signalling. Furthermore, PLR enhanced tryptophan-dependent indole-3-acetic acid (IAA) synthesis by inducing multiple auxin biosynthesis genes in Arabidopsis. Genome-wide sequencing of PLR integrated with the identification of IAA and its precursors in PLR exudates showed that tryptophan treatment significantly enhanced the ability of PLR to produce IAA and its precursors. Interestingly, PLR induced the expression of multiple nutrient (N, P, K, S) transporter genes in Arabidopsis in an auxin-independent manner. This study provides evidence of how PLR enhances plant growth through fine-tuning auxin biosynthesis and signalling in Arabidopsis, implying a potential application of PLR in crop yield improvement through accelerating root development.
PMID: 35196372
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3671-3685 doi: 10.1093/jxb/erac059
Ammonium transporters cooperatively regulate rice crown root formation responding to ammonium nitrogen.
MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Crown roots (CRs) are major components of the rice root system. They form at the basal node of the shoot, and their development is greatly influenced by environmental factors. Ammonium nitrogen is known to impact plant root development through ammonium transporters (AMTs), but it remains unclear whether ammonium and AMTs play roles in rice CR formation. In this study, we revealed a significant role of ammonium, rather than nitrate, in regulating rice CR development. High ammonium supply increases CR formation but inhibits CR elongation. Genetic evidence showed that ammonium regulation of CR development relies on ammonium uptake mediated jointly by ammonium transporters OsAMT1;1, OsAMT1;2; OsAMT1;3, and OsAMT2;1, but not on root acidification which was the result of ammonium uptake. OsAMTs are also needed for glutamine-induced CR formation. Furthermore, we showed that polar auxin transport dependent on the PIN auxin efflux carriers acts downstream of ammonium uptake and assimilation to activate local auxin signaling at CR primordia, in turn promoting CR formation. Taken together, our results highlight a critical role for OsAMTs in cooperatively regulating CR formation through regulating auxin transport under nitrogen-rich conditions.
PMID: 35176162
Development , IF:6.868 , 2022 Jul , V149 (13) doi: 10.1242/dev.200929
PILS proteins provide a homeostatic feedback on auxin signaling output.
Institute of Molecular Plant Biology (IMPB), Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.; Faculty of Biology, Department of Molecular Plant Physiology (MoPP), University of Freiburg, 79104 Freiburg, Germany.; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany.
Multiple internal and external signals modulate the metabolism, intercellular transport and signaling of the phytohormone auxin. Considering this complexity, it remains largely unknown how plant cells monitor and ensure the homeostasis of auxin responses. PIN-LIKES (PILS) intracellular auxin transport facilitators at the endoplasmic reticulum are suitable candidates to buffer cellular auxin responses because they limit nuclear abundance and signaling of auxin. We used forward genetics to identify gloomy and shiny pils (gasp) mutants that define the PILS6 protein abundance in a post-translational manner. Here, we show that GASP1 encodes an uncharacterized RING/U-box superfamily protein that impacts on auxin signaling output. The low auxin signaling in gasp1 mutants correlates with reduced abundance of PILS5 and PILS6 proteins. Mechanistically, we show that high and low auxin conditions increase and reduce PILS6 protein levels, respectively. Accordingly, non-optimum auxin concentrations are buffered by alterations in PILS6 abundance, consequently leading to homeostatic auxin output regulation. We envision that this feedback mechanism provides robustness to auxin-dependent plant development.
PMID: 35819066
Development , IF:6.868 , 2022 Jun , V149 (12) doi: 10.1242/dev.200403
A genetic framework for proximal secondary vein branching in the Arabidopsis thaliana embryo.
Group of Plant Vascular Development, Swiss Federal Institute of Technology (ETH) Zurich, CH-8092 Zurich, Switzerland.; Group of RNA Biology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8092 Zurich, Switzerland.; Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas (CSIC)-Universitat Politecnica de Valencia (UPV), 46022 Valencia, Spain.
Over time, plants have evolved flexible self-organizing patterning mechanisms to adapt tissue functionality for continuous organ growth. An example of this process is the multicellular organization of cells into a vascular network in foliar organs. An important, yet poorly understood component of this process is secondary vein branching, a mechanism employed to extend vascular tissues throughout the cotyledon surface. Here, we uncover two distinct branching mechanisms during embryogenesis by analyzing the discontinuous vein network of the double mutant cotyledon vascular pattern 2 (cvp2) cvp2-like 1 (cvl1). Similar to wild-type embryos, distal veins in cvp2 cvl1 embryos arise from the bifurcation of cell files contained in the midvein, whereas proximal branching is absent in this mutant. Restoration of this process can be achieved by increasing OCTOPUS dosage as well as by silencing RECEPTOR-LIKE PROTEIN KINASE 2 (RPK2) expression. Although RPK2-dependent rescue of cvp2 cvl1 is auxin- and CLE peptide-independent, distal branching involves polar auxin transport and follows a distinct regulatory mechanism. Our work defines a genetic network that confers plasticity to Arabidopsis embryos to spatially adapt vascular tissues to organ growth.
PMID: 35723181
Cells , IF:6.6 , 2022 Jul , V11 (14) doi: 10.3390/cells11142174
Magnetopriming Actuates Nitric Oxide Synthesis to Regulate Phytohormones for Improving Germination of Soybean Seeds under Salt Stress.
School of Biochemistry, Devi Ahilya Vishwavidyalaya, Khandwa Road, Indore 452001, India.; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.; ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.; Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.; Institute of Plant and Environmental Sciences, Slovak University of Agriculture, A. Hlinku 2, 94976 Nitra, Slovakia.; Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16500 Prague, Czech Republic.
In this study, the role of the signalling molecule nitric oxide (NO) in magnetopriming-mediated induction of salinity tolerance in soybean seeds is established. The cross-talk of NO with germination-related hormones gibberellic acid (GA), abscisic acid (ABA) and auxin (IAA) for their ability to reduce the Na(+)/K(+) ratio in the seeds germinating under salinity is highlighted. Salt tolerance index was significantly high for seedlings emerging from magnetoprimed seeds and sodium nitroprusside (SNP, NO-donor) treatment. The NO and superoxide (O2(*-)) levels were also increased in both of these treatments under non-saline and saline conditions. NO generation through nitrate reductase (NR) and nitric oxide synthase-like (NOS-like) pathways indicated the major contribution of NO from the NR-catalysed reaction. The relative expression of genes involved in the NO biosynthetic pathways reiterated the indulgence of NR in NO in magnetoprimed seeds, as a 3.86-fold increase in expression was observed over unprimed seeds under salinity. A 23.26-fold increase in relative expression of NR genes by the NO donor (SNP) was observed under salinity, while the NR inhibitor (sodium tungstate, ST) caused maximum reduction in expression of NR genes as compared to other inhibitors [L-NAME (N(G)-nitro-L-arginine methyl ester; inhibitor of nitric oxide synthase-like enzyme) and DPI (diphenylene iodonium; NADPH oxidase inhibitor)]. The ratio of ABA/GA and IAA/GA decreased in magnetoprimed and NO donor-treated seeds, suggesting homeostasis amongst hormones during germination under salinity. The magnetoprimed seeds showed low Na(+)/K(+) ratio in all treatments irrespective of NO inhibitors. Altogether, our results indicate that a balance of ABA, GA and IAA is maintained by the signalling molecule NO in magnetoprimed seeds which lowers the Na(+)/K(+) ratio to offset the adverse effects of salinity in soybean seeds.
PMID: 35883617
Plant J , IF:6.417 , 2022 Jun doi: 10.1111/tpj.15884
OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice.
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China.; Huazhong Agricultural University, Wuhan, 430070, China.; Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.; State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China.
As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice. RNA interference of OsSPL14 or miR529 and miR156 overexpression significantly increased the tiller number, whereas OsSPL14 overexpression decreased the tiller number. Histological analysis revealed that the OsSPL14-overexpressing line had normal initiation of axillary buds but inhibited outgrowth of tillers. Moreover, OsSPL14 was found to be responsive to indole-acetic acid and 1-naphthylphthalamic acid, and RNA interference of OsSPL14 reduced polar auxin transport and increased 1-naphthylphthalamic acid sensitivity of rice plants. Further analysis revealed that OsSPL14 directly binds to the promoter of PIN-FORMED 1b (OsPIN1b) and PIN-LIKE6b (PILS6b) to regulate their expression positively. OsPIN1b and PILS6b were highly expressed in axillary buds and proved involved in bud outgrowth. Loss of function of OsPIN1b or PILS6b increased the tiller number of rice. Taken together, our findings suggested that OsSPL14 could control axillary bud outgrowth and tiller number by activating the expression of OsPIN1b and PILS6b to fine-tune auxin transport in rice.
PMID: 35765202
Plant J , IF:6.417 , 2022 Jun doi: 10.1111/tpj.15868
H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple.
Graduate School of Agriculture, Kyoto University, Kyoto, Japan.; Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China.; School of Engineering, Utsunomiya University, Utsunomiya, Japan.; National Institute for Basic Biology, Okazaki, Japan.; The Graduate University for Advanced Studies, SOKENDAI, Miura-gun, Japan.; Faculty of Agriculture, Shinshu University, Kamiina-gun, Japan.; Agricultural Experimental Station, Ishikawa Prefectural University, Nonoichi, Japan.
Bud dormancy helps woody perennials survive winter and activate robust plant development in the spring. For apple (Malus x domestica), short-term chilling induces bud dormancy in autumn, then prolonged chilling leads to dormancy release and a shift to a quiescent state in winter, with subsequent warm periods promoting bud break in spring. Epigenetic regulation contributes to seasonal responses such as vernalization. However, how histone modifications integrate seasonal cues and internal signals during bud dormancy in woody perennials remains largely unknown. Here, we show that H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The global changes in gene expression strongly correlated with changes in H3K4me3, but not H3K27me3. High expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes, key regulators of dormancy, in autumn was associated with high H3K4me3 levels. In addition, known DAM/SHORT VEGETATIVE PHASE (SVP) target genes significantly overlapped with H3K4me3-modified genes as bud dormancy progressed. These data suggest that H3K4me3 contributes to the central dormancy circuit, consisting of DAM/SVP and abscisic acid (ABA), in autumn. In winter, the lower expression and H3K4me3 levels at DAMs and gibberellin metabolism genes control chilling-induced release of dormancy. Warming conditions in spring facilitate the expression of genes related to phytohormones, the cell cycle, and cell wall modification by increasing H3K4me3 toward bud break. Our study also revealed that activation of auxin and repression of ABA sensitivity in spring are conditioned at least partly through temperature-mediated epigenetic regulation in winter.
PMID: 35699670
Int J Mol Sci , IF:5.923 , 2022 Jul , V23 (15) doi: 10.3390/ijms23158208
The L-Type Lectin-like Receptor Kinase Gene TaLecRK-IV.1 Regulates the Plant Height in Wheat.
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; Department of Biological Sciences, Faculty of Science, University of Ngaoundere, Ngaoundere P.O. Box 454, Cameroon.
Dwarfing is important for the production of wheat (Triticumaestivum L.). In model plants, receptor-like kinases have been implicated in signal transduction, immunity, and development. However, functional roles of lectin receptor-like kinases in wheat are poorly understood. In this study, we identified an L-type lectin receptor-like kinase gene in wheat, designated as TaLecRK-IV.1, and revealed its role in plant height. Real time quantitative PCR analyses indicated that TaLecRK-IV.1 transcript level was lower in a dwarf wheat line harboring the Rht-D1b gene compared to its transcript level detected in a taller wheat line CI12633. Importantly, the virus-induced gene silencing results showed that silencing of TaLecRK-IV.1 in the wheat line CI12633 led to dwarf plants. The results of the disease resistance test performed after the gene silencing experiment suggest no significant role of TaLecRK-IV.1 in the resistance reaction of wheat line CI12633 to sharp eyespot. Gene expression analysis revealed that the transcript abundance of TaLecRK-IV.1 was more up-regulated after the exogenous application of gibberellic acid and auxin, two development-related phytohormones, compared to the gene transcript levels detected in the control plants (mock treatment). These findings support the potential implication of TaLecRK-IV.1 in the pathway controlling plant height rather than the disease resistance role, and suggest that TaLecRK-IV.1 may be a positive regulator of plant height through the gibberellic acid and auxin-signaling pathways.
PMID: 35897784
Int J Mol Sci , IF:5.923 , 2022 Jul , V23 (15) doi: 10.3390/ijms23158057
Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat.
Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.; Molecular Genetic Beijing Key Laboratory of Hybrid Wheat, Beijing 100097, China.; College of Horticulture, China Agricultural University, Beijing 100193, China.
Temperature-sensitive genic male sterile (TGMS) line Beijing Sterility 366 (BS366) has been utilized in hybrid breeding for a long time, but the molecular mechanism underlying male sterility remains unclear. Expression arrays, small RNA, and degradome sequencing were used in this study to explore the potential role of miRNA in the cold-induced male sterility of BS366. Microspore observation showed defective cell plates in dyads and tetrads and shrunken microspores at the vacuolated stage. Differential regulation of Golgi vesicle transport, phragmoplast formation, sporopollenin biosynthesis, pollen exine formation, and lipid metabolism were observed between cold and control conditions. Pollen development was significantly represented in the 352 antagonistic miRNA-target pairs in the integrated analysis of miRNA and mRNA profiles. The specific cleavage of ARF17 and TIR1 by miR160 and miR393 were found in the cold-treated BS366 degradome, respectively. Thus, the cold-mediated miRNAs impaired cell plate formation through repression of Golgi vesicle transport and phragmoplast formation. The repressed expression of ARF17 and TIR1 impaired pollen exine formation. The results of this study will contribute to our understanding of the roles of miRNAs in male sterility in wheat.
PMID: 35897633
Int J Mol Sci , IF:5.923 , 2022 Jul , V23 (14) doi: 10.3390/ijms23147574
Genome-Wide Identification of TaSAUR Gene Family Members in Hexaploid Wheat and Functional Characterization of TaSAUR66-5B in Improving Nitrogen Use Efficiency.
State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
Excessive input of nitrogen fertilizer not only causes a great waste of resources but brings about a series of ecological and environmental problems. Although Small Auxin Up-regulated RNAs (SAURs) participate in diverse biological processes, the function of SAURs in the nitrogen starvation response has not been well-studied. Here, we identified 308 TaSAURs in wheat and divided them into 10 subfamilies. The promoter regions of most TaSAURs contain hormone responsive elements, and their expression levels change under the treatment of different hormones, such as IAA, MeJA, and ABA. Interestingly, overexpression of one of the TaSAUR family members, a nitrogen starvation responsive gene, TaSAUR66-5B, can promote the growth of Arabidopsis and wheat roots. In addition, overexpression of TaSAUR66-5B in Arabidopsis up-regulates the expression levels of auxin biosynthesis related genes, suggesting that overexpression TaSAUR66-5B may promote root growth by increasing the biosynthesis of auxin. Furthermore, overexpression of TaSAUR66-5B in wheat can increase the biomass and grain yields of transgenic plants, as well as the nitrogen concentration and accumulation of both shoots and grains, especially under low nitrogen conditions. This study provides important genomic information of the TaSAUR gene family and lays a foundation for elucidating the functions of TaSAURs in improving nitrogen utilization efficiency in wheat.
PMID: 35886923
Int J Mol Sci , IF:5.923 , 2022 Jul , V23 (13) doi: 10.3390/ijms23137415
Morphological and Proteomic Analyses of Soybean Seedling Interaction Mechanism Affected by Fiber Crosslinked with Zinc-Oxide Nanoparticles.
Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.; R&D Laboratory for Applied Product, Asahi Kasei Corporation, Moriyama 524-0002, Japan.; Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan.; Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan.; Business Promotion Section Business Strategy Department, Bemberg Division, Asahi Kasei Corporation, Osaka 530-8205, Japan.
Nanoparticles (NPs) enhance soybean growth; however, their precise mechanism is not clearly understood. To develop a more effective method using NPs for the enhancement of soybean growth, fiber crosslinked with zinc oxide (ZnO) NPs was prepared. The solution of ZnO NPs with 200 nm promoted soybean growth at the concentration of 10 ppm, while fibers crosslinked with ZnO NPs promoted growth at a 1 ppm concentration. Soybeans grown on fiber cross-linked with ZnO NPs had higher Zn content in their roots than those grown in ZnO NPs solution. To study the positive mechanism of fiber crosslinked with ZnO NPs on soybean growth, a proteomic technique was used. Proteins categorized in photosynthesis and secondary metabolism accumulated more in soybeans grown on fiber crosslinked with ZnO NPs than in those grown in ZnO NPs solution. Furthermore, significantly accumulated proteins, which were NADPH oxidoreductase and tubulins, were confirmed using immunoblot analysis. The abundance of NADPH oxidoreductase increased in soybean by ZnO NPs application. These results suggest that fiber crosslinked with ZnO NPs enhances soybean growth through the increase of photosynthesis and secondary metabolism. Additionally, the accumulation of NADPH oxidoreductase might relate to the effect of auxin with fiber crosslinked with ZnO NPs on soybean growth.
PMID: 35806419
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (13) doi: 10.3390/ijms23137063
Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants.
Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.
PMID: 35806066
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (13) doi: 10.3390/ijms23137054
Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri.
School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
The SAUR (small auxin-up RNA) gene family is the biggest family of early auxin response genes in higher plants and has been associated with the control of a variety of biological processes. Although SAUR genes had been identified in several genomes, no systematic analysis of the SAUR gene family has been reported in Chinese white pear. In this study, comparative and systematic genomic analysis has been performed in the SAUR gene family and identified a total of 116 genes from the Chinese white pear. A phylogeny analysis revealed that the SAUR family could be classified into four groups. Further analysis of gene structure (introns/exons) and conserved motifs showed that they are diverse functions and SAUR-specific domains. The most frequent mechanisms are whole-genome duplication (WGD) and dispersed duplication (DSD), both of which may be important in the growth of the SAUR gene family in Chinese white pear. Moreover, cis-acting elements of the PbrSAUR genes were found in promoter regions associated with the auxin-responsive elements that existed in most of the upstream sequences. Remarkably, the qRT-PCR and transcriptomic data indicated that PbrSAUR13 and PbrSAUR52 were significantly expressed in fruit ripening. Subsequently, subcellular localization experiments revealed that PbrSAUR13 and PbrSAUR52 were localized in the nucleus. Moreover, PbrSAUR13 and PbrSAUR52 were screened for functional verification, and Dangshan pear and frandi strawberry were transiently transformed. Finally, the effects of these two genes on stone cells and lignin were analyzed by phloroglucinol staining, Fourier infrared spectroscopy, and qRT-PCR. It was found that PbrSAUR13 promoted the synthesis and accumulation of stone cells and lignin, PbrSAUR52 inhibited the synthesis and accumulation of stone cells and lignin. In conclusion, these results indicate that PbrSAUR13 and PbrSAUR52 are predominantly responsible for lignin inhibit synthesis, which provides a basic mechanism for further study of PbrSAUR gene functions.
PMID: 35806062
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (13) doi: 10.3390/ijms23137036
Progress and Applications of Plant Growth-Promoting Bacteria in Salt Tolerance of Crops.
Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan 250014, China.
Saline soils are a major challenge in agriculture, and salinization is increasing worldwide due to climate change and destructive agricultural practices. Excessive amounts of salt in soils cause imbalances in ion distribution, physiological dehydration, and oxidative stress in plants. Breeding and genetic engineering methods to improve plant salt tolerance and the better use of saline soils are being explored; however, these approaches can take decades to accomplish. A shorter-term approach to improve plant salt tolerance is to be inoculated with bacteria with high salt tolerance or adjusting the balance of bacteria in the rhizosphere, including endosymbiotic bacteria (living in roots or forming a symbiont) and exosymbiotic bacteria (living on roots). Rhizosphere bacteria promote plant growth and alleviate salt stress by providing minerals (such as nitrogen, phosphate, and potassium) and hormones (including auxin, cytokinin, and abscisic acid) or by reducing ethylene production. Plant growth-promoting rhizosphere bacteria are a promising tool to restore agricultural lands and improve plant growth in saline soils. In this review, we summarize the mechanisms of plant growth-promoting bacteria under salt stress and their applications for improving plant salt tolerance to provide a theoretical basis for further use in agricultural systems.
PMID: 35806037
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126841
Arabidopsis ERF012 Is a Versatile Regulator of Plant Growth, Development and Abiotic Stress Responses.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.; Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China.; State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China.
The AP2/ERF transcription factors are widely involved in the regulation of plant growth, development and stress responses. Arabidopsis ERF012 is differentially responsive to various stresses; however, its potential regulatory role remains elusive. Here, we show that ERF012 is predominantly expressed in the vascular bundles, lateral root primordium and vein branch points. ERF012 overexpression inhibits root growth, whereas it promotes root hair development and leaf senescence. In particular, ERF012 may downregulate its target genes AtC4H and At4CL1, key players in phenylpropanoid metabolism and cell wall formation, to hinder auxin accumulation and thereby impacting root growth and leaf senescence. Consistent with this, exogenous IAA application effectively relieves the effect of ERF012 overexpression on root growth and leaf senescence. Meanwhile, ERF012 presumably activates ethylene biosynthesis to promote root hair development, considering that the ERF012-mediated root hair development can be suppressed by the ethylene biosynthetic inhibitor. In addition, ERF012 overexpression displays positive and negative effects on low- and high-temperature responses, respectively, while conferring plant resistance to drought, salinity and heavy metal stresses. Taken together, this study provides a comprehensive evaluation of the functional versatility of ERF012 in plant growth, development and abiotic stress responses.
PMID: 35743283
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126784
BIG Modulates Stem Cell Niche and Meristem Development via SCR/SHR Pathway in Arabidopsis Roots.
State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China.; Hubei Hongshan Laboratory, Wuhan 430070, China.; State Key Laboratory of Hybrid Rice, The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
BIG, a regulator of polar auxin transport, is necessary to regulate the growth and development of Arabidopsis. Although mutations in the BIG gene cause severe root developmental defects, the exact mechanism remains unclear. Here, we report that disruption of the BIG gene resulted in decreased quiescent center (QC) activity and columella cell numbers, which was accompanied by the downregulation of WUSCHEL-RELATED HOMEOBOX5 (WOX5) gene expression. BIG affected auxin distribution by regulating the expression of PIN-FORMED proteins (PINs), but the root morphological defects of big mutants could not be rescued solely by increasing auxin transport. Although the loss of BIG gene function resulted in decreased expression of the PLT1 and PLT2 genes, genetic interaction assays indicate that this is not the main reason for the root morphological defects of big mutants. Furthermore, genetic interaction assays suggest that BIG affects the stem cell niche (SCN) activity through the SCRSCARECROW (SCR)/SHORT ROOT (SHR) pathway and BIG disruption reduces the expression of SCR and SHR genes. In conclusion, our findings reveal that the BIG gene maintains root meristem activity and SCN integrity mainly through the SCR/SHR pathway.
PMID: 35743225
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126754
Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L.
College of Forestry, Nanjing Forestry University, Nanjing 210037, China.; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Auxin participates in various physiological and molecular response-related developmental processes and is a pivotal hormone that regulates phenotypic formation in plants. Auxin response factors (ARFs) are vital transcription factors that mediate downstream auxin signaling by explicitly binding to auxin-responsive genes' promoters. Here, to investigate the possible developmental regulatory functions of ARFs in Ginkgo biloba, through employing comprehensive bioinformatics, we recognized 15 putative GbARF members. Conserved domains and motifs, gene and protein structure, gene duplication, GO enrichment, transcriptome expression profiles, and qRT-PCR all showed that Group I and III members were highly conserved. Among them, GbARF10b and GbARF10a were revealed as transcriptional activators in the auxin response for the development of Ginkgo male flowers through sequences alignment, cis-elements analysis and GO annotation; the results were corroborated for the treatment of exogenous SA. Moreover, the GbARFs expansion occurred predominantly by segmental duplication, and most GbARFs have undergone purifying selection. The Ka/Ks ratio test identified the functional consistence of GbARF2a and GbARF2c, GbARF10b, and GbARF10a in tissue expression profiles and male flower development. In summary, our study established a new research basis for exploring Ginkgo GbARF members' roles in floral organ development and hormone response.
PMID: 35743196
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126570
Genome-Wide Analysis of Genes Involved in the GA Signal Transduction Pathway in 'duli' Pear (Pyrus betulifolia Bunge).
College of Horticulture, Hebei Agricultural University, Baoding 071000, China.; School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK.
Gibberellic acid (GA) is an important phytohormone that regulates every aspect of plant growth and development. While elements involved in GA signaling have been identified and, hence, their functions have been well studied in model plants, such as Arabidopsis and rice, very little is known in pear. We, therefore, analyzed the genes related to GA signaling from the recently sequenced genome of the wildtype 'duli' pear (Pyrus betulifolia Bunge), a widely used rootstock for grafting in pear cultivation in China due to its vigorous growth and resistance to abiotic and biotic stress. In total, 15 genes were identified, including five GA receptors PbGID1s (GA-INSENSTIVE DWARF 1), six GA negative regulators, PbDELLAs, and four GA positive regulators, PbSLYs. Exogenous application of GA could promote the expression of PbGID1s but inhibit that of PbDELLAs and PbSLYs in tissue culture 'duli' pear seedlings. The expression profiles of these genes in field-grown trees under normal growth conditions, as well as in tissue-cultured seedlings treated with auxin (IAA), GA, paclobutrazol (PAC), abscisic acid (ABA), and sodium chloride (NaCl), were also studied, providing further evidence of the involvement of these genes in GA signaling in 'duli' pear plants. The preliminary results obtained in this report lay a good foundation for future research into GA signaling pathways in pear. Importantly, the identification and preliminary functional verification of these genes could guide molecular breeding in order to obtain the highly desired dwarf pear rootstocks for high-density plantation to aid easy orchard management and high yielding of pear fruits.
PMID: 35743013
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126390
Transcriptome and Metabolome Analysis Provide New Insights into the Process of Tuberization of Sechium edule Roots.
College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.; Institute for Processing and Storage of Agricultural Products, Chengdu Academy of Agricultural and Forest Sciences, Chengdu 611130, China.
Chayote (Sechium edule) produces edible tubers with high starch content after 1 year of growth but the mechanism of chayote tuberization remains unknown. 'Tuershao', a chayote cultivar lacking edible fruits but showing higher tuber yield than traditional chayote cultivars, was used to study tuber formation through integrative analysis of the metabolome and transcriptome profiles at three tuber-growth stages. Starch biosynthesis- and galactose metabolism-related genes and metabolites were significantly upregulated during tuber bulking, whereas genes encoding sugars will eventually be exported transporter (SWEET) and sugar transporter (SUT) were highly expressed during tuber formation. Auxin precursor (indole-3-acetamide) and ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, were upregulated, suggesting that both hormones play pivotal roles in tuber development and maturation. Our data revealed a similar tuber-formation signaling pathway in chayote as in potatoes, including complexes BEL1/KNOX and SP6A/14-3-3/FDL. Down-regulation of the BEL1/KNOX complex and upregulation of 14-3-3 protein implied that these two complexes might have distinct functions in tuber formation. Finally, gene expression and microscopic analysis indicated active cell division during the initial stages of tuber formation. Altogether, the integration of transcriptome and metabolome analyses unraveled an overall molecular network of chayote tuberization that might facilitate its utilization.
PMID: 35742832
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (11) doi: 10.3390/ijms23116352
The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.
Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.; VIB-UGent Center for Plant Systems, Technologiepark 71, 9052 Ghent, Belgium.; Department of Applied Genetics and Cell Biology (DAGZ), Institute of Molecular Plant Biology (IMPB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.; Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria.
Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.
PMID: 35683031
PLoS Genet , IF:5.917 , 2022 Jul , V18 (7) : Pe1010320 doi: 10.1371/journal.pgen.1010320
Cytidinediphosphate diacylglycerol synthase-Mediated phosphatidic acid metabolism is crucial for early embryonic development of Arabidopsis.
Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.; State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life and Science, Hubei University, Wuhan, China.
Embryonic development is a key developmental event in plant sexual reproduction; however, regulatory networks of plant early embryonic development, particularly the effects and functional mechanisms of phospholipid molecules are still unknown due to the limitation of sample collection and analysis. We innovatively applied the microspore-derived in vitro embryogenesis of Brassica napus and revealed the dynamics of phospholipid molecules, especially phosphatidic acid (PA, an important second messenger that plays an important role in plant growth, development, and stress responses), at different embryonic developmental stages by using a lipidomics approach. Further analysis of Arabidopsis mutants deficiency of CDS1 and CDS2 (cytidinediphosphate diacylglycerol synthase, key protein in PA metabolism) revealed the delayed embryonic development from the proembryo stage, indicating the crucial effect of CDS and PA metabolism in early embryonic development. Decreased auxin level and disturbed polar localization of auxin efflux carrier PIN1 implicate that CDS-mediated PA metabolism may regulate early embryogenesis through modulating auxin transport and distribution. These results demonstrate the dynamics and importance of phospholipid molecules during embryo development, and provide informative clues to elucidate the regulatory network of embryogenesis.
PMID: 35877676
Front Plant Sci , IF:5.753 , 2022 , V13 : P889045 doi: 10.3389/fpls.2022.889045
How Strigolactone Shapes Shoot Architecture.
Department of Biology, University of Fribourg, Fribourg, Switzerland.
Despite its central role in the control of plant architecture, strigolactone has been recognized as a phytohormone only 15 years ago. Together with auxin, it regulates shoot branching in response to genetically encoded programs, as well as environmental cues. A central determinant of shoot architecture is apical dominance, i.e., the tendency of the main shoot apex to inhibit the outgrowth of axillary buds. Hence, the execution of apical dominance requires long-distance communication between the shoot apex and all axillary meristems. While the role of strigolactone and auxin in apical dominance appears to be conserved among flowering plants, the mechanisms involved in bud activation may be more divergent, and include not only hormonal pathways but also sugar signaling. Here, we discuss how spatial aspects of SL biosynthesis, transport, and sensing may relate to apical dominance, and we consider the mechanisms acting locally in axillary buds during dormancy and bud activation.
PMID: 35903239
Front Plant Sci , IF:5.753 , 2022 , V13 : P875528 doi: 10.3389/fpls.2022.875528
New Insights Into the Activity of Apple Dihydrochalcone Phloretin: Disturbance of Auxin Homeostasis as Physiological Basis of Phloretin Phytotoxic Action.
Institute for Biological Research "Sinisa Stankovic" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia.; Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany, The Czech Academy of Sciences, Olomouc, Czechia.
Apple species are the unique naturally rich source of dihydrochalcones, phenolic compounds with an elusive role in planta, but suggested auto-allelochemical features related to "apple replant disease" (ARD). Our aim was to elucidate the physiological basis of the phytotoxic action of dihydrochalcone phloretin in the model plant Arabidopsis and to promote phloretin as a new prospective eco-friendly phytotoxic compound. Phloretin treatment induced a significant dose-dependent growth retardation and severe morphological abnormalities and agravitropic behavior in Arabidopsis seedlings. Histological examination revealed a reduced starch content in the columella cells and a serious disturbance in root architecture, which resulted in the reduction in length of meristematic and elongation zones. Significantly disturbed auxin metabolome profile in roots with a particularly increased content of IAA accumulated in the lateral parts of the root apex, accompanied by changes in the expression of auxin biosynthetic and transport genes, especially PIN1, PIN3, PIN7, and ABCB1, indicates the role of auxin in physiological basis of phloretin-induced growth retardation. The results reveal a disturbance of auxin homeostasis as the main mechanism of phytotoxic action of phloretin. This mechanism makes phloretin a prospective candidate for an eco-friendly bioherbicide and paves the way for further research of phloretin role in ARD.
PMID: 35873993
Front Plant Sci , IF:5.753 , 2022 , V13 : P929831 doi: 10.3389/fpls.2022.929831
Auxin Coordinates Achene and Receptacle Development During Fruit Initiation in Fragaria vesca.
College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.; Plant Synthetic Biology Center, Horticulture Biology and Metabolic Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.; College of Ecology and Resources Engineering, Wuyi University, Wuyishan, China.
In strawberries, fruit set is considered as the transition from the quiescent ovary to a rapidly growing fruit. Auxin, which is produced from the fertilized ovule in the achenes, plays a key role in promoting the enlargement of receptacles. However, detailed regulatory mechanisms for fruit set and the mutual regulation between achenes and receptacles are largely unknown. In this study, we found that pollination promoted fruit development (both achene and receptacle), which could be stimulated by exogenous auxin treatment. Interestingly, auxin was highly accumulated in achenes, but not in receptacles, after pollination. Further transcriptome analysis showed that only a small portion of the differentially expressed genes induced by pollination overlapped with those by exogenous auxin treatment. Auxin, but not pollination, was able to activate the expression of growth-related genes, especially in receptacles, which resulted in fast growth. Meanwhile, those genes involved in the pathways of other hormones, such as GA and cytokinin, were also regulated by exogenous auxin treatment, but not pollination. This suggested that pollination was not able to activate auxin responses in receptacles but produced auxin in fertilized achenes, and then auxin might be able to transport or transduce from achenes to receptacles and promote fast fruit growth at the early stage of fruit initiation. Our work revealed a potential coordination between achenes and receptacles during fruit set, and auxin might be a key coordinator.
PMID: 35873981
Front Plant Sci , IF:5.753 , 2022 , V13 : P943662 doi: 10.3389/fpls.2022.943662
Red and Blue Light Affect the Formation of Adventitious Roots of Tea Cuttings (Camellia sinensis) by Regulating Hormone Synthesis and Signal Transduction Pathways of Mature Leaves.
Tea Research Institute, Qingdao Agricultural University, Qingdao, China.; Rizhao Tea Research Institute, Rizhao, China.; Tea Research Institute, Shandong Academy of Agricultural Sciences, Rizhao, China.; College of Agronomy, Liaocheng University, Liaocheng, China.
Light is an important environmental factor which affects plant growth, through changes of intensity and quality. In this study, monochromatic white (control), red (660 nm), and blue (430 nm) light-emitting diodes (LEDs) were used to treat tea short cuttings. The results showed the most adventitious roots in blue light treated tea cuttings, but the lowest roots in that treated by red light. In order to explore the molecular mechanism of light quality affecting adventitious root formation, we performed full-length transcriptome and metabolome analyses of mature leaves under three light qualities, and then conducted weighted gene co-expression network analysis (WGCNA). Phytohormone analysis showed that Indole-3-carboxylic acid (ICA), Abscisic acid (ABA), ABA-glucosyl ester (ABA-GE), trans-Zeatin (tZ), and Jasmonic acid (JA) contents in mature leaves under blue light were significantly higher than those under white and red light. A crosstalk regulatory network comprising 23 co-expression modules was successfully constructed. Among them, the "MEblue" module which had a highly positive correlation with ICA (R = 0.92, P = 4e-04). KEGG analysis showed that related genes were significantly enriched in the "Plant hormone signal transduction (ko04075)" pathway. YUC (a flavin-containing monooxygenase), AUX1, AUX/IAA, and ARF were identified as hub genes, and gene expression analysis showed that the expression levels of these hub genes under blue light were higher than those under white and red light. In addition, we also identified 6 auxin transport-related genes, including PIN1, PIN3, PIN4, PILS5, PILS6, and PILS7. Except PILS5, all of these genes showed the highest expression level under blue light. In conclusion, this study elucidated the molecular mechanism of light quality regulating adventitious root formation of tea short cutting through WGCNA analysis, which provided an innovation for "rapid seedling" of tea plants.
PMID: 35873958
Front Plant Sci , IF:5.753 , 2022 , V13 : P837136 doi: 10.3389/fpls.2022.837136
Strigolactones and Cytokinin Interaction in Buds in the Control of Rice Tillering.
College of Biology Resources and Environmental Sciences, Jishou University, Jishou, China.; Key Laboratory of Plant Resources Conservation and Utilization, College of Hunan Province, Jishou, China.; Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China.
Shoot branching is among the most crucial morphological traits in rice (Oryza sativa L.) and is physiologically modulated by auxins, cytokinins (CKs), and strigolactones (SLs) cumulatively in rice. A number of studies focused on the interplay of these three hormones in regulating rice tiller extension. The present study primarily aimed at determining the impact of different treatments, which were used to regulate rice tiller and axillary bud development on node 2 at the tillering stage and full heading stage, respectively. Transcription levels of several genes were quantified through qRT-PCR analysis, and an endogenous auxin and four types of CKs were determined through LC-MS/MS. Both nutrient deficiency and exogenous SL supply were found to inhibit rice tiller outgrowth by reducing the CK content in the tiller buds. Furthermore, supplying the inhibitor of both exogenous SLs and endogenous SL synthesis could also affect the expression level of OsCKX genes but not the OsIPT genes. Comparison of OsCKX gene expression pattern under exogenous SL and CK supply suggested that the induction of OsCKX expression was most likely via a CK-induced independent pathway. These results combined with the expression of CK type-A RR genes in bud support a role for SLs in regulating bud outgrowth through the regulation of local CK levels. SL functioned antagonistically with CK in regulating the outgrowth of buds on node 2, by promoting the OsCKX gene expression in buds.
PMID: 35845690
Front Plant Sci , IF:5.753 , 2022 , V13 : P931105 doi: 10.3389/fpls.2022.931105
Dynamic Transcriptome Analysis Reveals Complex Regulatory Pathway Underlying Induction and Dose Effect by Different Exogenous Auxin IAA and 2,4-D During in vitro Embryogenic Redifferentiation in Cotton.
State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China.; College of Life Sciences, Huaibei Normal University, Huaibei City, China.
Plant somatic cells can reprogram into differentiated embryos through somatic embryogenesis (SE) on the condition of plant growth regulators (PGRs). RNA sequencing analysis was performed to investigate transcriptional profiling on cotton redifferentiated callus that was induced by different auxin types (IAA and 2,4-D), different concentrations (0, 0.025, and 0.05 mg L(-1)), and different incubation times (0, 5, and 20 days). Under the 2,4-D induction effect, signal transduction pathways of plant hormones were significantly enriched in the embryogenic response stage (5 days). These results indicated that auxin signal transduction genes were necessary for the initial response of embryogenic differentiation. In the pre-embryonic initial period (20 days), the photosynthetic pathway was significantly enriched. Most differentially expressed genes (DEGs) were downregulated under the induction of 2,4-D. Upon the dose effect of IAA and 2,4-D, respectively, pathways were significantly enriched in phenylpropanoid biosynthesis, fatty acid metabolism, and carbon metabolic pathways. Therefore, primary and secondary metabolism pathways were critical in cotton SE. These results showed that complex synergistic mechanisms involving multiple cellular pathways were the causes of the induction and dose effect of auxin-induced SE. This study reveals a systematic molecular response to auxin signals and reveals the way that regulates embryogenic redifferentiation during cotton SE.
PMID: 35845676
Front Plant Sci , IF:5.753 , 2022 , V13 : P938476 doi: 10.3389/fpls.2022.938476
eIF4E1 Regulates Arabidopsis Embryo Development and Root Growth by Interacting With RopGEF7.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China.; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences and Technology, Guangxi University, Nanning, China.
Eukaryotic translation initiation factor 4E1 (eIF4E1) is required for the initiation of protein synthesis. The biological function of eIF4E1 in plant-potyvirus interactions has been extensively studied. However, the role of eIF4E1 in Arabidopsis development remains unclear. In this study, we show that eIF4E1 is highly expressed in the embryo and root apical meristem. In addition, eIF4E1 expression is induced by auxin. eIF4E1 mutants show embryonic cell division defects and short primary roots, a result of reduced cell divisions. Furthermore, our results show that mutation in eIF4E1 severely reduces the accumulation of PIN-FORMED (PIN) proteins and decreases auxin-responsive gene expression at the root tip. Yeast two-hybrid assays identified that eIF4E1 interacts with an RAC/ROP GTPase activator, RopGEF7, which has been previously reported to be involved in the maintenance of the root apical meristem. The interaction between eIF4E1 and RopGEF7 is confirmed by protein pull-down and bimolecular fluorescent complementation assays in plant cells. Taken together, our results demonstrated that eIF4E1 is important for auxin-regulated embryo development and root growth. The eIF4E1-RopGEF7 interaction suggests that eIF4E1 may act through ROP signaling to regulate auxin transport, thus regulating auxin-dependent patterning.
PMID: 35845661
Front Plant Sci , IF:5.753 , 2022 , V13 : P905577 doi: 10.3389/fpls.2022.905577
Adaptation of the Invasive Plant (Sphagneticola trilobata L. Pruski) to a High Cadmium Environment by Hybridizing With Native Relatives.
Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China.; College of Life Science, Huizhou University, Huizhou, China.
Invasive species can evolve rapidly in the invasion areas to adapt to new habitats. Sphagneticola trilobata L. Pruski, an invasive species, was studied for its tolerance to cadmium (Cd) in the soil and compared with its natural hybrid. From the perspective of photosynthetic physiology, antioxidant characteristics, and leaf hormone levels, the differences between the leaves of the two species before and after Cd treatment were compared. The results showed that the hybrid had stronger tolerance to Cd stress than invasive species. After Cd stress, the indexes of gas-exchange [net photosynthetic rate (Pn), intercellular CO2 concentration (Ci), stomatal conductance (Gs), and transpiration rate (Tr)] of the hybrid was higher than invasive species, while the content of non-enzymatic antioxidants (flavonoids and total phenols) and antioxidant enzyme activities [peroxidase (POD) and superoxide dismutase (SOD)] was lower in hybrid than in invasive species. The changes in the content of plant hormones [auxin (IAA) and abscisic acid (ABA)] under Cd stress showed that hybrid can still maintain growth and prevent leaf senescence. Furthermore, the differences in gene expression between hybrid and invasive species in photosynthetic physiology, the antioxidant capacity of leaves, and endogenous hormone (IAA and ABA) synthesis pathway also showed that hybrid has stronger Cd tolerance than invasive species. This suggests that invasive species will realize the invasion through hybridization with the native relatives to overcome the stress from environmental factors. The study implied that hybridization between invasive species and native relatives is an important way for invasive species to spread in a wider and new environment that invasive species have not experienced in the area of origin.
PMID: 35845659
Front Plant Sci , IF:5.753 , 2022 , V13 : P757852 doi: 10.3389/fpls.2022.757852
Interaction With Fungi Promotes the Accumulation of Specific Defense Molecules in Orchid Tubers and May Increase the Value of Tubers for Biotechnological and Medicinal Applications: The Case Study of Interaction Between Dactylorhiza sp. and Tulasnella calospora.
Potato Research Institute, Ltd., Havlickuv Brod, Czechia.; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia.; Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia.; Department of Biology of Ecosystems, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia.; W. Bock GmbH & Co. KG, Bremen, Germany.; Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Turkey.
Terrestrial orchids can form tubers, organs modified to store energy reserves. Tubers are an attractive source of nutrients, and salep, a flour made from dried orchid tubers, is the source of traditional beverages. Tubers also contain valuable secondary metabolites and are used in traditional medicine. The extensive harvest of wild orchids is endangering their populations in nature; however, orchids can be cultivated and tubers mass-produced. This work illustrates the importance of plant-fungus interaction in shaping the content of orchid tubers in vitro. Orchid plants of Dactylorhiza sp. grown in asymbiotic culture were inoculated with a fungal isolate from Tulasnella calospora group and, after 3 months of co-cultivation, tubers were analyzed. The fungus adopted the saprotrophic mode of life, but no visible differences in the morphology and biomass of the tubers were detected compared to the mock-treated plants. To elucidate the mechanisms protecting the tubers against fungal infestation, proteome, metabolome, and lipidome of tubers were analyzed. In total, 1,526, 174, and 108 proteins, metabolites, and lipids were quantified, respectively, providing a detailed snapshot of the molecular process underlying plant-microbe interaction. The observed changes at the molecular level showed that the tubers of inoculated plants accumulated significantly higher amounts of antifungal compounds, including phenolics, alkaloid Calystegine B2, and dihydrophenanthrenes. The promoted antimicrobial effects were validated by observing transient inhibition of Phytophthora cactorum growth. The integration of omics data highlighted the promotion of flavonoid biosynthesis, the increase in the formation of lipid droplets and associated production of oxylipins, and the accumulation of auxin in response to T. calospora. Taken together, these results provide the first insights into the molecular mechanisms of defense priming in orchid tubers and highlight the possible use of fungal interactors in biotechnology for the production of orchid secondary metabolites.
PMID: 35845638
Front Plant Sci , IF:5.753 , 2022 , V13 : P904198 doi: 10.3389/fpls.2022.904198
Integrate QTL Mapping and Transcription Profiles Reveal Candidate Genes Regulating Flowering Time in Brassica napus.
State Key Laboratory of Arid Land Crop Sciences, Gansu Agricultural University, Lanzhou, China.
Flowering at the proper time is an important part of acclimation to the ambient environment and season and maximizes the plant yield. To reveal the genetic architecture and molecular regulation of flowering time in oilseed rape (Brassica napus), we performed an RNA-seq analysis of the two parents after vernalization at low temperature and combined this with quantitative trait loci (QTL) mapping in an F2 population. A genetic linkage map that included 1,017 markers merged into 268 bins and covered 793.53 cM was constructed. Two QTLs associated with flowering time were detected in the F2 population. qFTA06 was the major QTL in the 7.06 Mb interval on chromosome A06 and accounted for 19.3% of the phenotypic variation. qFTC08 was located on chromosome C06 and accounted for 8.6% of the phenotypic variation. RNA-seq analysis revealed 4,626 differentially expressed genes (DEGs) between two parents during vernalization. Integration between QTL mapping and RNA-seq analysis revealed six candidate genes involved in the regulation of flowering time through the circadian clock/photoperiod, auxin and ABA hormone signal, and cold signal transduction and vernalization pathways. These results provide insights into the molecular genetic architecture of flowering time in B. napus.
PMID: 35837459
Front Plant Sci , IF:5.753 , 2022 , V13 : P938697 doi: 10.3389/fpls.2022.938697
Mucilaginibacter sp. K Improves Growth and Induces Salt Tolerance in Nonhost Plants via Multilevel Mechanisms.
School of Biology, Food and Environment, Hefei University, Hefei, China.; Department of Plant Science, McGill University, Montreal, QC, Canada.
Soil salinity negatively modulates plant growth and development, contributing to severe decreases in the growth and production of crops. Mucilaginibacter sp. K is a root endophytic bacterium that was previously reported by our laboratory to stimulate growth and confer salt tolerance in Arabidopsis (Arabidopsis thaliana). The main purpose of the present study is to elucidate the physiological and molecular machinery responsible for the prospective salt tolerance as imparted by Mucilaginibacter sp. K. We first report that auxin, gibberellin, and MPK6 signalings were required for strain K-induced growth promotion and salt tolerance in Arabidopsis. Then, this strain was assessed as a remediation strategy to improve maize performance under salinity stress. Under normal growth conditions, the seed vigor index, nitrogen content, and plant growth were significantly improved in maize. After NaCl exposure, strain K significantly promoted the growth of maize seedlings, ameliorated decline in chlorophyll content and reduced accretion of MDA and ROS compared with the control. The possible mechanisms involved in salt resistance in maize could be the improved activities of SOD and POD (antioxidative system) and SPS (sucrose biosynthesis), upregulated content of total soluble sugar and ABA, and reduced Na(+) accumulation. These physiological changes were then confirmed by induced gene expression for ion transportation, photosynthesis, ABA biosynthesis, and carbon metabolism. In summary, these results suggest that strain K promotes plant growth through increases in photosynthesis and auxin- and MPK6-dependent pathways; it also bestows salt resistance on plants through protection against oxidative toxicity, Na(+) imbalance, and osmotic stress, along with the activation of auxin-, gibberellin-, and MPK6-dependent signaling pathways. This is the first detailed report of maize growth promotion by a Mucilaginibacter sp. strain from wild plant. This strain could be used as a favorable biofertilizer and a salinity stress alleviator for maize, with further ascertainment as to its reliability of performance under field conditions and in the presence of salt stress.
PMID: 35832221
Front Plant Sci , IF:5.753 , 2022 , V13 : P924044 doi: 10.3389/fpls.2022.924044
Comparative Transcriptomic, Anatomical and Phytohormone Analyses Provide New Insights Into Hormone-Mediated Tetraploid Dwarfing in Hybrid Sweetgum (Liquidambar styraciflua x L. formosana).
National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.; College of Landscape Architecture, Beijing University of Agriculture, Beijing, China.; Guangxi Bagui Forest and Flowers Seedlings Co., Ltd., Nanning, China.
Polyploid breeding is an effective approach to improve plant biomass and quality. Both fast growth and dwarf types of in vitro or ex vitro plants are produced after polyploidization. However, little is known regarding the dwarf type mechanism in polyploids grown in vitro. In this study, the morphological and cytological characteristics were measured in tetraploid and diploid hybrid sweetgum (Liquidambar styraciflua x L. formosana) with the same genetic background. RNA sequencing (RNA-Seq) was used to analyse shoot and root variations between tetraploid and diploid plants; important metabolites were validated. The results showed that the shoot and root lengths were significantly shorter in tetraploids than in diploids after 25 d of culture. Most tetraploid root cells were wider and more irregular, and the length of the meristematic zone was shorter, while tetraploid cells were significantly larger than diploid cells. Differentially expressed genes (DEGs) were significantly enriched in the plant growth and organ elongation pathways, such as plant hormone biosynthesis and signal transduction, sugar and starch metabolism, and cell cycles. Hormone biosynthesis and signal transduction genes, such as YUCCA, TAA1, GH3, SAUR, CPS, KO, KAO, GA20ox, GA3ox, BAS1 and CYCD3, which help to regulate organ elongation, were generally downregulated. The auxin, gibberellin, and brassinolide (BL) contents in roots and stems were significantly lower in tetraploids than in diploids, which may greatly contribute to slow growth in the roots and stems of tetraploid regenerated plants. Exogenous gibberellic acid (GA3) and indole-3-acetic acid (IAA), which induced plant cell elongation, could significantly promote growth in the stems and roots of tetraploids. In summary, comparative transcriptomics and metabolite analysis showed that the slow growth of regenerated tetraploid hybrid sweetgum was strongly related to auxin and gibberellin deficiency. Our findings provide insights into the molecular mechanisms that underlie dwarfism in allopolyploid hybrid sweetgum.
PMID: 35832220
Front Plant Sci , IF:5.753 , 2022 , V13 : P928386 doi: 10.3389/fpls.2022.928386
The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses.
Centro de Biotecnologia y Genomica de Plantas,Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentacion (INIA /CSIC), Madrid, Spain.; Umea Plant Science Center, Umea University, Umea, Sweden.; Institute of Biology, University of Graz, Graz, Austria.; Institute of Botany, Technische Universitat Dresden, Dresden, Germany.; Departamento de Biotecnologia-Biologia Vegetal, Escuela Tecnica Superior de Ingenieria Agronomica, Alimentaria y de Biosistemas, Universidad Politecnica de Madrid (UPM), Madrid, Spain.
The accumulation of the auxin precursor indole-3-acetamide (IAM) in the ami1 mutant has recently been reported to reduce plant growth and to trigger abiotic stress responses in Arabidopsis thaliana. The observed response includes the induction of abscisic acid (ABA) biosynthesis through the promotion of NCED3 expression. The mechanism by which plant growth is limited, however, remained largely unclear. Here, we investigated the transcriptional responses evoked by the exogenous application of IAM using comprehensive RNA-sequencing (RNA-seq) and reverse genetics approaches. The RNA-seq results highlighted the induction of a small number of genes, including the R2R3 MYB transcription factor genes MYB74 and MYB102. The two MYB factors are known to respond to various stress cues and to ABA. Consistent with a role as negative plant growth regulator, conditional MYB74 overexpressor lines showed a considerable growth reduction. RNA-seq analysis of MYB74 mutants indicated an association of MYB74 with responses to osmotic stress, water deprivation, and seed development, which further linked MYB74 with the observed ami1 osmotic stress and seed phenotype. Collectively, our findings point toward a role for MYB74 in plant growth control and in responses to abiotic stress stimuli.
PMID: 35812959
Front Plant Sci , IF:5.753 , 2022 , V13 : P917493 doi: 10.3389/fpls.2022.917493
Multi-Omics Analysis Reveals a Regulatory Network of ZmCCT During Maize Resistance to Gibberella Stalk Rot at the Early Stage.
Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China.; State Key Laboratory of Agricultural Microbiology and Provincial Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases in maize; however, the regulatory mechanism of resistance to GSR remains largely unknown. We performed a comparative multi-omics analysis to reveal the early-stage resistance of maize to GSR. We inoculated F. graminearum to the roots of susceptible (Y331) and resistant (Y331-DeltaTE) near-isogenic lines containing GSR-resistant gene ZmCCT for multi-omics analysis. Transcriptome detected a rapid reaction that confers resistance at 1-3 hpi as pattern-triggered immunity (PTI) response to GSR. Many key properties were involved in GSR resistance, including genes in photoperiod and hormone pathways of salicylic acid and auxin. The activation of programmed cell death-related genes and a number of metabolic pathways at 6 hpi might be important to prevent further colonization. This is consistent with an integrative analysis of transcriptomics and proteomics that resistant-mediated gene expression reprogramming exhibited a dynamic pattern from 3 to 6 hpi. Further metabolomics analysis revealed that the amount of many chemical compounds was altered in pathways associated with the phenylpropanoid biosynthesis and the phenylalanine metabolism, which may play key roles to confer the GSR resistance. Taken together, we generated a valuable resource to interpret the defense mechanism during early GSR resistance.
PMID: 35812937
Front Plant Sci , IF:5.753 , 2022 , V13 : P935540 doi: 10.3389/fpls.2022.935540
Developmental Characteristics and Auxin Response of Epiphytic Root in Dendrobium catenatum.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.
Dendrobium catenatum, a traditional precious Chinese herbal medicine, belongs to epiphytic orchids. Its special life mode leads to the specialization of roots, but there is a lack of systematic research. The aerial root in D. catenatum displays diverse unique biological characteristics, and it initially originates from the opposite pole of the shoot meristem within the protocorm. The root development of D. catenatum is not only regulated by internal cues but also adjusts accordingly with the change in growth environments. D. catenatum root is highly tolerant to auxin, which may be closely related to its epiphytic life. Exogenous auxin treatment has dual effects on D. catenatum roots: relatively low concentration promotes root elongation, which is related to the induced expression of cell wall synthesis genes; excessive concentration inhibits the differentiation of velamen and exodermis and promotes the overproliferation of cortical cells, which is related to the significant upregulation of WOX11-WOX5 regeneration pathway genes and cell division regulatory genes. Overexpression of D. catenatum WOX12 (DcWOX12) in Arabidopsis inhibits cell and organ differentiation, but induces cell dedifferentiation and callus production. Therefore, DcWOX12 not only retains the characteristics of ancestors as stem cell regulators, but also obtains stronger cell fate transformation ability than homologous genes of other species. These findings suggest that the aerial root of D. catenatum evolves special structure and developmental characteristics to adapt to epiphytic life, providing insight into ideal root structure breeding of simulated natural cultivation in D. catenatum and a novel target gene for improving the efficiency of monocot plant transformation.
PMID: 35812932
Front Plant Sci , IF:5.753 , 2022 , V13 : P862398 doi: 10.3389/fpls.2022.862398
Constitutive Active CPK30 Interferes With Root Growth and Endomembrane Trafficking in Arabidopsis thaliana.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; VIB Center for Plant Systems Biology, Ghent, Belgium.; Universite Paris-Saclay, CNRS, INRAE, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France.; Universite de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France.; Department of Plants and Crops, Ghent University, Ghent, Belgium.; Institute of Science and Technology Austria, Klosterneuburg, Austria.; Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, South Korea.
Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.
PMID: 35783951
Front Plant Sci , IF:5.753 , 2022 , V13 : P886268 doi: 10.3389/fpls.2022.886268
N-3-Oxo-Octanoyl Homoserine Lactone Primes Plant Resistance Against Necrotrophic Pathogen Pectobacterium carotovorum by Coordinating Jasmonic Acid and Auxin-Signaling Pathways.
State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.; Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.; Biology Institute, Hebei Academy of Sciences, Shijiazhuang, China.; Julu Institute of Applied Technology, Xingtai, China.
Many Gram-negative bacteria use small signal molecules, such as N-acyl-homoserine lactones (AHLs), to communicate with each other and coordinate their collective behaviors. Recently, increasing evidence has demonstrated that long-chained quorum-sensing signals play roles in priming defense responses in plants. Our previous work indicated that a short-chained signal, N-3-oxo-octanoyl homoserine lactone (3OC8-HSL), enhanced Arabidopsis resistance to the hemi-biotrophic bacteria Pseudomonas syringae pv. tomato DC3000 through priming the salicylic acid (SA) pathway. Here, we found that 3OC8-HSL could also prime resistance to the necrotrophic bacterium Pectobacterium carotovorum ssp. carotovorum (Pcc) through the jasmonic acid (JA) pathway, and is dependent on auxin responses, in both Chinese cabbage and Arabidopsis. The subsequent Pcc invasion triggered JA accumulation and increased the down-stream genes' expressions of JA synthesis genes (LOX, AOS, and AOC) and JA response genes (PDF1.2 and VSP2). The primed state was not observed in the Arabidopsis coi1-1 and jar1-1 mutants, which indicated that the primed resistance to Pcc was dependent on the JA pathway. The 3OC8-HSL was not transmitted from roots to leaves and it induced indoleacetic acid (IAA) accumulation and the DR5 and SAUR auxin-responsive genes' expressions in seedlings. When Arabidopsis and Chinese cabbage roots were pretreated with exogenous IAA (10 muM), the plants had activated the JA pathway and enhanced resistance to Pcc, which implied that the JA pathway was involved in AHL priming by coordinating with the auxin pathway. Our findings provide a new strategy for the prevention and control of soft rot in Chinese cabbage and provide theoretical support for the use of the quorum-sensing AHL signal molecule as a new elicitor.
PMID: 35774826
Front Plant Sci , IF:5.753 , 2022 , V13 : P889615 doi: 10.3389/fpls.2022.889615
Trehalose Outperforms Chitosan, Humic Acid and Gamma-Aminobutyric Acid in Promoting the Growth of Field Maize.
Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.; Institution of Plant Nutrition and Environmental Resources, Henan Academy of Agricultural Sciences, Zhengzhou, China.
Despite the fact that there are many distinct types of plant growth regulators (PGRs), the diverse ways in which they regulate plant development are rarely compared. In this study, four PGRs (trehalose, chitosan, humic acid and gamma-aminobutyric acid) were selected and sprayed folially, and plant samples were collected while maize was at vegetative leaf stages 6, 10, and 14 (V6, V10, and V14, respectively) to reveal the effects of different PGRs on photosynthesis, dry matter accumulation, oxidative stress, carbon and nitrogen metabolism, hormone levels, and gene expression of maize. Results showed that 100 mg/L PGRs did not induce oxidative damage or repair activities in maize. Trehalose significantly increased chlorophyll content at V6 and promoted dry matter (roots and shoots) accumulation at V6 and V10. The activities of carbon and nitrogen metabolizing enzymes were significantly enhanced by trehalose treatment, which promoted the accumulation of sucrose and soluble sugar, but did not affect the biosynthesis of auxin and gibberellin at V6. Changes in carbon and nitrogen metabolism enzymes are regulated by transcription of related synthetic genes. Lower starch content and higher sucrose content in trehalose-treated maize leaves are important biological characteristics. Further analysis revealed that the effect of trehalose on the metabolic activity of maize was a short-term promoting effect (0-12 days), while the effect on maize growth was a long-term cumulative effect (13-28 days). Overall, exogenous trehalose induced stronger carbon and nitrogen metabolic activity, higher photosynthetic capacity and more dry matter accumulation than chitosan, humic acid and gamma-aminobutyric acid.
PMID: 35774813
Front Plant Sci , IF:5.753 , 2022 , V13 : P923183 doi: 10.3389/fpls.2022.923183
Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.).
Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.; Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzho, China.
Longan (Dimocarpus longan Lour.) is a tropical/subtropical fruit tree of significant economic importance. Floral induction is an essential process for longan flowering and plays decisive effects on the longan yield. Due to the instability of flowering, it is necessary to understand the molecular mechanisms of floral induction in longan. In this study, mRNA and long noncoding RNA (lncRNA) transcriptome sequencing were performed using the apical buds of fruiting branches as materials. A total of 7,221 differential expressions of mRNAs (DEmRNAs) and 3,238 differential expressions of lncRNAs (DElncRNAs) were identified, respectively. KEGG enrichment analysis of DEmRNAs highlighted the importance of starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways during floral induction. Combining the analysis of weighted gene co-expression network (WGCNA) and expression pattern of DEmRNAs in the three pathways, specific transcriptional characteristics at each stage during floral induction and regulatory network involving co-expressed genes were investigated. The results showed that sucrose metabolism and auxin signal transduction may be crucial for the growth and maturity of autumn shoots in September and October (B1-B2 stage); starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways participated in the regulation of floral bud physiological differentiation together in November and December (B3-B4 stage) and the crosstalk among three pathways was also found. Hub genes in the co-expression network and key DEmRNAs in three pathways were identified. The circadian rhythm genes FKF1 and GI were found to activate SOC1gene through the photoperiod core factor COL genes, and they were co-expressed with auxin, gibberellin, abscisic acid, ethylene signaling genes, and sucrose biosynthesis genes at B4 stage. A total of 12 hub-DElncRNAs had potential for positively affecting their distant target genes in three putative key pathways, predominantly in a co-transcriptional manner. A hypothetical model of regulatory pathways and key genes and lncRNAs during floral bud induction in longan was proposed finally. Our studies will provide valuable clues and information to help elucidate the potential molecular mechanisms of floral initiation in longan and woody fruit trees.
PMID: 35774802
Front Plant Sci , IF:5.753 , 2022 , V13 : P902694 doi: 10.3389/fpls.2022.902694
Melatonin-Induced Protection Against Plant Abiotic Stress: Mechanisms and Prospects.
Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, China.; Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan.; Department of Agronomy, Sub-Campus Depalpur, Okara, University of Agriculture Faisalabad, Faisalabad, Pakistan.; Biology Department, Collage of Science, Jouf University, Sakaka, Saudi Arabia.; Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia.; Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia.; Department of Agriculture, Guru Nanak Dev University, Amritsar, India.; Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, Egypt.; Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey.; Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah, Saudi Arabia.
Global warming in this century increases incidences of various abiotic stresses restricting plant growth and productivity and posing a severe threat to global food production and security. The plant produces different osmolytes and hormones to combat the harmful effects of these abiotic stresses. Melatonin (MT) is a plant hormone that possesses excellent properties to improve plant performance under different abiotic stresses. It is associated with improved physiological and molecular processes linked with seed germination, growth and development, photosynthesis, carbon fixation, and plant defence against other abiotic stresses. In parallel, MT also increased the accumulation of multiple osmolytes, sugars and endogenous hormones (auxin, gibberellic acid, and cytokinins) to mediate resistance to stress. Stress condition in plants often produces reactive oxygen species. MT has excellent antioxidant properties and substantially scavenges reactive oxygen species by increasing the activity of enzymatic and non-enzymatic antioxidants under stress conditions. Moreover, the upregulation of stress-responsive and antioxidant enzyme genes makes it an excellent stress-inducing molecule. However, MT produced in plants is not sufficient to induce stress tolerance. Therefore, the development of transgenic plants with improved MT biosynthesis could be a promising approach to enhancing stress tolerance. This review, therefore, focuses on the possible role of MT in the induction of various abiotic stresses in plants. We further discussed MT biosynthesis and the critical role of MT as a potential antioxidant for improving abiotic stress tolerance. In addition, we also addressed MT biosynthesis and shed light on future research directions. Therefore, this review would help readers learn more about MT in a changing environment and provide new suggestions on how this knowledge could be used to develop stress tolerance.
PMID: 35755707
Front Plant Sci , IF:5.753 , 2022 , V13 : P918112 doi: 10.3389/fpls.2022.918112
The Adaxial/Abaxial Patterning of Auxin and Auxin Gene in Leaf Veins Functions in Leafy Head Formation of Chinese Cabbage.
Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China.; National Engineering Research Center for Vegetables, Beijing, China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China.; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China.; Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Leaf curling is an essential prerequisite for the formation of leafy heads in Chinese cabbage. However, the part or tissue that determines leaf curvature remains largely unclear. In this study, we first introduced the auxin-responsive marker DR5::GUS into the Chinese cabbage genome and visualized its expression during the farming season. We demonstrated that auxin response is adaxially/abaxially distributed in leaf veins. Together with the fact that leaf veins occupy considerable proportions of the Chinese cabbage leaf, we propose that leaf veins play a crucial supporting role as a framework for heading. Then, by combining analyses of QTL mapping and a time-course transcriptome from heading Chinese cabbage and non-heading pak choi during the farming season, we identified the auxin-related gene BrPIN5 as a strong candidate for leafy head formation. PIN5 displays an adaxial/abaxial expression pattern in leaf veins, similar to that of DR5::GUS, revealing an involvement of BrPIN5 in leafy head development. The association of BrPIN5 function with heading was further confirmed by its haplo-specificity to heading individuals in both a natural population and two segregating populations. We thus conclude that the adaxial/abaxial patterning of auxin and auxin genes in leaf veins functions in the formation of the leafy head in Chinese cabbage.
PMID: 35755702
Front Plant Sci , IF:5.753 , 2022 , V13 : P924490 doi: 10.3389/fpls.2022.924490
Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress.
Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China.; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China.; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China.; College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China.
Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.
PMID: 35755690
Front Plant Sci , IF:5.753 , 2022 , V13 : P902902 doi: 10.3389/fpls.2022.902902
Design, Synthesis, and Action Mechanism of 1,3-Benzodioxole Derivatives as Potent Auxin Receptor Agonists and Root Growth Promoters.
College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.; College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou, China.; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
Deeper and longer roots allow crops to survive and flourish, but our understanding of the plant growth regulators promoting root system establishment is limited. Here, we report that, a novel auxin receptor agonist, named K-10, had a remarkable promotive effect on root growth in both Arabidopsis thaliana and Oryza sativa through the enhancement of root-related signaling responses. Using computer-aided drug discovery approaches, we developed potent lead compound by screening artificial chemicals on the basis of the auxin receptor TIR1 (Transport Inhibitor Response 1), and a series of N-(benzo[d] [1,3] dioxol-5-yl)-2-(one-benzylthio) acetamides, K-1 to K-22, were designed and synthesized. The results of bioassay showed that K-10 exhibited an excellent root growth-promoting activity far exceeding that of NAA (1-naphthylacetic acid). A further morphological investigation of the auxin related mutants (yucQ, tir1) revealed that K-10 had auxin-like physiological functions and was recognized by TIR1, and K-10 significantly enhanced auxin response reporter's (DR5:GUS) transcriptional activity. Consistently, transcriptome analysis showed that K-10 induced a common transcriptional response with auxin and down-regulated the expression of root growth-inhibiting genes. Further molecular docking analysis revealed that K-10 had a stronger binding ability with TIR1 than NAA. These results indicated that this class of derivatives could be a promising scaffold for the discovery and development of novel auxin receptor agonists, and the employment of K-10 may be effective for enhancing root growth and crop production.
PMID: 35755644
Front Plant Sci , IF:5.753 , 2022 , V13 : P898786 doi: 10.3389/fpls.2022.898786
Integrative Analysis of the GRAS Genes From Chinese White Pear (Pyrus bretschneideri): A Critical Role in Leaf Regeneration.
School of Life Sciences, Anhui Agricultural University, Hefei, China.; Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia.
GRAS is a transcription regulator factor, which plays an important role in plant growth and development. Previous analyses found that several GRAS functions have been identified, such as axillary bud meristem formation, radial root elongation, gibberellin signaling, light signaling, and abiotic stress. The GRAS family has been comprehensively evaluated in several species. However, little finding is on the GRAS transcription factors (TFs) in Chinese white pear. In this study, 99 PbGRAS were systemically characterized and renamed PbGRAS1 to PbGRAS99 according to their chromosomal localizations. Phylogenetic analysis and structural features revealed that could be classified into eight subfamilies (LISCL, Ls, SHR, HAM, SCL, PAT, SCR, and DELLA). Further analysis of introns/exons and conserved motifs revealed that they are diverse and functionally differentiated in number and structure. Synteny analysis among Pyrus bretschenedri, Prunus mume, Prunus avium, Fragaria vesca, and Prunus persica showed that GRAS duplicated regions were more conserved. Dispersed duplication events are the most common mechanism and may play a crucial role in the expansion of the GRAS gene family. In addition, cis-acting elements of the PbGRAS gene were found in promoter regions associated with hormone and environmental stress responses. Notably, the expression pattern detected by qRT-PCR indicated that PbGRAS genes were differentially expressed under gibberellin (GA), abscisic acid (ABA), and auxin (IAA) conditions, which are responsive to abiotic stress. PbGRAS89 and PbGRAS99 were highly expressed at different stages of hormone treatment and may play important role in leaf development. Therefore, we selected PbGRAS89 and PbGRAS99 to clone and construct pCAMBIA1301-PbGRAS89, 99 and transferred them into Arabidopsis thaliana. Finally, we observed and compared the changes of overexpressed plants and wild-type plants during regeneration. This method was used to analyze their roles in leaf regeneration of Chinese white pear. In addition, we also constructed pCAMBIA1305-PbGRAS89, 99, and transferred them into onion cells to determine the subcellular localization. Subcellular localization experiments showed that PbGRAS89 and PbGRAS99 were localized in the nucleus. In summary, the results of this study indicate that PbGRAS89 and PbGRAS99 are mainly responsible for leaf regeneration of Chinese white pear, which plays a positive role in callus formation and provides rich resources for studying GRAS gene functions.
PMID: 35734253
Front Plant Sci , IF:5.753 , 2022 , V13 : P917354 doi: 10.3389/fpls.2022.917354
Growth-Defense Trade-Offs Induced by Long-term Overgrazing Could Act as a Stress Memory.
School of Ecology and Environment, Inner Mongolia University, Hohhot, China.; Department of Biology, Edge Hill University, Ormskirk, United Kingdom.; Inner Mongolia Mongolian Grass Seed Industry Science and Technology Research Institute Co., Ltd., Hohhot, China.
Long-term overgrazing (OG) is one of the key drivers of global grassland degradation with severe loss of productivity and ecosystem functions, which may result in stress memory such as smaller stature of grassland plants. However, how the OG-induced stress memory could be regulated by phytohormones is unknown. In this study, we investigated the changes of four phytohormones of cloned offspring of Leymus chinensis that were developed from no-grazing (NG) plants and OG plants with a grazing history of 30 years. The concentrations of auxin (IAA) and gibberellic acid (GA) in OG plant leaves were 45% and 20% lower than control, respectively. Meanwhile, the level of abscisic acid (ABA) in OG leaves nearly doubled compared with that in NG leaves. The situation was quite similar in roots. Unexpectedly, no significant changes in the jasmonic acid (JA) level were observed between OG and NG plants. The changes in gene expression patterns between OG and NG plants were also investigated by transcriptomic analysis. In total, 302 differentially expressed genes (DEGs) were identified between OG and NG plants, which were mainly classified into the functions of synthesis, receptor, and signal transduction processes of phytohormones. The expression of 24 key genes related to the biosynthesis and signal transduction of IAA and GA was downregulated in OG plants. Among them, OASA1 and AO1 (regulating the biosynthesis of IAA and ABA, respectively) were reduced significantly by 88 and 92%, respectively. In addition, the content of secondary metabolites related to plant defense such as flavonoids and phenols was also increased in leaves. Taken together, the decrease of positive plant growth-related hormones (IAA and GA) together with the increase of plant stress-related hormones or factors (ABA, flavonoids, and phenols) induced the growth-defense trade-offs for L. chinensis adaptation to long-term OG stress. The findings reported in this study shed new light on the mechanism of plant-animal interaction in the grassland ecosystem and provide a deeper insight into optimizing grazing management and sustainable utilization of grassland.
PMID: 35720531
Theor Appl Genet , IF:5.699 , 2022 Jul , V135 (7) : P2543-2554 doi: 10.1007/s00122-022-04137-5
Genetic and transcriptomic dissection of an artificially induced paired spikelets mutant of wheat (Triticum aestivum L.).
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China.; University of Chinese Academy of Sciences, Beijing, People's Republic of China.; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China.; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China. hailong@cib.ac.cn.
KEY MESSAGE: Morphological, genetic and transcriptomic characterizations of an EMS-induced wheat paired spikelets (PS) mutant were performed. A novel qualitative locus WPS1 on chromosome 1D was identified. Grain yield of wheat is significantly associated with inflorescence or spike architecture. However, few genes related to wheat spike development have been identified and their underlying mechanisms are largely unknown. In this study, we characterized an ethyl methanesulfonate (EMS)-induced wheat mutant, wheat paired spikelets 1 (wps1). Unlike a single spikelet that usually develops at each node of rachis, a secondary spikelet appeared below the primary spikelet at most of the rachis nodes of wps1. The microscope observation showed that the secondary spikelet initiated later than the primary spikelet. Genetic analysis suggested that the PS of wps1 is controlled by a single dominant nuclear gene, designated WHEAT PAIRED SPIKELETS 1 (WPS1). Further RNA-seq based bulked segregant analysis and molecular marker mapping localized WPS1 in an interval of 208.18-220.92 Mb on the chromosome arm 1DL, which is different to known genes related to spike development in wheat. By using wheat omics data, TraesCS1D02G155200 encoding a HD-ZIP III transcription factor was considered as a strong candidate gene for WPS1. Transcriptomic analysis indicated that PS formation in wps1 is associated with auxin-related pathways and may be regulated by networks involving TB1, Ppd1, FT1, VRN1, etc. This study laid the solid foundation for further validation of the causal gene of WPS1 and explored its regulatory mechanism in PS formation and inflorescence development, which may benefit to kernel yield improvement of wheat based on optimization or design of spike architecture in the future.
PMID: 35695919
Mol Plant Pathol , IF:5.663 , 2022 Jun doi: 10.1111/mpp.13234
A novel strategy for improving watermelon resistance to cucumber green mottle mosaic virus by exogenous boron application.
Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China.; Centre for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China.; Xinmin City Agricultural Technology Extension Centre, Shenyang, China.
The molecular mode controlling cucumber green mottle mosaic virus (CGMMV)-induced watermelon blood flesh disease (WBFD) is largely unknown. In this study, we have found that application of exogenous boron suppressed CGMMV infection in watermelon fruit and alleviated WBFD symptoms. Our transcriptome analysis showed that the most up-regulated differentially expressed genes (DEGs) were associated with polyamine and auxin biosynthesis, abscisic acid catabolism, defence-related pathways, cell wall modification, and energy and secondary metabolism, while the down-regulated DEGs were mostly involved in ethylene biosynthesis, cell wall catabolism, and plasma membrane functions. Our virus-induced gene silencing results showed that silencing of SPDS expression in watermelon resulted in a higher putrescine content and an inhibited CGMMV infection correlating with no WBFD symptoms. SBT and TUBB1 were also required for CGMMV infection. In contrast, silencing of XTH23 and PE/PEI7 (low-level lignin, cellulose and pectin) and ATPS1 (low-level glutathione) promoted CGMMV accumulation. Furthermore, RAP2-3, MYB6, WRKY12, H2A, and DnaJ11 are likely to participate in host antiviral resistance. In addition, a higher (spermidine + spermine):putrescine ratio, malondialdehyde content, and lactic acid content were responsible for fruit decay and acidification. Our results provide new knowledge on the roles of boron in watermelon resistance to CGMMV-induced WBFD. This new knowledge can be used to design better control methods for CGMMV in the field and to breed CGMMV resistant watermelon and other cucurbit crops.
PMID: 35671152
iScience , IF:5.458 , 2022 Jul , V25 (7) : P104683 doi: 10.1016/j.isci.2022.104683
Transcriptional reprogramming during floral fate acquisition.
Laboratoire Reproduction et Developpement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France.; Univ. Grenoble Alpes, CNRS, CEA, INRAE, BIG-LPCV, 38000 Grenoble, France.; Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland.; Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Universite Paris-Sud, Universite d'Evry, Universite Paris-Saclay, Batiment 630, Plateau de Moulon, 91192 Gif sur Yvette, France.; Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE Universite Paris-Diderot, Sorbonne Paris-Cite, Batiment 630, Plateau de Moulon, 91192 Gif sur Yvette, France.; IRHS-UMR1345, Universite d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouze, France.; Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, UK.; Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton, AB T6G 2E9, Canada.; The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK.
Coordinating growth and patterning is essential for eukaryote morphogenesis. In plants, auxin is a key regulator of morphogenesis implicated throughout development. Despite this central role, our understanding of how auxin coordinates cell fate and growth changes is still limited. Here, we addressed this question using a combination of genomic screens to delve into the transcriptional network induced by auxin at the earliest stage of flower development, prior to morphological changes. We identify a shoot-specific network suggesting that auxin initiates growth through an antagonistic regulation of growth-promoting and growth-repressive hormones, quasi-synchronously to floral fate specification. We further identify two DNA-binding One Zinc Finger (DOF) transcription factors acting in an auxin-dependent network that could interface growth and cell fate from the early stages of flower development onward.
PMID: 35856019
Nanomaterials (Basel) , IF:5.076 , 2022 Jun , V12 (12) doi: 10.3390/nano12122099
Potassium Chloroaurate-Mediated In Vitro Synthesis of Gold Nanoparticles Improved Root Growth by Crosstalk with Sucrose and Nutrient-Dependent Auxin Homeostasis in Arabidopsis thaliana.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.; ICAR-Indian Institute of Rice Research, Hyderabad 500030, India.; Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea.; Aerosol and Air Quality Research Laboratory, Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.; Department of Biology, University City Campus, Saint Joseph's University, 600 S. 43rd St., Philadelphia, PA 19104, USA.; School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.; Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India.
In a hydroponic system, potassium chloroaurate (KAuCl4) triggers the in vitro sucrose (Suc)-dependent formation of gold nanoparticles (AuNPs). AuNPs stimulate the growth of the root system, but their molecular mechanism has not been deciphered. The root system of Arabidopsis (Arabidopsis thaliana) exhibits developmental plasticity in response to the availability of various nutrients, Suc, and auxin. Here, we showed the roles of Suc, phosphorus (P), and nitrogen (N) in facilitating a AuNPs-mediated increase in root growth. Furthermore, the recuperating effects of KAuCl4 on the natural (IAA) auxin-mediated perturbation of the root system were demonstrated. Arabidopsis seedlings harboring the cell division marker CycB1;1::CDB-GUS provided evidence of the restoration efficacy of KAuCl4 on the IAA-mediated inhibitory effect on meristematic cell proliferation of the primary and lateral roots. Arabidopsis harboring synthetic auxin DR5rev::GFP exhibited a reinstating effect of KAuCl4 on IAA-mediated aberration in auxin subcellular localization in the root. KAuCl4 also exerted significant and differential recuperating effects on the IAA-mediated altered expression of the genes involved in auxin signaling and biosynthetic pathways in roots. Our results highlight the crosstalk between KAuCl4-mediated improved root growth and Suc and nutrient-dependent auxin homeostasis in Arabidopsis.
PMID: 35745438
Plant Methods , IF:4.993 , 2022 Jul , V18 (1) : P94 doi: 10.1186/s13007-022-00929-4
Deep learning for detecting herbicide weed control spectrum in turfgrass.
College of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.; Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, China.; Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.; College of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China. chenyongjsnj@163.com.; Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, China. jialin.yu@pku-iaas.edu.cn.
BACKGROUND: Precision spraying of postemergence herbicides according to the herbicide weed control spectrum can substantially reduce herbicide input. The objective of this research was to evaluate the effectiveness of using deep convolutional neural networks (DCNNs) for detecting and discriminating weeds growing in turfgrass based on their susceptibility to ACCase-inhibiting and synthetic auxin herbicides. RESULTS: GoogLeNet, MobileNet-v3, ShuffleNet-v2, and VGGNet were trained to discriminate the vegetation into three categories based on the herbicide weed control spectrum: weeds susceptible to ACCase-inhibiting herbicides, weeds susceptible to synthetic auxin herbicides, and turfgrass without weed infestation (no herbicide). ShuffleNet-v2 and VGGNet showed high overall accuracy (>/= 0.999) and F1 scores (>/= 0.998) in the validation and testing datasets to detect and discriminate weeds susceptible to ACCase-inhibiting and synthetic auxin herbicides. The inference time of ShuffleNet-v2 was similar to MobileNet-v3, but noticeably faster than GoogLeNet and VGGNet. ShuffleNet-v2 was the most efficient and reliable model among the neural networks evaluated. CONCLUSION: These results demonstrated that the DCNNs trained based on the herbicide weed control spectrum could detect and discriminate weeds based on their susceptibility to selective herbicides, allowing the precision spraying of particular herbicides to susceptible weeds and thereby saving more herbicides. The proposed method can be used in a machine vision-based autonomous spot-spraying system of smart sprayers.
PMID: 35879797
Plant Cell Physiol , IF:4.927 , 2022 Jul doi: 10.1093/pcp/pcac104
OsAMT1;1 and OsAMT1;2 Coordinate Root Morphological and Physiological Responses to Ammonium for Efficient Nitrogen Foraging in Rice.
Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, 100193 Beijing, China.; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Optimal plant growth and development rely on morphological and physiological adaptions of root system to forage heterogeneously distributed nitrogen (N) in soils. Rice grows mainly in the paddy soil where ammonium (NH4+) is present as the major N source. Although root NH4+ foraging behaviors are expected to be agronomically relevant, the underlying mechanism remains largely unknown. Here, we showed that NH4+ supply transiently enhanced the high-affinity NH4+ uptake and stimulated lateral root (LR) branching and elongation. These synergistic physiological and morphological responses were closely related to NH4+-induced expression of ammonium transporters OsAMT1;1 and OsAMT1;2 in roots. The two independent double mutants (dko) defective in OsAMT1;1 and OsAMT1;2 failed to induce NH4+ uptake and stimulate LR formation, suggesting that OsAMT1s conferred the substrate-dependent root NH4+ foraging. In dko plants, NH4+ was unable to activate expression of OsPIN2, and OsPIN2 mutant (lra1) exhibited strong reduction in NH4+-triggered LR branching, suggesting that auxin pathway was likely involved in OsAMT1s-dependent LR branching. Importantly, OsAMT1s-dependent root NH4+ foraging behaviors facilitated rice growth and N acquisition under fluctuating NH4+ supply. These results revealed an essential role of OsAMT1s in synergizing root morphological and physiological processes, allowing for efficient root NH4+ foraging to optimize N capture under fluctuating N availabilities.
PMID: 35861152
Plant Cell Physiol , IF:4.927 , 2022 Jun doi: 10.1093/pcp/pcac084
Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize.
Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee-247667, Uttarakhand, India.
The evolution of the root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, thus becoming a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus displaying species-specific diversity in the adventitious root types. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics, and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of action and interaction of crucial genetic and hormonal regulators. In this review, we provide a comprehensive state-of-the-art on the key regulators involved during different stages of AR development in two important crop plants, rice, and maize. We have reviewed the role of major phytohormones, microRNAs, transcription factors, and their crosstalk during adventitious root development in these cereal crops.
PMID: 35713294
Plant Cell Physiol , IF:4.927 , 2022 Jun doi: 10.1093/pcp/pcac078
Root Cap at Soil Interface: A Driving Force Towards Plant Adaptation and Development.
Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, 517507, Andhra Pradesh, India.
Land plants have developed robust roots to grow in diverse soil ecosystems. The distal end of the root tip has specialized organ called the "root cap." The root cap assists the roots in penetrating the ground, absorbing water & minerals, avoiding heavy metals, and regulating the rhizosphere microbiota. Furthermore, root cap derived auxin governs the lateral roots patterning and directs root growth under varying soil conditions. The root cap formation is hypothesized as one of the key innovations during root evolution. Morphologically diversified root caps in early land plant lineage and later in angiosperms aids in improving the adaptation of roots and, thereby, plants in diverse soil environments. This review article presents a retrospective view of the root cap's important morphology and physiology characteristics for the root-soil interaction and their response towards various abiotic and biotic stimuli. Recent single-cell RNAseq data shed light on root cap cell-type enriched genes. We complied root cap cell-type enriched genes from Arabidopsis, rice, maize and tomato and analyzed their transcription factor binding site enrichment. Further, the putative gene regulatory networks derived from root cap enriched genes and their transcription factor regulators highlight the species-specific biological functions of root cap genes across the four plant species.
PMID: 35662353
Plant Cell Physiol , IF:4.927 , 2022 Jul , V63 (7) : P932-943 doi: 10.1093/pcp/pcac055
SMAX1 Integrates Karrikin and Light Signals into GA-Mediated Hypocotyl Growth during Seedling Establishment.
Department of Chemistry, Seoul National University, Seoul 08826, South Korea.; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, South Korea.
Morphogenic adaptation of young seedlings to light environments is a critical developmental process that ensures plant survival and propagation, as they emerge from the soil. Photomorphogenic responses are facilitated by a network of light and growth hormonal signals, such as auxin and gibberellic acid (GA). Karrikins (KARs), a group of butenolide compounds produced from burning plant materials in wildfires, are known to stimulate seed germination in fire-prone plant species. Notably, recent studies support that they also regulate seedling growth, while underlying molecular mechanisms have been unexplored yet. Here, we demonstrate that SUPPRESSOR OF MAX2 1 (SMAX1), a negative regulator of KAR signaling, integrates light and KAR signals into GA-DELLA pathways that regulate hypocotyl growth during seedling establishment. We found that SMAX1 facilitates degradation of DELLA proteins in the hypocotyls. Interestingly, light induces the accumulation of SMAX1 proteins, and SMAX1-mediated degradation of DELLA is elevated in seedling establishment during the dark-to-light transition. Our observations indicate that SMAX1-mediated integration of light and KAR signals into GA pathways elaborately modulates seedling establishment.
PMID: 35477800
Biomolecules , IF:4.879 , 2022 Jun , V12 (7) doi: 10.3390/biom12070899
Transcriptome Analysis of Lycoris chinensis Bulbs Reveals Flowering in the Age-Mediated Pathway.
Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China.
Lycoris is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsible for floral transition in bulbous flowers is lacking, and only a few genes that regulate flowering have been identified with few reports on the floral transition in Lycoris. In this study, we identified many differentially expressed genes (DEGs) and transcription factors (TFs) by RNA-Seq in L. chinensis bulbs of different ages, including one- to four-year-old nonflowering bulbs and four-year-old flowering bulbs. Some DEGs were enriched in Gene Ontology (GO) terms between the three- and four-year-old bulbs, and there most genes were enriched in terms of metabolic process and catalytic activity. In the four-year old bulbs, most of the DEGs that may be involved in flowering were classified under the GO term biological process, which was a totally different result from the vegetative bulbs. Some DEGs between flowering and nonflowering bulbs were enriched in plant hormone signal transduction, including the hormones auxin, cytokinin, abscisic acid, and ethylene, but no DEGs were enriched in the gibberellin pathway. Auxin is the main endogenous phytohormone involved in bulb growth and development, but cytokinin, abscisic acid, and ethylene were shown to increase in flowering bulbs. In addition, energy-metabolism-related genes maintain a high expression level in large bulbs, and some positive regulators (SPL, COL, and AP1) and early flowering genes were also shown to be highly expressed in the meristems of flowering bulbs. It suggested that sugar molecules may be the energy source that regulates the signal transduction of flowering by connecting with phytohormone signaling in Lycoris. A total of 1911 TFs were identified and classified into 89 categories, where the top six families with the largest gene numbers were C2H2, NAC, AP2/ERF-ERF, C3H, MYB-related, and WRKY. Most DEGs were in the AP2/ERF-ERF family, and most of them were downregulated in 4-year-old flowering bulbs. A number of families were reported to be involved in plant flowering, including NAC, AP2/ERF, MYB, WRKY, bZIP, MADS, and NF-Y. These results can act as a genetic resource to aid in the explanation of the genetic mechanism responsible for the flowering of Lycoris and other bulbous flowers.
PMID: 35883454
Biomolecules , IF:4.879 , 2022 Jun , V12 (6) doi: 10.3390/biom12060811
Hormonal Crosstalk and Root Suberization for Drought Stress Tolerance in Plants.
Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Korea.; Department of Biology, Chungbuk National University, Cheong-ju 28644, Korea.; Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheong-ju 28644, Korea.
Higher plants in terrestrial environments face to numerous unpredictable environmental challenges, which lead to a significant impact on plant growth and development. In particular, the climate change caused by global warming is causing drought stress and rapid desertification in agricultural fields. Many scientific advances have been achieved to solve these problems for agricultural and plant ecosystems. In this review, we handled recent advances in our understanding of the physiological changes and strategies for plants undergoing drought stress. The activation of ABA synthesis and signaling pathways by drought stress regulates root development via the formation of complicated signaling networks with auxin, cytokinin, and ethylene signaling. An abundance of intrinsic soluble sugar, especially trehalose-6-phosphate, promotes the SnRK-mediated stress-resistance mechanism. Suberin deposition in the root endodermis is a physical barrier that regulates the influx/efflux of water and nutrients through complex hormonal and metabolic networks, and suberization is essential for drought-stressed plants to survive. It is highly anticipated that this work will contribute to the reproduction and productivity improvements of drought-resistant crops in the future.
PMID: 35740936
Pest Manag Sci , IF:4.845 , 2022 Jul , V78 (7) : P2759-2766 doi: 10.1002/ps.6863
Soybean dose-response to 2,4-D and dicamba at vegetative and reproductive growth stages.
Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USA.; Department of Agronomy and Horticulture, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE, USA.; Corteva Agriscience, Wilmington, DE, USA.; Department of Crop, Soil and Environmental Sciences, University of Arkansas, Lonoke, AR, USA.
BACKGROUND: Field experiments were conducted across multiple sites in 2012 and 2013 to describe sensitivity of soybean to 2,4-D (six doses) and dicamba (seven doses) at V3 and R1 growth stages. Further experiments were conducted under greenhouse conditions in 2017 and 2018 to compare soybean response to several dicamba herbicides across a broader range of doses than those tested in the field. RESULTS: Soybean yield loss was 6.1-fold greater from 2,4-D exposure at V3 compared to R1 and 1.4 times greater from dicamba exposure at R1 than at V3. In V3 exposures, soybean was 15.4 times more sensitive to dicamba than 2,4-D and 134.4-fold more sensitive to dicamba when exposed at R1. Plant injury and height correlations to grain yield resulted in coefficients ranging from 0.65 to 0.91. In greenhouse experiments, five dicamba products were tested at up to 19 doses and as low as 0.002 g ae ha(-1) (3.6 x 10(-6) % of maximum single use-rate); however, no differences were observed among formulations used in dicamba-resistant crops versus traditional formulations. A no observable effects dose was not identified due to responses observed even at the lowest doses tested, although hormesis effects were observed in plant height. CONCLUSION: These data suggest that the sensitivity of soybean to dicamba is much greater than what has previously been reported. However, as has been indicated by previous work, that injury does not always result in yield loss. (c) 2022 Society of Chemical Industry.
PMID: 35254733
Rice (N Y) , IF:4.783 , 2022 Jul , V15 (1) : P40 doi: 10.1186/s12284-022-00587-z
miR167d-ARFs Module Regulates Flower Opening and Stigma Size in Rice.
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China. j316wenmingwang@163.com.
Flower opening and stigma exertion are two critical traits for cross-pollination during seed production of hybrid rice (Oryza sativa L.). In this study, we demonstrate that the miR167d-ARFs module regulates stigma size and flower opening that is associated with the elongation of stamen filaments and the cell arrangement of lodicules. The overexpression of miR167d (OX167d) resulted in failed elongation of stamen filaments, increased stigma size, and morphological alteration of lodicule, resulting in cleistogamy. Blocking miR167d by target mimicry also led to a morphological alteration of the individual floral organs, including a reduction in stigma size and alteration of lodicule cell morphology, but did not show the cleistogamous phenotype. In addition, the four target genes of miR167d, namely ARF6, ARF12, ARF17, and ARF25, have overlapping functions in flower opening and stigma size. The loss-of-function of a single ARF gene did not influence the flower opening and stigma size, but arf12 single mutant showed a reduced plant height and aborted apical spikelets. However, mutation in ARF12 together with mutation in either ARF6, ARF17, or ARF25 led to the same defective phenotypes that were observed in OX167d, including the failed elongation of stamen filaments, increased stigma size, and morphological alteration of lodicule. These findings indicate that the appropriate expression of miR167d is crucial and the miR167d-ARFs module plays important roles in the regulation of flower opening and stigma size in rice.
PMID: 35876915
Plant Sci , IF:4.729 , 2022 Jul : P111401 doi: 10.1016/j.plantsci.2022.111401
The Citrus sinensis Tiller Angle Control 1 (CsTAC1) Gene Regulates Tree Architecture in Sweet Oranges by Modulating the Endogenous Hormone Content.
Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA. Electronic address: manjul@ufl.edu.; Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Pomology Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt.; Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31512, Egypt.; Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA.
Citrus is a major fruit crop cultivated on a global scale. Citrus trees are long lived perennials with a large canopy. Understanding the genetic control of tree architecture could provide tools for breeding and selection of citrus cultivars suitable for high density planting with improved light exposure. Tree architecture is modulated by the TILLER ANGLE CONTROL 1 (TAC1) gene which plays an important role in the regulation of the shoot angle. Herein, we used CRISPR/Cas9 technology to knockout the CsTAC1 gene for the biochemical and molecular analysis of its function. Nine transgenic lines were obtained, and five edited plants were confirmed based on T7EI mismatch detection assay and Sanger sequencing. The transgenic citrus lines exhibited pleiotropic phenotypes, including differences in branch angle and stem growth. Additionally, silencing CsTAC1 led to the upregulation of the CsLAZY1 gene in two of the tested lines. Analysis of the phytohormonal profile revealed that TAC1-edited plants exhibited lower auxin contents and increased cytokinin levels in the leaves compared to the wild-type plants. The GA7 gibberellin level was enhanced in most of the edited lines. Collectively, TAC1 affects branch angle in association with hormone signals in citrus.
PMID: 35905898
Plant Sci , IF:4.729 , 2022 Sep , V322 : P111371 doi: 10.1016/j.plantsci.2022.111371
Auxin facilitates cell wall phosphorus reutilization in a nitric oxide-ethylene dependent manner in phosphorus deficient rice (Oryza sativa L.).
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: xiaofangzhu@issas.ac.cn.
Auxin is involved in stress responses of plants, such as phosphorus (P) deficiency in rice. Studies on whether auxin participates in cell-wall inorganic phosphorous (Pi) reutilization in Pi-starved rice are scarce. This study explored the mechanisms underlying auxin-facilitated cell-wall Pi-reutilization in rice roots. Pi deficiency rapidly induced auxin accumulation in roots; exogenous auxin [alpha-naphthaleneacetic acid (NAA), a permeable analog of auxin] elevated soluble Pi content in roots and shoots by increasing pectin content by enhancing activity of pectin methylesterase, and upregulating the transcript level of PHOSPHORUS-TRANSPORTER-2, such that more Pi was translocated to the shoot. Irrespective of the Pi status, exogenous auxin induced nitric oxide (NO) and ethylene production, while exogenous sodium nitroprusside (an NO donor) and 1-aminocyclopropane-1-carboxylic acid (a precursor of ethylene) had no effect on auxin content, suggesting that auxin may act upstream of NO and ethylene. The beneficial effect of NAA in increasing soluble Pi content in roots and shoots disappeared when 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (a scavenger of NO) or aminoethoxyvinylglycine (an inhibitor of ethylene) were applied, suggesting that auxin facilitates cell-wall Pi-reutilization in a NO-ethylene-dependent manner in Pi-deficient rice. Our study results suggest auxin application as an effective agronomic practice for improving plant Pi nutrition in P-deficient conditions.
PMID: 35809682
Plant Sci , IF:4.729 , 2022 Sep , V322 : P111366 doi: 10.1016/j.plantsci.2022.111366
A MADS-box transcription factor, SlMADS1, interacts with SlMACROCALYX to regulate tomato sepal growth.
Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.; Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.; Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD UK.; Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: daqifu@cau.edu.cn.
In flowering plants, sepals play important roles in the development of flowers and fruit, and both processes are regulated by MADS-box (MADS) transcription factors (TFs). SlMADS1 was previously reported to act as a negative regulator of fruit ripening. In this study, expression analysis shown that its transcripts were very highly expressed during the development of sepals. To test the role of SlMADS1, we generated KO-SlMADS1 (knock-out) tomato mutants by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9) technology and over-expression of SlMADS1 (OE-SlMADS1). The sepals and individual cells of KO-SlMADS1 mutants were significantly elongated, compared with the wild type (WT), whereas the sepals of OE-SlMADS1 tomatoes were significantly shorter and their cells were wider. RNA-seq (RNA-sequencing) of sepal samples showed that ethylene-, gibberellin-, auxin-, cytokinin- and cell wall metabolism-related genes were significantly affected in both KO-SlMADS1 and OE-SlMADS1 plants with altered sepal size. Since SlMACROCALYX (MC) is known to regulate the development of tomato sepals, we also studied the relationship between SlMC and SlMADS1 and the result showed that SlMADS1 interacts directly with SlMC. In addition, we also found that manipulating SlMADS1 expression alters the development of tomato plant leaves, roots and plant height. These results enrich our understanding of sepal development and the function of SlMADS1 throughout the plant.
PMID: 35779674
Plant Sci , IF:4.729 , 2022 Sep , V322 : P111349 doi: 10.1016/j.plantsci.2022.111349
The carbohydrate elicitor Riclinoctaose facilitates defense and growth of potato roots by inducing changes in transcriptional and metabolic profiles.
Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China.; Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China.; Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China. Electronic address: jingli.seb@njust.edu.cn.
Promoting both root growth and defense is conducive to the production of potatoes (Solanum tuberosum L.), while the role of elicitors in this topic hasn't been fully understood. To investigate the effect of Riclinoctaose (RiOc) on root growth and defense, potato tissue cuttings were cultivated with different concentration of RiOc (0, 50, 200 mg/L) for 5 weeks and changes in root morphology, transcription, enzymatic and metabolomic profiles were monitored over time. The results indicated that RiOc triggered the salicylic acid (SA)-mediated defense response and facilitated the growth of adventitious and lateral roots in a dose- and time-dependent manner. MPK3/MPK6, SA- and auxin-signaling pathways and transcription factors such as WUS, SCR and GRAS4/GRAS9 participated in this process. Moreover, the (1)H NMR based metabolome profiling demonstrated that potato roots altered the primary metabolism to respond to the RiOc elicitation and efficiency in production and allocation of defense and growth-related metabolites was improved. After 5-week treatment, the level of glucose, N-acetylglucosamine, glutamine, asparagine, isoleucine, valine, 3-hydroxyisovalerate and ferulate increased, while acetate, acetoacetate, fucose, and 2-hydroxyphenylacetate declined. In conclusion, RiOc played dual roles in activating the SA-mediated defense response and in promoting growth of potato roots by inducing changes in root transcription and metabolism.
PMID: 35709981
Plant Sci , IF:4.729 , 2022 Jul , V320 : P111279 doi: 10.1016/j.plantsci.2022.111279
The high concentrations of abscisic, jasmonic, and salicylic acids produced under long days do not accelerate flowering in Chenopodium ficifolium 459.
Institute of Experimental Botany, Czech Academy of Sciences, Rozvojova 263, 16502 Prague, Czech Republic.; Institute of Experimental Botany, Czech Academy of Sciences, Rozvojova 263, 16502 Prague, Czech Republic. Electronic address: storchova@ueb.cas.cz.
The survival and adaptation of angiosperms depends on the proper timing of flowering. The weedy species Chenopodium ficifolium serves as a useful diploid model for comparing the transition to flowering with the important tetraploid crop Chenopodium quinoa due to the close phylogenetic relationship. The detailed transcriptomic and hormonomic study of the floral induction was performed in the short-day accession C. ficifolium 459. The plants grew more rapidly under long days but flowered later than under short days. The high levels of abscisic, jasmonic, and salicylic acids at long days were accompanied by the elevated expression of the genes responding to oxidative stress. The increased concentrations of stress-related phytohormones neither inhibited the plant growth nor accelerated flowering in C. ficifolium 459 at long photoperiods. Enhanced content of cytokinins and the stimulation of cytokinin and gibberellic acid signaling pathways under short days may indicate the possible participation of these phytohormones in floral initiation. The accumulation of auxin metabolites suggests the presence of a dynamic regulatory network in C. ficifolium 459.
PMID: 35643618
Front Genet , IF:4.599 , 2022 , V13 : P891702 doi: 10.3389/fgene.2022.891702
RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative.
Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.; Aquatic and Crop Resource Development Research Center, National Research Council of Canada, Saskatoon, SK, Canada.
Lentil is an important pulse crop not only because of its high nutrient value but also because of its ecological advantage in a sustainable agricultural system. Our previous work showed that the cultivated lentil and wild lentil germplasm respond differently to light environments, especially to low R/FR-induced shade conditions. Little is known about how cultivated and wild lentils respond to shade at the level of gene expression and function. In this study, transcriptomic profiling of a cultivated lentil (Lupa, L. culinaris) and a wild lentil (BGE 016880, L. orientalis) at several growth stages is presented. De novo transcriptomes were assembled for both genotypes, and differential gene expression analysis and gene ontology enrichment analysis were performed. The transcriptomic resources generated in this study provide fundamental information regarding biological processes and genes associated with shade responses in lentils. BGE 016880 and Lupa shared a high similarity in their transcriptomes; however, differential gene expression profiles were not consistent between these two genotypes. The wild lentil BGE 016880 had more differentially expressed genes than the cultivated lentil Lupa. Upregulation of genes involved in gibberellin, brassinosteroid, and auxin synthesis and signaling pathways, as well as cell wall modification, in both genotypes explains their similarity in stem elongation response under the shade. Genes involved in jasmonic acid and flavonoid biosynthesis pathways were downregulated in BGE 016880 only, and biological processes involved in defense responses were significantly enriched in the wild lentil BGE 016880 only. Downregulation of WRKY and MYB transcription factors could contribute to the reduced defense response in BGE 016880 but not in Lupa under shade conditions. A better understanding of shade responses of pulse crop species and their wild relatives will play an important role in developing genetic strategies for crop improvement in response to changes in light environments.
PMID: 35795209
Front Genet , IF:4.599 , 2022 , V13 : P929490 doi: 10.3389/fgene.2022.929490
Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes.
Instituto de Ecologia A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico.; Instituto de Ecologia A.C. (INECOL), Red de Biologia Evolutiva, Xalapa, Mexico.; Investigador por Mexico-CONACyT en el Instituto de Ecologia A.C. (INECOL), Xalapa, Mexico.; Departamento de Botanica, Instituto de Biologia, Universidad Nacional Autonoma de Mexico (UNAM), Ciudad de Mexico, Mexico.; Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico.; Centro de Investigacion en Ciencias Biologicas, Universidad Autonoma de Tlaxcala, Tlaxcala, Mexico.; Laboratorio de Genetica de la Conservacion, Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Morelia, Mexico.; INBIOTECA, Universidad Veracruzana, Xalapa, Mexico.
The mistletoe Psittacanthus schiedeanus, a keystone species in interaction networks between plants, pollinators, and seed dispersers, infects a wide range of native and non-native tree species of commercial interest. Here, using RNA-seq methodology we assembled the whole circularized quadripartite structure of P. schiedeanus chloroplast genome and described changes in the gene expression of the nuclear genomes across time of experimentally inoculated seeds. Of the 140,467 assembled and annotated uniGenes, 2,000 were identified as differentially expressed (DEGs) and were classified in six distinct clusters according to their expression profiles. DEGs were also classified in enriched functional categories related to synthesis, signaling, homoeostasis, and response to auxin and jasmonic acid. Since many orthologs are involved in lateral or adventitious root formation in other plant species, we propose that in P. schiedeanus (and perhaps in other rootless mistletoe species), these genes participate in haustorium formation by complex regulatory networks here described. Lastly, and according to the structural similarities of P. schiedeanus enzymes with those that are involved in host cell wall degradation in fungi, we suggest that a similar enzymatic arsenal is secreted extracellularly and used by mistletoes species to easily parasitize and break through tissues of the host.
PMID: 35769994
Plant Cell Rep , IF:4.57 , 2022 Jul doi: 10.1007/s00299-022-02899-2
Heterologous expression of a Fraxinus velutina SnRK2 gene in Arabidopsis increases salt tolerance by modifying root development and ion homeostasis.
Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, China.; Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Academy of Forestry, Jinan, 250014, China. pangcaihong@shandong.cn.; Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, China. chenminrundong@126.com.; Dongying Institute, Shandong Normal University, No. 2 Kangyang Road, Dongying, 257000, China. chenminrundong@126.com.
KEY MESSAGE: FvSnRK2182 is involved in regulating the growth and stress response. SnRK2 family members are positive regulators of downstream signals in the abscisic acid (ABA) signaling pathway, playing key roles in the plant responses to abiotic stresses. Fraxinus velutina Torr. is a candidate phytoremediator of saline-alkali areas, and is a valuable research subject because of its adaptability in saline soil. We identified a SnRK2 gene in F. velutina (named FvSnRK2182), which was significantly upregulated under salt stress. A bioinformatics analysis showed that FvSnRK2182 has a Ser/Thr kinase domain typical of the SnRK2 subfamily. Compared with wild-type (WT) Arabidopsis, its heterologous expression in Arabidopsis resulted in higher auxin content during seed germination and seedling growth, leading to longer primary roots and more lateral roots. The transgenic lines were better able to tolerate treatments with NaCl (100 mM) and/or ABA (0.2 and 0.5 microM), producing a greater biomass than the WT plants. Under NaCl treatment, the shoots of the transgenic lines had lower Na(+) contents and higher K(+) contents than the WT plants, and the genes encoding the ion transport-related proteins SOS1, HKT1, NHX1, and AKT1 were significantly upregulated. In addition, the expression of the genes functioning downstream of SnRK2 in the ABA signaling pathway (Rboh, AREB4, ABF2, and ABF3) were significantly upregulated in transgenic lines under NaCl stress. These results showed that expressing FvSnRK2182 in Arabidopsis significantly increased their resistance to ABA and salt stress by regulating root development and maintaining ion homeostasis, which suggests that FvSnRK2182 may be involved in regulating the growth and stress response of F. velutina.
PMID: 35794394
Plant Cell Rep , IF:4.57 , 2022 Jul doi: 10.1007/s00299-022-02898-3
Cellular responses of oil palm genotypes during somatic embryogenesis involve participation of procambial cells, DNA demethylation, and auxin accumulation.
CNPq/Embrapa Postoctoral Fellowship Program, Embrapa Recursos Geneticos e Biotecnologia, Brasilia, DF, Brazil.; Laboratorio de Microscopia, Embrapa Recursos Geneticos e Biotecnologia, Brasilia, DF, Brazil.; Laboratorio de Microscopia, Embrapa Recursos Geneticos e Biotecnologia, Brasilia, DF, Brazil. jonny.pereira@embrapa.br.; Laboratorio de Cultura de Tecidos e Genetica Vegetal, Embrapa Recursos Geneticos e Biotecnologia, Brasilia, DF, Brazil. jonny.pereira@embrapa.br.
KEY MESSAGE: Cell markers of somatic embryogenesis initiation from leaf tissues in oil palm involve the participation of procambial cells, DNA demethylation, and auxin accumulation. Low callogenesis and genotype-dependent response have been mentioned in the development of somatic embryogenesis protocols of Elaeis oleifera x E. guineensis elite hybrids, which requires more detailed investigations of the process. Thus, the initial cellular responses of immature leaves of adult genotypes of this hybrid were investigated for the first time, emphasizing histological, epigenetic, and endogenous auxin changes. Leaf segments from two genotypes, one responsive to somatic embryogenesis (B351733) and another non-responsive (B352933), were inoculated in Murashige and Skoog medium with 450 microM of 4-amino-3, 5, 6-trichloropicolinic acid. For anatomical analysis, samples of both genotypes were collected at 0, 20, 90, and 105 days of cultivation. Samples of both genotypes were also taken at different cultivation periods to analyze DNA methylation status (% 5-mC-5 methylcytosine) via ELISA test. Immunolocalization assays were performed with anti-indole-3-acetic acid and anti-5-methyl-deoxycytosine antibodies from samples of hybrid B351733. We distinguished two groups of cells reactive to the induction of embryogenic callogenesis, parenchymatous sheath cells, and procambial cells; however, only the latter are directly involved with the formation of calluses. The data obtained indicate that the formation of calluses in hybrid B351733 is related to DNA hypomethylation, while the non-responsiveness of leaf explants in hybrid B352932 is related to DNA hypermethylation. The in situ immunolocalization enabled the identification of initial markers of the callogenic process, such as IAA accumulation and hypomethylation. Identifying these events brings the possibility of establishing strategies for efficient manipulation of somatic embryogenesis protocols in palm trees.
PMID: 35776139
Plant Cell Rep , IF:4.57 , 2022 Jul , V41 (7) : P1613-1626 doi: 10.1007/s00299-022-02882-x
Transcriptome analysis reveals the effects of strigolactone on shoot regeneration of apple.
State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.; State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China. liwei0522898@163.com.; State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China. rschan@cau.edu.cn.
KEY MESSAGE: We have demonstrated that strigolactone inhibitor, Tis108, could be used to improve shoot regeneration of apple, and provided insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Lack of an efficient transformation system largely stagnated the application of transgenic and CRISPR technology in apple rootstock. High shoot regeneration ability is an important basis for establishing an effective transformation system. In this study, we first demonstrated the inhibitory effects of strigolactones on the adventitious shoot formation of apple rootstock M26. Next, we successfully verified that strigolactone-biosynthesis inhibitor, Tis108, could be used to improve the shoot regeneration of woody plants. Our results also suggest strigolactone-biosynthesis gene, MdCCD7, can be a target gene for biotechnological improvements of shoot regeneration capacity. Furthermore, we have employed transcriptome analysis to reveal the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Differentially expressed genes associated with photosynthesis, secondary growth, and organ development were identified. WGCNA suggests SLs might affect shoot regeneration through interaction with other hormones, especially, auxin, cytokinin, and ethylene. We were able to identify important candidate genes mediating the cross-talk between strigolactone and other hormones during the process of adventitious shoot formation. Overall, our findings not only propose a useful chemical for improving shoot regeneration in practice but also provide insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation.
PMID: 35680714
Microb Ecol , IF:4.552 , 2022 Jul doi: 10.1007/s00248-022-02080-y
Screening of Phosphate Solubilization Identifies Six Pseudomonas Species with Contrasting Phytostimulation Properties in Arabidopsis Seedlings.
Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacan, Mexico.; Catedratico CONACYT-Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacan, Mexico.; Instituto de Ecologia, Red de Estudios Moleculares Avanzados, Cluster BioMimic(R), Carretera Antigua a Coatepec 351, El Haya, A.C, 91073, Veracruz, Mexico.; Catedratico CONACYT-Instituto de Ecologia, Red de Estudios Moleculares Avanzados, Cluster BioMimic(R), Carretera Antigua a Coatepec 351, El Haya, A.C, 91073, Veracruz, Mexico.; Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacan, Mexico. jbucio@umich.mx.
The interaction of plants with bacteria and the long-term success of their adaptation to challenging environments depend upon critical traits that include nutrient solubilization, remodeling of root architecture, and modulation of host hormonal status. To examine whether bacterial promotion of phosphate solubilization, root branching and the host auxin response may account for plant growth, we isolated and characterized ten bacterial strains based on their high capability to solubilize calcium phosphate. All strains could be grouped into six Pseudomonas species, namely P. brassicae, P. baetica, P. laurylsulfatiphila, P. chlororaphis, P. lurida, and P. extremorientalis via 16S rRNA molecular analyses. A Solibacillus isronensis strain was also identified, which remained neutral when interacting with Arabidopsis roots, and thus could be used as inoculation control. The interaction of Arabidopsis seedlings with bacterial streaks from pure cultures in vitro indicated that their phytostimulation properties largely differ, since P. brassicae and P. laurylsulfatiphila strongly increased shoot and root biomass, whereas the other species did not. Most bacterial isolates, except P. chlororaphis promoted lateral root formation, and P. lurida and P. chlororaphis strongly enhanced expression of the auxin-inducible gene construct DR5:GUS in roots, but the most bioactive probiotic bacterium P. brassicae could not enhance the auxin response. Inoculation with P. brassicae and P. lurida improved shoot and root growth in medium supplemented with calcium phosphate as the sole Pi source. Collectively, our data indicate the differential responses of Arabidopsis seedlings to inoculation with several Pseudomonas species and highlight the potential of P. brassicae to manage phosphate nutrition and plant growth in a more eco-friendly manner.
PMID: 35867140
Physiol Plant , IF:4.5 , 2022 Jun : Pe13728 doi: 10.1111/ppl.13728
De novo transcriptome sequencing of Capsicum frutescens. L and comprehensive analysis of salt stress alleviating mechanism by Bacillus atrophaeus WU-9.
School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, PR China.; School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, PR China.
Salt stress, as one of the most severe environmental stresses, can cause a series of changes in plants. However, the explanation of plant salt stress alleviating mechanism of plant growth-promoting rhizobacteria (PGPR) was hindered by the limited availability of transcriptomic information for salt stress-treated plants grown in a microorganism-controled environment. Our previous reports have selected Bacillus atrophaeus WU-9 as PGPR significantly alleviating pepper (Capsicum frutescens. L) salt stress. In this work, the RNA-seq analysis of salt stress-treated and untreated plants, grown with and without WU-9 in a microorganism-controled environment, was used to reveal the plant salt stress alleviating mechanisms of WU-9. Twelve sequencing libraries, prepared by treating with WU-9 and salt (150 mM NaCl for 36 h), were constructed by RNA-Seq technique. Non-inoculated seedlings mainly respond to salt stress through regulation of signal transduction, such as ethylene-activated signaling pathway, signaling and cell communication, etc. And ethylene signal participated in salt stress response in pepper through regulating defense responses, fruit ripening and senescence. WU-9 inoculation under salt stress mainly improves salt tolerance and plant growth by regulating salt stress-responding ethylene and auxin signal transduction, utilization of proline, photosynthesis, antioxidant enzyme activities and cell enlargement. Furthermore, 86 differentially expressed genes (DEGs) and 20 transcription factors were identified as associated with salt stress response and tolerance. Thus, this innovative transcriptomic study identified the salt stress response and alleviation in C. frutescens. L with PGPR inoculation. This result provided novel insights into the salinity alleviation in pepper regulated by PGPR. This article is protected by copyright. All rights reserved.
PMID: 35675473
Sci Rep , IF:4.379 , 2022 Jul , V12 (1) : P12057 doi: 10.1038/s41598-022-16255-7
Key regulatory pathways, microRNAs, and target genes participate in adventitious root formation of Acer rubrum L.
Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.; College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People's Republic of China.; Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing University of Agriculture, Beijing, 102206, People's Republic of China. zhangkezhongbua@163.com.; College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China. zhangkezhongbua@163.com.; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People's Republic of China. zhangkezhongbua@163.com.; Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing University of Agriculture, Beijing, 102206, People's Republic of China. 2562860102@qq.com.; College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China. 2562860102@qq.com.; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People's Republic of China. 2562860102@qq.com.
Red maple (Acer rubrum L.) is a type of colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms of AR formation in A. rubrum. To address this knowledge gap, we sequenced the transcriptome and small RNAs (sRNAs) of the A. rubrum variety 'Autumn Fantasy' using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. We identified 82,468 differentially expressed genes (DEGs) between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two key regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene auxin response factor 10 (ArARF10) were selected based on KEGG pathway and cluster analyses. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. Experiments overexpressing ArARF10 and Ar-miR160a, indicated that ArARF10 promoted AR formation, while Ar-miR160a inhibited AR formation. Transcription factors (TFs) and miRNAs related to auxin regulation that promote AR formation in A. rubrum were identified. Differential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.
PMID: 35835811
Sci Rep , IF:4.379 , 2022 Jul , V12 (1) : P11505 doi: 10.1038/s41598-022-15309-0
Phyllanthus amarus shoot cultures as a source of biologically active lignans: the influence of selected plant growth regulators.
Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Gdansk, Gdansk, Poland.; Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Gdansk, Gdansk, Poland. krauze@gumed.edu.pl.
This is the first comprehensive study of the influence of plant growth regulators (PGRs) on the development of shoots and accumulation of biologically active lignans-phyllanthin and hypophyllanthin, in the shoot culture of P. amarus Schum. & Thonn. (Euphorbiaceae) obtained by direct organogenesis. The following PGRs were included in the experiments-cytokinins: kinetin (Kin), 6-benzylaminopurine (BAP), 2-isopentenyladenine (2iP), 1-phenyl-3-(1,2,3-thiadiazol-5-yl)urea, thidiazuron (TDZ) and auxin, indole-3-butyric acid (IBA) and used at various concentrations. Depending on PGRs and their concentrations, differences in the culture response and lignan accumulation were observed. The highest content of the investigated compounds was found in the shoot culture grown on Murashige and Skoog's (MS) medium supplemented with Kin 0.25 mg/L. The sum of phyllanthin and hypophyllanthin was ~ 10 mg/g of dry weight (DW), which was similar or even higher than that in the plant material obtained from natural conditions. The results of the research provide new data on the selection of the optimal growth medium for the production of plant material with a significant level of phyllanthin and hypophyllanthin biosynthesis. The obtained data may also be valuable in designing systems for large-scale cultivation of P. amarus shoots with high productivity of hepatoprotective lignans.
PMID: 35798810
Sci Rep , IF:4.379 , 2022 Jun , V12 (1) : P10883 doi: 10.1038/s41598-022-14631-x
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information.
Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA.; Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.; Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. decook@ksu.edu.; Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA. pbogdan@usc.edu.
Cellular biological networks represent the molecular interactions that shape function of living cells. Uncovering the organization of a biological network requires efficient and accurate algorithms to determine the components, termed communities, underlying specific processes. Detecting functional communities is challenging because reconstructed biological networks are always incomplete due to technical bias and biological complexity, and the evaluation of putative communities is further complicated by a lack of known ground truth. To address these challenges, we developed a geometric-based detection framework based on Ollivier-Ricci curvature to exploit information about network topology to perform community detection from partially observed biological networks. We further improved this approach by integrating knowledge of gene function, termed side information, into the Ollivier-Ricci curvature algorithm to aid in community detection. This approach identified essential conserved and varied biological communities from partially observed Arabidopsis protein interaction datasets better than the previously used methods. We show that Ollivier-Ricci curvature with side information identified an expanded auxin community to include an important protein stability complex, the Cop9 signalosome, consistent with previous reported links to auxin response and root development. The results show that community detection based on Ollivier-Ricci curvature with side information can uncover novel components and novel communities in biological networks, providing novel insight into the organization and function of complex networks.
PMID: 35760826
Sci Rep , IF:4.379 , 2022 Jun , V12 (1) : P10453 doi: 10.1038/s41598-022-14568-1
Single trait versus principal component based association analysis for flowering related traits in pigeonpea.
ICAR-National Institute for Plant Biotechnology, New Delhi, India.; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India.; ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.; ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India.; ICAR-National Institute for Plant Biotechnology, New Delhi, India. kish2012@gmail.com.
Pigeonpea, a tropical photosensitive crop, harbors significant diversity for days to flowering, but little is known about the genes that govern these differences. Our goal in the current study was to use genome wide association strategy to discover the loci that regulate days to flowering in pigeonpea. A single trait as well as a principal component based association study was conducted on a diverse collection of 142 pigeonpea lines for days to first and fifty percent of flowering over 3 years, besides plant height and number of seeds per pod. The analysis used seven association mapping models (GLM, MLM, MLMM, CMLM, EMLM, FarmCPU and SUPER) and further comparison revealed that FarmCPU is more robust in controlling both false positives and negatives as it incorporates multiple markers as covariates to eliminate confounding between testing marker and kinship. Cumulatively, a set of 22 SNPs were found to be associated with either days to first flowering (DOF), days to fifty percent flowering (DFF) or both, of which 15 were unique to trait based, 4 to PC based GWAS while 3 were shared by both. Because PC1 represents DOF, DFF and plant height (PH), four SNPs found associated to PC1 can be inferred as pleiotropic. A window of +/- 2 kb of associated SNPs was aligned with available transcriptome data generated for transition from vegetative to reproductive phase in pigeonpea. Annotation analysis of these regions revealed presence of genes which might be involved in floral induction like Cytochrome p450 like Tata box binding protein, Auxin response factors, Pin like genes, F box protein, U box domain protein, chromatin remodelling complex protein, RNA methyltransferase. In summary, it appears that auxin responsive genes could be involved in regulating DOF and DFF as majority of the associated loci contained genes which are component of auxin signaling pathways in their vicinity. Overall, our findings indicates that the use of principal component analysis in GWAS is statistically more robust in terms of identifying genes and FarmCPU is a better choice compared to the other aforementioned models in dealing with both false positive and negative associations and thus can be used for traits with complex inheritance.
PMID: 35729192
Plant Physiol Biochem , IF:4.27 , 2022 Jul , V186 : P182-196 doi: 10.1016/j.plaphy.2022.07.002
Exogenous spermidine regulates the anaerobic enzyme system through hormone concentrations and related-gene expression in Phyllostachys praecox roots under flooding stress.
State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.; College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.; State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China. Electronic address: syzhuang@issas.ac.cn.
PURPOSE: Acclimation to hypoxia and anoxia is important in various ecological systems, especially flooded soil. Phyllostachys pracecox is sensitive to flooding, and therefore, it is important to explore ways of alleviating hypoxia stress in the roots. In this study, we investigated the regulatory effect of spermidine (Spd) on flooded P. praecox seedlings. METHODS: A batch experiment was carried out in roots treated with Spd under flooding for eight days. The following factors were subsequently measured: growth, survival rate, root respiratory activity, soluble protein and anaerobic respiration enzyme contents (pyruvate decarboxylase, PDC; alcohol dehydrogenase, ADH; lactate dehydrogenase, LDH; alanine aminotransferase, AlaAT), S-adenosylmethionine decarboxylase (SAMDC), nitrate reductase (NR), ACC oxidase (ACO) and ACC synthetase (ACS) activities, free Spd, spermine (Spm) and the diamine precursor putrescine (Put) content, indole-3-acetic acid (IAA) and abscisic acid (ABA) content, ethylene emissions and expression of hormone-related genes. RESULTS: Application of Spd promoted root growth (root length, volume, surface and dry weight) and root respiratory inhibition, improved the soluble protein content, and reduced the O2(.-) production rate, H2O2 and MDA content to alleviate the damage of roots under flooding. A significant increase in SAMDC activity, and ABA and IAA contents were also observed, along with a reduction in ethylene emissions, NR, ACO and ACS activities (p < 0.05). Exogenous Spd increased the free Spd and Spm contents in the P. praecox roots, but decreased the free Put content. Taken together, these findings suggest that hypoxia stress was alleviated. Moreover, exogenous Spd up-regulated the expression of auxin-related genes ARF1, AUX1, AUX2, AUX3 and AUX4, and down-regulated the expression of ethylene-related ACO and ACS genes during flooding. In addition, correlation and RDA analysis showed that ARF1, ACO and ACS significantly promoted the expression of auxin, ACO and ACS enzyme activities, respectively (p < 0.05), while ADH, NR, AlaAT, ethylene emissions, Put, Spd, ACS and ACO were significantly correlated with ACS, ACO, and auxin-related gene expression (p < 0.05). Overall, ethylene emissions, ACS and ACO were identified as the main drivers of ethylene and auxin-related gene structure. CONCLUSIONS: These results suggest that Spd regulated hormone concentrations, the content of Spd, Spm and Put, and related gene expression, in turn regulating physiological changes such as anaerobic enzyme activity, mitigating flooding stress in the roots and improving overall growth. Spd therefore has the potential to improve the adaptability of P. praecox to flooding stress.
PMID: 35868108
Plant Physiol Biochem , IF:4.27 , 2022 Jul , V186 : P31-39 doi: 10.1016/j.plaphy.2022.06.029
Ultra-low concentration of chlorine dioxide regulates stress-caused premature leaf senescence in tobacco by modulating auxin, ethylene, and chlorophyll biosynthesis.
Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: 1535950539@qq.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: 1328454086@qq.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: 2135291758@qq.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: 1938840527@qq.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: 1796482382@qq.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: 2296365488@qq.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: xuetao_26@163.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: zhaofenglan2004@163.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: biosw2006@126.com.; Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China. Electronic address: yboduan@163.com.
Exploring novel growth regulators for premature senescence regulation is important for tobacco production. In the present study, chlorine dioxide (ClO2) was explored as a novel plant growth regulator for tobacco growth, particularly its effect on leaf senescence and root development. The results showed that 0.15 muM ClO2 maintained the lushness of detached leaves and whole plants. Also, the leaves of ClO2-treated plants exhibited a chlorophyll content of 58% higher than in CK (control) plants (P < 0.05). Besides, ClO2 treatment increased the biomass of roots and aboveground parts by 54 and 16%, respectively. The ClO2-treated plants also showed enhanced activities of antioxidant enzymes and significantly reduced malondialdehyde contents (P < 0.05). Moreover, ClO2 treatment remarkably alleviated drought-caused premature senescence in the tobacco plants and partly rescued the exogenous ethylene-caused plant dwarfism. The indole-3-acetic acid content in ClO2-treated plants was higher than in non-treated plants (P < 0.05), but ethylene content was significantly lower (P < 0.05). Gene expression analysis showed that ClO2 treatment remarkably suppressed ethylene synthase genes. However, the auxin biosynthesis and transport genes were up-regulated, with NtIAA17 increasing by five folds (P < 0.05). Further, ClO2 remarkably up-regulated the expression of chlorophyll biosynthesis genes, with a >20-fold increase in NtHEMA1 and NtCHLH expressions. These results designate ClO2 as a potential regulator for improving tobacco productivity by retaining higher chlorophyll content and promoting root growth.
PMID: 35803089
Plant Physiol Biochem , IF:4.27 , 2022 Aug , V185 : P260-267 doi: 10.1016/j.plaphy.2022.06.013
Mechanism of pod shattering in the forage legume Medicago ruthenica.
Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China.; Grassland and Resources Environment Institute, Inner Mongolia Agriculture University, Hohhot, China.; Grassland Supervision Office, Chahar Right Back Banner, Ulanqab, China.; Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China. Electronic address: zhiyongli1216@126.com.; Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China; Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China. Electronic address: lijun1538@126.com.
Pod shattering is a seed dispersal strategy and an important agronomical trait in domesticated crops. The relationship between pod shattering and pod morphology in the genus Medicago is well known; however, the detailed mechanism underlying pod dehiscence in Medicago ruthenica, a perennial legume used for forage production, is unknown. Here, the pod ventral sutures of shatter-resistant and shatter-susceptible M. ruthenica genotypes were examined at 8, 12, 16, and 20 d after flowering. The mechanism of pod shattering was analyzed through microscopic observations, polygalacturonase (PG) and cellulase (CE) activity analyses, and RNA-sequencing (RNA-Seq), and the results were verified via reverse transcriptase-quantitative polymerase chain reaction. Pod shattering at the ventral suture in M. ruthenica occurs via a combination of two mechanisms: degradation of the middle lamella at the abscission layers (ALs) and detachment of lignified cells on either side of the ALs triggered by physical forces. Increased PG and CE activities in the pod ventral suture are essential for AL cell-autolysis in the shatter-susceptible genotype. RNA-Seq revealed that 11 genes encoding PG and CE were highly expressed in the ventral sutures of the shatter-susceptible genotype. The expression levels of auxin biosynthesis-related genes decreased in the AL cells and they were negatively associated with pod dehiscence. These results enhance our understanding of the pod shattering mechanism not only in M. ruthenica but also in other leguminous plants.
PMID: 35717734
Plant Physiol Biochem , IF:4.27 , 2022 Aug , V185 : P244-259 doi: 10.1016/j.plaphy.2022.06.006
Auxin regulates growth, photosynthetic efficiency and mitigates copper induced toxicity via modulation of nutrient status, sugar metabolism and antioxidant potential in Brassica juncea.
Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.; Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, 11942, Saudi Arabia.; Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India. Electronic address: hayat_68@yahoo.co.in.
The involvement of auxin (IAA) in growth and development of plants is well known, but its role in the mitigation of metal stress, especially copper (Cu), is not fully understood; therefore, it is time to explore its involvement in minimizing the stress. A pot experiment was conducted to assess the protective function of IAA, applied to the foliage, on photosynthetic machinery, carbohydrate metabolism, and growth of Brassica juncea, grown with Cu (30 or 60 mg kg(-1) of soil). Among the different concentrations (10(-10), 10(-8), or 10(-6) M), 10(-8) M of IAA alone enhanced the photosynthetic characteristics, sugar accumulation and vegetative growth with minimal cellular oxidative stress level. Moreover, the same concentration of auxin was most effective in decreasing the stress levels generated by Cu and maintained it nearly to that of the control in terms of photosynthetic attributes, gas exchange parameters, PSII activity, electron transport rate, and growth attributes. Auxin also maintained the membrane stability and ultrastructure of chloroplast, stomatal morphology with a reduction in malondialdehyde (MDA), electrolyte leakage (EL) and cell death in test plants even under Cu stress. IAA also improved the translocation of Cu from root to the aerial parts, thus enhanced the Cu-reclamation in metal contaminated soils. Our findings suggest that the application of 10(-8) M of IAA maintains the overall growth of plants and may be used as an effective agent to improve growth, photosynthesis and phyto-remediation potential of B. juncea in Cu contaminated soil.
PMID: 35717733
Plant Physiol Biochem , IF:4.27 , 2022 Jul , V183 : P46-55 doi: 10.1016/j.plaphy.2022.05.003
Probing into the unique relationship between a soil bacterium, Pseudomonas putida AKMP7 and Arabidopsis thaliana: A case of "conditional pathogenesis".
Department of Biological Sciences, Birla Institute of Technology and Science (Pilani), Hyderabad Campus, India.; Department of Biological Sciences, Birla Institute of Technology and Science (Pilani), Hyderabad Campus, India. Electronic address: sridev.mohapatra@hyderabad.bits-pilani.ac.in.
Plant growth-promoting rhizobacteria (PGPR) are beneficial soil bacteria that colonise the rhizosphere and help plants in growth, development, and stress tolerance. While there is a significant body of research elucidating their benefits to plants, studies on the "abnormal" or "unexpected" behavior of these bacteria are almost non-existent. One such study from our laboratory has previously reported a unique situation in which a certain strain of drought and thermo-tolerant PGPR, namely, Pseudomonas putida AKMP7, becomes pathogenic towards Arabidopsis thaliana under drought conditions, but not under normal (well-watered) conditions. In this study, we have probed deeper into this phenomenon of "conditional pathogenesis". We found that, AKMP7 imparts an enhancement in plant growth under well-watered conditions, while, causing a deterioration in plant health under drought conditions. In an attempt to understand the underlying reasons for this phenomenon, we analysed the phytohormones released by Pseudomonas putida AKMP7 using LC-ESI-MS/MS technique. We identified that AKMP7 releases zeatin (a cytokinin), the auxin derivative -indole acetamide and amino acid-conjugates of auxin (indole-3-acetyl-L-alanine, indole-3-acetyl-L-phenylalanine and indole-3-acetyl-L-aspartate) in the growth medium. By treating the plants with commercially obtained forms of these phytohormones, individually or in combination with AKMP7, we identified that zeatin and auxin derivative indole acetamide can play a crucial role in the conditional pathogenesis exhibited by this bacterium on A. thaliana under drought conditions. Our work lays a foundation for further understanding the precise molecular mechanisms involved in this unique phenomenon of conditional/opportunistic pathogenesis.
PMID: 35567874
BMC Plant Biol , IF:4.215 , 2022 Jul , V22 (1) : P361 doi: 10.1186/s12870-022-03756-w
Gene expression profiling before and after internode culture for adventitious shoot formation in ipecac.
Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan.; Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.; Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan. umehara@toyo.jp.; Department of Applied Biosciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan. umehara@toyo.jp.
BACKGROUND: In ipecac (Carapichea ipecacuanha (Brot.) L. Andersson), adventitious shoots can be induced simply by placing internodal segments on phytohormone-free culture medium. The shoots form locally on the epidermis of the apical region of the segments, but not the basal region. Levels of endogenous auxin and cytokinin transiently increase in the segments after 1 week of culture. RESULTS: Here, we conducted RNA-seq analysis to compare gene expression patterns in apical and basal regions of segments before culture and after 1 week of culture for adventitious shoot formation. The results revealed 8987 differentially expressed genes in a de novo assembly of 76,684 genes. Among them, 276 genes were upregulated in the apical region after 1 week of culture relative to before culture and the basal region after 1 week of culture. These genes include 18 phytohormone-response genes and shoot-formation-related genes. Validation of the gene expression by quantitative real-time PCR assay confirmed that the expression patterns were similar to those of the RNA-seq data. CONCLUSIONS: The transcriptome data show that expression of cytokinin biosynthesis genes is induced along with the acquisition of cellular pluripotency and the initiation of cell division by wounding in the apical region of internodal segments, that trigger adventitious shoot formation without callusing.
PMID: 35869421
BMC Plant Biol , IF:4.215 , 2022 Jul , V22 (1) : P348 doi: 10.1186/s12870-022-03695-6
Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage.
National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.; Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.; National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China. liwh416@163.com.; National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China. tangjihua1@163.com.; The Shennong Laboratory, Zhengzhou, Henan, 450002, China. tangjihua1@163.com.
BACKGROUND: Heterosis is widely used in many crops and is important for global food safety, and maize is one of the most successful crops to take advantage of heterosis. Gene expression patterns control the development of the maize ear, but the mechanisms by which heterosis affects transcriptional-level control are not fully understood. RESULTS: In this study, we sampled ear inflorescence meristems (IMs) from the single-segment substitution maize (Zea mays) line lx9801(hlEW2b), which contains the heterotic locus hlEW2b associated with ear width, as well as the receptor parent lx9801, the test parent Zheng58, and their corresponding hybrids Zheng58 x lx9801(hlEW2b) (HY) and Zheng58 x lx9801 (CK). After RNA sequencing and transcriptomic analysis, 2531 unique differentially expressed genes (DEGs) were identified between the two hybrids (HY vs. CK). Our results showed that approximately 64% and 48% of DEGs exhibited additive expression in HY and CK, whereas the other genes displayed a non-additive expression pattern. The DEGs were significantly enriched in GO functional categories of multiple metabolic processes, plant organ morphogenesis, and hormone regulation. These essential processes are potentially associated with heterosis performance during the maize ear developmental stage. In particular, 125 and 100 DEGs from hybrids with allele-specific expression (ASE) were specifically identified in HY and CK, respectively. Comparison between the two hybrids suggested that ASE genes were involved in different development-related processes that may lead to the hybrid vigor phenotype during maize ear development. In addition, several critical genes involved in auxin metabolism and IM development were differentially expressed between the hybrids and showed various expression patterns (additive, non-additive, and ASE). Changes in the expression levels of these genes may lead to differences in auxin homeostasis in the IM, affecting the transcription of core genes such as WUS that control IM development. CONCLUSIONS: Our research suggests that additive, non-additive, and allele-specific expression patterns may fine-tune the expression of crucial DEGs that modulate carbohydrate and protein metabolic processes, nitrogen assimilation, and auxin metabolism to optimal levels, and these transcriptional changes may play important roles in maize ear heterosis. The results provide new information that increases our understanding of the relationship between transcriptional variation and heterosis during maize ear development, which may be helpful for clarifying the genetic and molecular mechanisms of heterosis.
PMID: 35843937
BMC Plant Biol , IF:4.215 , 2022 Jul , V22 (1) : P330 doi: 10.1186/s12870-022-03730-6
Transporter NRT1.5/NPF7.3 suppresses primary root growth under low K(+) stress by regulating the degradation of PIN-FORMED2.
Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.; Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China. 08321@njnu.edu.cn.
BACKGROUND: The availability of potassium is one of the main environmental factors for modifying the plasticity of root architecture. Many potassium channels and transporters are involved in regulating primary root growth in response to low potassium stress. NRT1.5/NPF7.3 transporter is a NO3(-)/H(+) and K(+)/H(+) cotransporter, and participates in NO3(-) and K(+) translocation from the roots to the shoots. However, the underlying mechanism of NRT1.5-regulated primary root growth under low potassium stress is unclear. RESULTS: We show that NRT1.5/NPF7.3 inhibited primary root growth under low potassium conditions by regulating the accumulation of PIN2 protein and auxin levels. Under low potassium conditions, the mutants nrt1.5 and lks2 exhibited longer primary roots, longer meristem regions and elongation zones of primary roots, and more cell activity in the meristem region compared to WT plants, revealing the involvement of NRT1.5 in LK (low potassium)-inhibition primary root growth. In addition, exogenous auxin (IAA), auxin analogue (NAA, 2.4-D) or auxin precursor (IBA) promoted the primary root growth of WT and the complementation line NRT1.5 COM plants. In addition, the application of NPA inhibited the primary root growth of the nrt1.5 and lks2 mutants. Auxin accumulation was higher in the root tip of nrt1.5 plants than in WT plants, indicating that NRT1.5 regulates root growth inhibition by regulating auxin distribution. Furthermore, PIN2 was degraded more quickly in nrt1.5 plants under LK stress. CONCLUSIONS: Our findings reveal that NRT1.5 inhibits primary root growth by modulating the auxin level in the root tip via the degradation of PIN2.
PMID: 35804293
BMC Plant Biol , IF:4.215 , 2022 Jul , V22 (1) : P319 doi: 10.1186/s12870-022-03701-x
Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis).
Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China.; Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, 666201, China.; Tea Research Institute of Enshi Academy of Agricultural Sciences, Enshi, 445000, China.; Tea Research Institute of Enshi Academy of Agricultural Sciences, Enshi, 445000, China. hbeshsz@yahoo.com.cn.; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China. wangly@tricaas.com.; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China. weikang@tricaas.com.
BACKGROUND: Tea plant breeding or cultivation mainly involves propagation via cuttings, which not only ensures the inheritance of the excellent characteristics of the mother plant but also facilitates mechanized management. The formation of adventitious root (AR) determines the success of cutting-based propagation, and auxin is an essential factor involved in this process. To understand the molecular mechanism underlying AR formation in nodal tea cuttings, transcriptome and endogenous hormone analysis was performed on the stem bases of red (mature)- and green (immature)-stem cuttings of 'Echa 1 hao' tea plant as affected by a pulse treatment with naphthalene acetic acid (NAA). RESULTS: In this study, NAA significantly promoted AR formation in both red- and green-stem cuttings but slightly reduced callus formation. External application of NAA reduced the levels of endogenous indole-3-acetic acid (IAA) and cytokinin (TZR, trans-zeatin riboside). The number of DEGs (NAA vs. CK) identified in the green-stem cuttings was significantly higher than that in the red-stem cuttings, which corresponded to a higher rooting rate of green-stem cuttings under the NAA treatment. A total of 82 common DEGs were identified as being hormone-related and involved in the auxin, cytokinin, abscisic acid, ethylene, salicylic acid, brassinosteroid, and jasmonic acid pathways. The negative regulation of NAA-induced IAA and GH3 genes may explain the decrease of endogenous IAA. NAA reduced endogenous cytokinin levels and further downregulated the expression of cytokinin signalling-related genes. By the use of weighted gene co-expression network analysis (WGCNA), several hub genes, including three [cellulose synthase (CSLD2), SHAVEN3-like 1 (SVL1), SMALL AUXIN UP RNA (SAUR21)] that are highly related to root development in other crops, were identified that might play important roles in AR formation in tea cuttings. CONCLUSIONS: NAA promotes the formation of AR of tea cuttings in coordination with endogenous hormones. The most important endogenous AR inductor, IAA, was reduced in response to NAA. DEGs potentially involved in NAA-mediated AR formation of tea plant stem cuttings were identified via comparative transcriptome analysis. Several hub genes, such as CSLD2, SVL1 and SAUR21, were identified that might play important roles in AR formation in tea cuttings.
PMID: 35787241
BMC Plant Biol , IF:4.215 , 2022 Jun , V22 (1) : P282 doi: 10.1186/s12870-022-03652-3
Transcriptome analysis reveals multiple effects of nitrogen accumulation and metabolism in the roots, shoots, and leaves of potato (Solanum tuberosum L.).
Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016, Qinghai, China.; Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016, Qinghai, China. jianwang2197@163.com.
BACKGROUND: Nitrogen (N) is a major element and fundamental constituent of grain yield. N fertilizer plays an essential role in the roots, shoots, and leaves of crop plants. Here, we obtained two N-sensitive potato cultivars. RESULTS: The plants were cultivated in the pots using N-deficient and N-sufficient conditions. Crop height, leaf chlorophyll content, dry matter, and N-accumulation significantly decreased under N-deficient conditions. Furthermore, we performed a comprehensive analysis of the phenotype and transcriptome, GO terms, and KEGG pathways. We used WGCNA of co-expressed genes, and 116 differentially expressed hub genes involved in photosynthesis, nitrogen metabolism, and secondary metabolites to generate 23 modules. Among those modules, six NRT gene families, four pigment genes, two auxin-related genes, and two energy-related genes were selected for qRT-PCR validation. CONCLUSIONS: Overall, our study demonstrates the co-expressed genes and potential pathways associated with N transport and accumulation in potato cultivars' roots, shoots, and leaves under N-deficient conditions. Therefore, this study provides new ideas to conduct further research on improving nitrogen use efficiency in potatoes.
PMID: 35676629
Tree Physiol , IF:4.196 , 2022 Jul doi: 10.1093/treephys/tpac089
The dark septate endophyte Phialocephala sphaeroides suppresses conifer pathogen transcripts and promotes root growth of Norway spruce.
College of Forestry, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.; Department of Forest Sciences, P.O. box 27, University of Helsinki, FIN-00014 Helsinki, Finland.
Plant associated microbes including dark septate endophytes (DSE) of forest trees play diverse functional roles in host fitness including growth promotion and increased defence. However, little is known about the impact on the fungal transcriptome and metabolites during tripartite interaction involving plant host, endophyte and pathogen. To understand the transcriptional regulation of endophyte and pathogen during co-infection, Norway spruce (Picea abies) seedlings were infected with DSE Phialocephala sphaeroides, or conifer root-rot pathogen Heterobasidion parviporum, or both. P. sphaeroides showed low but stable transcripts abundance (a decrease of 40%) during interaction with Norway spruce and conifer pathogen. By contrast, H. parviporum transcripts were significantly reduced (92%) during co-infection. With RNAseq analysis, P. sphaeroides experienced a shift from cell growth to anti-stress and antagonistic responses, while it repressed the ability of H. parviporum to access carbohydrate nutrients by suppressing its carbohydrate/polysaccharide degrading enzyme machinery. The pathogen on the other hand secreted cysteine peptidase to restrict free growth of P. sphaeroides. The expression of both DSE P. sphaeroides and pathogen H. parviporum genes encoding plant growth promotion products were equally detected in both dual and tripartite interaction systems. This was further supported by the presence of tryptophan-dependent indolic compound in liquid culture of P. sphaeroides. Norway spruce and Arabidopsis seedlings treated with P. sphaeroides culture filtrate exhibited auxin-like phenotypes, such as enhanced root hairs, and primary root elongation at low concentration but shortened primary root at high concentration. The results suggested that the presence of the endophyte had strong repressive or suppressive effect on H. parviporum transcripts encoding genes involved in nutrient acquisition.
PMID: 35878416
Tree Physiol , IF:4.196 , 2022 Jul , V42 (7) : P1411-1431 doi: 10.1093/treephys/tpac008
Roles of auxin in the inhibition of shoot branching in 'Dugan' fir.
Department of Forest Genetics & Biotechnology, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, No.159 Longpan Road, Nanjing, Jiangsu 210037, China.; Department of Molecular Biology and Biochemistry, College of Biology and Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, Jiangsu 210037, China.
Shoot branching substantially impacts vegetative and reproductive growth as well as wood characteristics in perennial woody species by shaping the shoot system architecture. Although plant hormones have been shown to play a fundamental role in shoot branching in annual species, their corresponding actions in perennial woody plants are largely unknown, in part due to the lack of branching mutants. Here, we demonstrated the role of plant hormones in bud dormancy transition toward activation and outgrowth in woody plants by comparing the physiological and molecular changes in the apical shoot stems of 'Yangkou' 020 fir and 'Dugan' fir, two Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) clones with normal and completely abolished branching phenotypes, respectively. Our studies showed that the defect in bud outgrowth was the cause of failed shoot branching in 'Dugan' fir whereas apically derived signals acted as triggers of this ectopic bud activity. Further studies indicated that auxin played a key role in inhibiting bud outgrowth in 'Dugan' fir. During bud dormancy release, the differential auxin resistant 1/Like AUX1 (AUX1/LAX) and PIN-formed (PIN) activity resulted in an ectopic auxin/indole-3-acetic acid (IAA) accumulation in the apical shoot stem of 'Dugan' fir, which could inhibit the cell cycle in the axillary meristem by decreasing cytokinin (CK) biosynthesis but increasing abscisic acid (ABA) production and response through the signaling pathway. In contrast, during bud activation and outgrowth, the striking increase in auxin biosynthesis and PIN activity in the shoot tip of 'Dugan' fir may trigger the correlative inhibition of axillary buds by modulating the polar auxin transport stream (PATS) and connective auxin transport (CAT) in shoots, and by influencing the biosynthesis of secondary messengers, including CK, gibberellin (GA) and ABA, thereby inducing the paradormancy of axillary buds in 'Dugan' fir by apical dominance under favorable conditions. The findings of this study provide important insights into the roles of plant hormones in bud outgrowth control in perennial woody plants.
PMID: 35088089
Mol Plant Microbe Interact , IF:4.171 , 2022 Jun doi: 10.1094/MPMI-05-22-0113-TA
Berberine Bridge Enzyme-Like Oligosaccharide Oxidases Act as Enzymatic Transducers Between Microbial Glycoside Hydrolases and Plant Peroxidases.
University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; anna.scortica@guest.univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; moira.giovannoni@univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; valentina.scafati@guest.univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; francesco.angelucci@univaq.it.; University of Rome La Sapienza Department of Biology and Biotechnology Charles Darwin, 125566, Roma, Lazio, Italy; felice.cervone@uniroma1.it.; University of Rome La Sapienza Department of Biology and Biotechnology Charles Darwin, 125566, Roma, Lazio, Italy; giulia.delorenzo@uniroma1.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; manuel.benedetti@univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; mariabenedetta.mattei@univaq.it.
OG-oxidase 1 (OGOX1) and CD-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide oxidases that oxidize oligogalacturonides (OGs) and cellodextrins (CDs), cell wall fragments with nature of damage-associated molecular patterns (DAMPs). The oxidation of OGs and CDs attenuates their elicitor activity and concomitantly releases H2O2. By using a multiple enzyme-based assay, we demonstrate that the H2O2 generated downstream of the combined action between a fungal polygalacturonase and OGOX1 or an endoglucanase and CELLOX can be directed by plant peroxidases (PODs) either towards a reaction possibly involved in plant defence such as the oxidation of monolignol or a reaction possibly involved in a developmental event such as the oxidation of auxin (IAA), pointing to OGOX1 and CELLOX as enzymatic transducers between microbial glycoside hydrolases and plant PODs.
PMID: 35704684
Anal Bioanal Chem , IF:4.142 , 2022 Aug , V414 (20) : P6259-6269 doi: 10.1007/s00216-022-04198-x
Effect of ion source polarity and dopants on the detection of auxin plant hormones by ion mobility-mass spectrometry.
Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynska dolina F2, 84248, Bratislava, Slovakia. vahideh.ilbeigi@fmph.uniba.sk.; Department of Chemistry, Faculty of Science, Imam Khomeini International University, Qazvin, Iran.; Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynska dolina F2, 84248, Bratislava, Slovakia.; Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynska dolina F2, 84248, Bratislava, Slovakia. stefan.matejcik@fmph.uniba.sk.
Ion mobility spectrometry (IMS) equipped with a corona discharge (CD) ion source was used for measurement of three auxin plant hormones including indole-3-acetic acid (IAA), indole-3-propionic acid (IPA), and indole-3-butyric acid (IBA). The measurements were performed in both positive and negative polarities of the CD ion source. Dopant gases NH3, CCl4, and CHBr3 were used to modify the ionization mechanism. A time-of-flight mass spectrometer (TOFMS) orthogonal to the IMS cell was used for identification of the product ions. Density functional theory was used to rationalize formation of the ions, theoretically. The mixtures of the auxins were analyzed by CD-IMS. The separation performance depended on the ion polarity and the dopants. In the positive polarity without dopants, auxins were ionized via protonation and three distinguished peaks were observed. Application of NH3 dopant resulted in two ionization channels, protonation, and NH4(+) attachment leading to peak overlapping. In the negative polarity, two ionization reactions were operative, via deprotonation and O2(-) attachment. The separation of the monomer peaks was not achieved while the peaks of anionic dimers [2 M-H](-) were separated well. The best LOD (4 ng) was obtained in negative polarity with CCl4 dopant. Methylation (esterification) of IAA improved LODs by about one order.
PMID: 35794348
Microorganisms , IF:4.128 , 2022 Jun , V10 (7) doi: 10.3390/microorganisms10071290
Azospirillum brasilense Bacteria Promotes Mn(2+) Uptake in Maize with Benefits to Leaf Photosynthesis.
Missouri Research Reactor Center, University of Missouri, Columbia, MO 65211, USA.; Chemistry Department, University of Missouri, Columbia, MO 65211, USA.; School of Natural Resources, University of Missouri, Columbia, MO 65211, USA.; Biochemistry Department, University of Missouri, Columbia, MO 65211, USA.; Division of Plant Sciences and Technology, University of Missouri, Columbia, MO 65211, USA.; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
Azospirillum brasilense is a prolific grass-root colonizing bacteria well-known for its ability to promote plant growth in several cereal crops. Here we show that one of the mechanisms of action in boosting plant performance is through increased assimilation of the micronutrient manganese by the host. Using radioactive (52)Mn(2+) (t(1/2) 5.59 d), we examined the uptake kinetics of this micronutrient in young maize plants, comparing the performance of three functional mutants of A. brasilense, including HM053, a high auxin-producing and high N2-fixing strain; ipdC, a strain with a reduced auxin biosynthesis capacity; and FP10, a strain deficient in N2-fixation that still produces auxin. HM053 had the greatest effect on host (52)Mn(2+) uptake, with a significant increase seen in shoot radioactivity relative to non-inoculated controls. LA-ICP-MS analysis of root sections revealed higher manganese distributions in the endodermis of HM053-inoculated plants and overall higher manganese concentrations in leaves. Finally, increased leaf manganese concentration stimulated photosynthesis as determined by measuring leaf fixation of radioactive (11)CO2 with commensurate increases in chlorophyll concentration.
PMID: 35889009
Planta , IF:4.116 , 2022 Jul , V256 (2) : P44 doi: 10.1007/s00425-022-03936-w
ARF2 positively regulates flavonols and proanthocyanidins biosynthesis in Arabidopsis thaliana.
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.; Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. pangyongzhen@caas.cn.
MAIN CONCLUSION: Auxin response factor 2 acts as a positive regulator to fine-tune the spatial and temporal accumulation of flavonoid compounds, mainly flavonols and proanthocyanidins in Arabidopsis. Auxin response factor (ARF) proteins are reported to involve in auxin-mediated regulation of flavonoid biosynthesis. However, the detailed regulation mechanism of ARF remains still unknown. Here, we provide genetic and molecular evidence that one of the twenty-three ARF members-ARF2-positively regulates flavonoid biosynthesis at multi-level in tissue-specific manner in Arabidopsis thaliana. Loss-of-function mutation of ARF2 led to significant reduction in flavonoid content (e.g., flavonols and proanthocyanidins) in the seedlings and seeds of the Arabidopsis arf2 mutants. Over-expression of ARF2 increased flavonols and proanthocyanidins content in Arabidopsis. Additionally, the changes of flavonoid content correlate well with the transcript abundance of several regulatory genes (e.g., MYB11, MYB12, MYB111, TT2, and GL3), and key biosynthetic genes (e.g., CHS, F3'H, FLS, ANS, ANR, TT12, TT19, and TT15), in the arf2 mutant and ARF2 over-expression lines. Transient transactivation assays with site-directed mutagenesis confirmed that ARF2 directly regulates the expression of MYB12 and FLS genes in the flavonol pathway and ANR in the proanthocyanidin pathway, and indirectly regulates MYB11 and MYB111 genes in the flavonol pathway, and ANS, TT12, TT19 and TT15 genes in the proanthocyanidin pathway. Further genetic results indicated that ARF2 acts upstream of MYB12 to regulate flavonol accumulation, and of TT2 to regulate proanthocyanidins accumulation. In particular, yeast two-hybrid assays revealed that ARF2 physically interacts with TT2, a master regulator of proanthocyanidins biosynthesis. Combined together, these results indicated that ARF2 functions as a positive regulator for the fine-tuned spatial and temporal regulation of flavonoids (mainly flavonols and proanthocyanidins) accumulation in Arabidopsis.
PMID: 35857143
Planta , IF:4.116 , 2022 Jun , V256 (1) : P6 doi: 10.1007/s00425-022-03916-0
The genome of a mangrove plant, Avicennia marina, provides insights into adaptation to coastal intertidal habitats.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China. zhenghl@xmu.edu.cn.
MAIN CONCLUSION: Whole-genome duplication, gene family and lineage-specific genes analysis based on high-quality genome reveal the adaptation mechanisms of Avicennia marina to coastal intertidal habitats. Mangrove plants grow in a complex habitat of coastal intertidal zones with high salinity, hypoxia, etc. Therefore, it is an interesting question how mangroves adapt to the unique intertidal environment. Here, we present a chromosome-level genome of the Avicennia marina, a typical true mangrove with a size of 480.43 Mb, contig N50 of 11.33 Mb and 30,956 annotated protein-coding genes. We identified 621 Avicennia-specific genes that are mainly related to flavonoid and lignin biosynthesis, auxin homeostasis and response to abiotic stimulus. We found that A. marina underwent a novel specific whole-genome duplication, which is in line with a brief era of global warming that occurred during the paleocene-eocene maximum. Comparative genomic and transcriptomic analyses outline the distinct evolution and sophisticated regulations of A. marina adaptation to the intertidal environments, including expansion of photosynthesis and oxidative phosphorylation gene families, unique genes and pathways for antibacterial, detoxifying antioxidant and reactive oxygen species scavenging. In addition, we also analyzed salt gland secretion-related genes, and those involved in the red bark-related flavonoid biosynthesis, while significant expansions of key genes such as NHX, 4CL, CHS and CHI. High-quality genomes in future investigations will facilitate the understand of evolution of mangrove and improve breeding.
PMID: 35678934
Genes (Basel) , IF:4.096 , 2022 Jul , V13 (7) doi: 10.3390/genes13071203
Leaf Development in Medicago truncatula.
Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
Forage yield is largely dependent on leaf development, during which the number of leaves, leaflets, leaf size, and shape are determined. In this mini-review, we briefly summarize recent studies of leaf development in Medicago truncatula, a model plant for legumes, with a focus on factors that could affect biomass of leaves. These include: floral development and related genes, lateral organ boundary genes, auxin biosynthesis, transportation and signaling genes, and WOX related genes.
PMID: 35885986
Genes (Basel) , IF:4.096 , 2022 Jun , V13 (6) doi: 10.3390/genes13061041
An Aux/IAA Family Member, RhIAA14, Involved in Ethylene-Inhibited Petal Expansion in Rose (Rosa hybrida).
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China.; Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.
Flower size, a primary agronomic trait in breeding of ornamental plants, is largely determined by petal expansion. Generally, ethylene acts as an inhibitor of petal expansion, but its effect is restricted by unknown developmental cues. In this study, we found that the critical node of ethylene-inhibited petal expansion is between stages 1 and 2 of rose flower opening. To uncover the underlying regulatory mechanism, we carried out a comparative RNA-seq analysis. Differentially expressed genes (DEGs) involved in auxin-signaling pathways were enriched. Therefore, we identified an auxin/indole-3-acetic acid (Aux/IAA) family gene, RhIAA14, whose expression was development-specifically repressed by ethylene. The silencing of RhIAA14 reduced cell expansion, resulting in diminished petal expansion and flower size. In addition, the expressions of cell-expansion-related genes, including RhXTH6, RhCesA2, RhPIP2;1, and RhEXPA8, were significantly downregulated following RhIAA14 silencing. Our results reveal an Aux/IAA that serves as a key player in orchestrating petal expansion and ultimately contributes to flower size, which provides new insights into ethylene-modulated flower opening and the function of the Aux/IAA transcription regulator.
PMID: 35741802
Plant Mol Biol , IF:4.076 , 2022 Jul doi: 10.1007/s11103-022-01298-1
SlBBX28 positively regulates plant growth and flower number in an auxin-mediated manner in tomato.
Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.; Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de Sao Paulo, Sao Paulo, SP, Brazil.; Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.; Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, SP, Brazil. mmrossi@usp.br.
KEY MESSAGE: SlBBX28 is a positive regulator of auxin metabolism and signaling, affecting plant growth and flower number in tomato B-box domain-containing proteins (BBXs) comprise a family of transcription factors that regulate several processes, such as photomorphogenesis, flowering, and stress responses. For this reason, attention is being directed toward the functional characterization of these proteins, although knowledge in species other than Arabidopsis thaliana remains scarce. Particularly in the tomato, Solanum lycopersicum, only three out of 31 SlBBX proteins have been functionally characterized to date. To deepen the understanding of the role of these proteins in tomato plant development and yield, SlBBX28, a light-responsive gene, was constitutively silenced, resulting in plants with smaller leaves and fewer flowers per inflorescence. Moreover, SlBBX28 knockdown reduced hypocotyl elongation in darkness-grown tomato. Analyses of auxin content and responsiveness revealed that SlBBX28 promotes auxin-mediated responses. Altogether, the data revealed that SlBBX28 promotes auxin production and signaling, ultimately leading to proper hypocotyl elongation, leaf expansion, and inflorescence development, which are crucial traits determining tomato yield.
PMID: 35798935
Plant Mol Biol , IF:4.076 , 2022 Jun doi: 10.1007/s11103-022-01289-2
The interaction between exogenous IBA with sucrose, light and ventilation alters the expression of ARFs and Aux/IAA genes in Carica papaya plantlets.
Centro de Investigacion Cientifica de Yucatan A.C., Calle 43 No. 130, Colonia Chuburna de Hidalgo, C.P. 97205, Merida, Yucatan, Mexico. estrella.humberto@inifap.gob.mx.; Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martinez de la Torre-Tlapacoyan, C.P. 93600, Tlapacoyan, Veracruz, Mexico. estrella.humberto@inifap.gob.mx.; Centro de Investigacion Cientifica de Yucatan A.C., Calle 43 No. 130, Colonia Chuburna de Hidalgo, C.P. 97205, Merida, Yucatan, Mexico.; Independent Researcher, Calle 6a 279 a, Jardines de Vista Alegre, Merida, Yucatan, Mexico.; Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Boulevard Hochelaga, Quebec City, QC, G1V 0A6, Canada.; Centro de Investigacion Cientifica de Yucatan A.C., Calle 43 No. 130, Colonia Chuburna de Hidalgo, C.P. 97205, Merida, Yucatan, Mexico. jorgesm@cicy.mx.
KEY MESSAGE: The interaction between exogenous IBA with sucrose, light and ventilation, alters the expression of ARFs and Aux/IAA genes in in vitro grown Carica papaya plantlets. In vitro papaya plantlets normally show low rooting percentages during their ex vitro establishment that eventually leads to high mortality when transferred to field conditions. Indole-3-butyric acid (IBA) auxin is normally added to culture medium, to achieve adventitious root formation on in vitro papaya plantlets. However, the molecular mechanisms occurring when IBA is added to the medium under varying external conditions of sugar, light and ventilation have not been studied. Auxin response factors (ARF) are auxin-transcription activators, while auxin/indole-3-acetic acid (Aux/IAA) are auxin-transcription repressors, that modulate key components involved in auxin signaling in plants. In the present study, we identified 12 CpARF and 18 CpAux/IAA sequences in the papaya genome. The cis-acting regulatory elements associated to those CpARFs and CpAux/IAA gene families were associated with stress and hormone responses. Furthermore, a comprehensive characterization and expression profiling analysis was performed on 6 genes involved in rhizogenesis formation (CpARF5, 6, 7 and CpAux/IAA11, 13, 14) from in vitro papaya plantlets exposed to different rhizogenesis-inducing treatments. In general, intact in vitro plantlets were not able to produce adventitious roots, when IBA (2 mg L(-1)) was added to the culture medium; they became capable to produce roots and increased their ex-vitro survival. However, the best rooting and survival % were obtained when IBA was added in combination with adequate sucrose supply (20 g L(-1)), increased light intensity (750 micromol photon m(-2) s(-1)) and ventilation systems within the culture vessel. Interestingly, it was precisely under those conditions that promoted high rooting and survival %, where the highest expression of CpARFs, but the lowest expression of CpAux/IAAs occurred. One interesting case occurred when in vitro plantlets were exposed to high levels of light in the absence of added IBA, as high rooting and survival occurred, even though no exogenous auxin was added. In fact, plantlets from this treatment showed the right expression profile between auxin activators/repressors genes, in both stem base and root tissues.
PMID: 35725838
Plants (Basel) , IF:3.935 , 2022 Jul , V11 (15) doi: 10.3390/plants11151898
Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening.
College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.; Department of Horticultural Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan.; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.; Department of Animal Sciences, Ghazi University, Dera Ghazi Khan 32200, Pakistan.; Ayub Agricultural Research Institute, Faisalabad 38850, Pakistan.
Auxin/indole-3-acetic acid (Aux/IAA) is a transcriptional repressor in the auxin signaling pathway that plays a role in several plant growth and development as well as fruit and embryo development. However, it is unclear what role they play in Japanese apricot (Prunus mume) fruit development and maturity. To investigate the role of Aux/IAA genes in fruit texture, development, and maturity, we comprehensively identified and expressed 19 PmIAA genes, and demonstrated their conserved domains and homology across species. The majority of PmIAA genes are highly responsive and expressed in different hormone treatments. PmIAA2, PmIAA5, PmIAA7, PmIAA10, PmIAA13, PmIAA18, and PmIAA19 showed a substantial increase in expression, suggesting that these genes are involved in fruit growth and maturity. During fruit maturation, alteration in the expression of PmIAA genes in response to 1-Methylcyclopropene (1-MCP) treatment revealed an interaction between auxin and ethylene. The current study investigated the response of Aux/IAA development regulators to auxin during fruit ripening, with the goal of better understanding their potential application in functional genomics.
PMID: 35893602
Plants (Basel) , IF:3.935 , 2022 Jul , V11 (14) doi: 10.3390/plants11141867
Morphological and Physiological Indicators for Screening Cell Lines with High Potential for Somatic Embryo Maturation at an Early Stage of Somatic Embryogenesis in Pinus Koraiensis.
State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China.; State Forestry and Grassland Administration Engineering Technology Research Center of Korean Pine, Harbin 150040, China.; Laboratory of Forest Genetics and Breeding, Institution of the Russian Academy of Sciences, V.N. Sukachev Institute of Forest Siberian Branch of RAS, 660036 Krasnoyarsk, Russia.; Department of Cell Biology, Institute of Plant Physiology, K.A. Timiryazev Russian Academy of Sciences, 127276 Moscow, Russia.; Department of Plant Physiology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia.
Many cell lines in the embryogenic callus cannot produce somatic embryos (SEs) even if they meet the optimal SE maturation culture conditions during conifer somatic embryogenesis. This phenomenon hinders the progress of the industrial-scale reproduction of conifers. Therefore, there is an urgent need to obtain morphological and physiological markers to screen embryogenic calli in response to SE maturation conditions. To detect cell lines with high somatic embryogenesis potential during the proliferation process, we counted the number of pro-embryos and early SEs (ESEs) in different cell lines and storage substances, endogenous hormones, and polyamine contents. The results showed that the yield of P. koraiensis SEs was heavily dependent on genotype (p = 0.001). There were high levels of PE III (pro-embryo III) number, ESE number, and soluble protein content, in the response cell lines (R cell lines), which were 1.6-, 3-, and 1.1-fold those of the obstructive cell lines (B cell lines), respectively. The B cell line had high levels of starch, auxin (IAA), Put, Spd, and putrescine: spermine (Put: Spm) compared to the R cell line. In addition, the numbers of PE III, ESEs, and soluble protein content were significantly positively correlated with SE yield. In contrast, the contents of starch, abscisic acid (ABA), Put, Spm, and Spd were significantly negatively correlated with SE yield. To ensure the accuracy of the results, we used nine cell lines to test the results. The PE III and ESE numbers and the Spm and Spd contents were positively correlated with SE yield, while the levels of starch, ABA, IAA, Put: Spd, and Put: Spm were negatively correlated with SE yield. Thus, we recommend using high PE III and ESEs as morphological indicators and low levels of starch, IAA, ABA, and Put: Spm as physiological markers to screen cell lines with a high somatic embryogenesis potential. In addition, we also found that the relationship between Spd, Spm, and SE yield was opposite in the two experimental results. Therefore, we speculate that the differences in Spd and Spm content are mainly affected by genotype. In conclusion, this study obtained the morphological and physiological markers of some high-somatic embryogenic cell lines by comparing the differences between nine somatic embryogenic cell lines. Our results can guide the improvement of conifer somatic embryogenesis technology and can provide a theoretical basis for accelerating the application of biotechnology in large-scale artificial breeding.
PMID: 35890500
Plants (Basel) , IF:3.935 , 2022 Jul , V11 (14) doi: 10.3390/plants11141817
Plant Development of Early-Maturing Spring Wheat (Triticum aestivum L.) under Inoculation with Bacillus sp. V2026.
Agrophysical Scientific Research Institute, Grazhdansky Pr. 14, 195220 St. Petersburg, Russia.; All-Russia Research Institute for Agricultural Microbiology, Podbelskogohwy 3, Pushkin, 196608 St. Petersburg, Russia.
The effect of a plant growth-promoting bacterium (PGPB) Bacillus sp. V2026, a producer of indolyl-3-acetic acid (IAA) and gibberellic acid (GA), on the ontogenesis and productivity of four genotypes of early-maturing spring wheat was studied under controlled conditions. The inoculation of wheat plants with Bacillus sp. V2026 increased the levels of endogenous IAA and GA in wheat of all genotypes and the level of trans-Zeatin in Sonora 64 and Leningradskaya rannyaya cvs but decreased it in AFI177 and AFI91 ultra-early lines. Interactions between the factors "genotype" and "inoculation" were significant for IAA, GA, and trans-Zeatin concentrations in wheat shoots and roots. The inoculation increased the levels of chlorophylls and carotenoids and reduced lipid peroxidation in leaves of all genotypes. The inoculation resulted in a significant increase in grain yield (by 33-62%), a reduction in the time for passing the stages of ontogenesis (by 2-3 days), and an increase in the content of macro- and microelements and protein in the grain. Early-maturing wheat genotypes showed a different response to inoculation with the bacterium Bacillus sp. V2026. Cv. Leningradskaya rannyaya was most responsive to inoculation with Bacillus sp. V2026.
PMID: 35890450
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (13) doi: 10.3390/plants11131728
HD-Zip III Gene Family: Identification and Expression Profiles during Leaf Vein Development in Soybean.
College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China.; Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu 611130, China.; Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu 611130, China.
Leaf veins constitute the transport network for water and photosynthetic assimilates in vascular plants. The class III homeodomain-leucine zipper (HD-Zip III) gene family is central to the regulation of vascular development. In this research, we performed an overall analysis of the HD-Zip III genes in soybean (Glycine max L. Merr.). Our analysis included the phylogeny, conservation domains and cis-elements in the promoters of these genes. We used the quantitative reverse transcription-polymerase chain reaction to characterize the expression patterns of HD-Zip III genes in leaf vein development and analyze the effects of exogenous hormone treatments. In this study, twelve HD-Zip III genes were identified from the soybean genome and named. All soybean HD-Zip III proteins contained four highly conserved domains. GmHB15-L-1 transcripts showed steadily increasing accumulation during all stages of leaf vein development and were highly expressed in cambium cells. GmREV-L-1 and GmHB14-L-2 had nearly identical expression patterns in soybean leaf vein tissues. GmREV-L-1 and GmHB14-L-2 transcripts remained at stable high levels at all xylem developmental stages. GmREV-L-1 and GmHB14-L-2 were expressed at high levels in the vascular cambium and xylem cells. Overall, GmHB15-L-1 may be an essential regulator that is responsible for the formation or maintenance of soybean vein cambial cells. GmREV-L-1 and GmHB14-L-2 were correlated with xylem differentiation in soybean leaf veins. This study will pave the way for identifying the molecular mechanism of leaf vein development.
PMID: 35807680
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (13) doi: 10.3390/plants11131727
Changes in the Activity of the CLE41/PXY/WOX Signaling Pathway in the Birch Cambial Zone under Different Xylogenesis Patterns.
Forest Research Institute, Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskayast., 185910 Petrozavodsk, Russia.
The balance between cell proliferation and differentiation into other cell types is crucial for meristem indeterminacy, and both growth aspects are under genetic control. The peptide-receptor signaling module regulates the activity of the cambial stem cells and the differentiation of their derivatives, along with cytokinins and auxin. We identified the genes encoding the signaling module CLE41-PXY and the regulator of vascular cambium division WOX4 and studied their expression during the period of cambial growth in the radial row: the conducting phloem/cambial zone and the differentiating xylem in two forms of Betula pendula, silver birch and Karelian birch. We have shown that the expression maximum of the BpCLE41/44a gene precedes the expression maximum of the BpPXY gene. Non-figured Karelian birch plants with straight-grained wood are characterized by a more intensive growth and the high expression of CLE41/44-PXY-WOX4. Figured Karelian birch plants, where the disturbed ratio and spatial orientation of structural elements characterizes the wood, have high levels of BpWOX4 expression and a decrease in xylem growth as well as the formation of xylem with a lower vessel density. The mutual influences of CLE41-PXY signaling and auxin signaling on WOX4 gene activity and the proliferation of cambium stem cells are discussed.
PMID: 35807679
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (13) doi: 10.3390/plants11131679
BnKAT2 Positively Regulates the Main Inflorescence Length and Silique Number in Brassica napus by Regulating the Auxin and Cytokinin Signaling Pathways.
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.; Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.; Chongqing Engineering Research Center for Rapeseed, Chongqing 400715, China.; Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550018, China.
Brassica napus is the dominant oil crop cultivated in China for its high quality and high yield. The length of the main inflorescence and the number of siliques produced are important traits contributing to rapeseed yield. Therefore, studying genes related to main inflorescence and silique number is beneficial to increase rapeseed yield. Herein, we focused on the effects of BnKAT2 on the main inflorescence length and silique number in B. napus. We explored the mechanism of BnKAT2 increasing the effective length of main inflorescence and the number of siliques through bioinformatics analysis, transgenic technology, and transcriptome sequencing analysis. The full BnKAT2(BnaA01g09060D) sequence is 3674 bp, while its open reading frame is 2055 bp, and the encoded protein comprises 684 amino acids. BnKAT2 is predicted to possess two structural domains, namely KHA and CNMP-binding domains. The overexpression of BnKAT2 effectively increased the length of the main inflorescence and the number of siliques in B. napus, as well as in transgenic Arabidopsis thaliana. The type-A Arabidopsis response regulator (A-ARR), negative regulators of the cytokinin, are downregulated in the BnKAT2-overexpressing lines. The Aux/IAA, key genes in auxin signaling pathways, are downregulated in the BnKAT2-overexpressing lines. These results indicate that BnKAT2 might regulate the effective length of the main inflorescence and the number of siliques through the auxin and cytokinin signaling pathways. Our study provides a new potential function gene responsible for improvement of main inflorescence length and silique number, as well as a candidate gene for developing markers used in MAS (marker-assisted selection) breeding to improve rapeseed yield.
PMID: 35807631
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (13) doi: 10.3390/plants11131654
From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity.
Institute of Plantecology, Justus-Liebig-University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany.; Institute of Botany, Leibniz Universitaet Hannover, Herrenhaeuser Str. 2, 30416 Hannover, Germany.; AK Biotechnology, VDI-BV-Hannover, Hanomagstr. 12, 30449 Hannover, Germany.
Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food-soil-climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant-soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.
PMID: 35807605
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (13) doi: 10.3390/plants11131620
Plants' Physio-Biochemical and Phyto-Hormonal Responses to Alleviate the Adverse Effects of Drought Stress: A Comprehensive Review.
Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.; Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr 75169, Iran.; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.; Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.; Department of Botany, Islamia College, Peshawar 25120, Pakistan.; Department of Botany, University of Peshawar, Peshawar 25120, Pakistan.; Department of Botany, Division of Science and Technology, University of Education, Lahore 54770, Pakistan.; Department of Botany, Bahauddin Zakariya University, Multan 60800, Pakistan.; Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 Calea Manastur Street, 400372 Cluj-Napoca, Romania.
Water, a necessary component of cell protoplasm, plays an essential role in supporting life on Earth; nevertheless, extreme changes in climatic conditions limit water availability, causing numerous issues, such as the current water-scarce regimes in many regions of the biome. This review aims to collect data from various published studies in the literature to understand and critically analyze plants' morphological, growth, yield, and physio-biochemical responses to drought stress and their potential to modulate and nullify the damaging effects of drought stress via activating natural physiological and biochemical mechanisms. In addition, the review described current breakthroughs in understanding how plant hormones influence drought stress responses and phytohormonal interaction through signaling under water stress regimes. The information for this review was systematically gathered from different global search engines and the scientific literature databases Science Direct, including Google Scholar, Web of Science, related studies, published books, and articles. Drought stress is a significant obstacle to meeting food demand for the world's constantly growing population. Plants cope with stress regimes through changes to cellular osmotic potential, water potential, and activation of natural defense systems in the form of antioxidant enzymes and accumulation of osmolytes including proteins, proline, glycine betaine, phenolic compounds, and soluble sugars. Phytohormones modulate developmental processes and signaling networks, which aid in acclimating plants to biotic and abiotic challenges and, consequently, their survival. Significant progress has been made for jasmonates, salicylic acid, and ethylene in identifying important components and understanding their roles in plant responses to abiotic stress. Other plant hormones, such as abscisic acid, auxin, gibberellic acid, brassinosteroids, and peptide hormones, have been linked to plant defense signaling pathways in various ways.
PMID: 35807572
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (12) doi: 10.3390/plants11121618
UVB Irradiation-Induced Transcriptional Changes in Lignin- and Flavonoid Biosynthesis and Indole/Tryptophan-Auxin-Responsive Genes in Rice Seedlings.
Department of Crop Science, Chungbuk National University, Cheongju 28644, Korea.
Global warming accelerates the destruction of the ozone layer, increasing the amount of UVB reaching the Earth's surface, which in turn alters plant growth and development. The effects of UVB-induced alterations of plant secondary and cell wall metabolism were previously documented; however, there is little knowledge of its effects on rice seedlings during the developmental phase of leaves. In this study, we examined secondary metabolic responses to UVB stress using a transcriptomic approach, focusing on the biosynthetic pathways for lignin, flavonoid, and indole/tryptophan-auxin responses. As new leaves emerged, they were irradiated with UVB for 5 days (for 3 h/day(-1)). The genes encoding the enzymes related to lignin (4CL, CAD, and POD) and flavonoid biosynthesis (CHS, CHI, and FLS) were highly expressed on day 1 (younger leaves) and day 5 (older leaves) after UVB irradiation. The expression of the genes encoding the enzymes related to tryptophan biosynthesis (AS, PRT, PRAI, IGPS, and TS) increased on day 3 of UVB irradiation, and the level of tryptophan increased and showed the same temporal pattern of occurrence as the expression of the cognate gene. Interestingly, the genes encoding BBX4 and BBX11, negative regulators of UVB signaling, and SAUR27 and SAUR55, auxin response enzymes, were downregulated on day 3 of UVB irradiation. When these results are taken together, they suggest that secondary metabolic pathways in rice seedlings are influenced by the interaction between UVB irradiation and the leaf developmental stage. Thus, the strategies of protection against, adaptation to, and mitigation of UVB might be delicately regulated, and, in this context, our data provide valuable information to understand UVB-induced secondary metabolism in rice seedlings.
PMID: 35736769
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (12) doi: 10.3390/plants11121601
The Mutation of Rice MEDIATOR25, OsMED25, Induces Rice Bacterial Blight Resistance through Altering Jasmonate- and Auxin-Signaling.
Faculty of Agriculture, Kagawa University, Miki 761-0795, Japan.; Philippine Rice Research Institute, Central Experiment Station, Science City of Munoz 3119, Philippines.; International Center for Research and Education in Agriculture, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
Rice bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most severe diseases of rice. However, the regulatory mechanisms of rice defense against Xoo remain poorly understood. The rice MEDIATOR25, OsMED25-a subunit of the mediator multiprotein complex that acts as a universal adaptor between transcription factors (TFs) and RNA polymerase II-plays an important role in jasmonic acid (JA)-mediated lateral root development in rice. In this study, we found that OsMED25 also plays an important role in JA- and auxin-mediated resistance responses against rice bacterial blight. The osmed25 loss-of-function mutant exhibited high resistance to Xoo. The expression of JA-responsive defense-related genes regulated by OsMYC2, which is a positive TF in JA signaling, was downregulated in osmed25 mutants. Conversely, expression of some OsMYC2-independent JA-responsive defense-related genes was upregulated in osmed25 mutants. Furthermore, OsMED25 interacted with some AUXIN RESPONSE FACTORS (OsARFs) that regulate auxin signaling, whereas the mutated osmed25 protein did not interact with the OsARFs. The expression of auxin-responsive genes was downregulated in osmed25 mutants, and auxin-induced susceptibility to Xoo was not observed in osmed25 mutants. These results indicate that OsMED25 plays an important role in the stable regulation of JA- and auxin-mediated signaling in rice defense response.
PMID: 35736751
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (12) doi: 10.3390/plants11121580
A Small Gtp-Binding Protein GhROP3 Interacts with GhGGB Protein and Negatively Regulates Drought Tolerance in Cotton (Gossypium hirsutum L.).
College of Life Science, Xinjiang Agricultural University, Nongda East Road, Urumqi 830001, China.; College of Agronomy, Laboratory of Agricultural Biotechnology, Xinjiang Agricultural University, Nongda East Road, Urumqi 830001, China.; Research Center of Cotton Engineering, Ministry of Education, Xinjiang Agricultural University, Nongda East Road, Urumqi 830001, China.
As a plant-specific Rho-like small G protein, the ROP (Rho-related GTPase of plants) protein regulates the growth and development of plants and various stress responses in the form of molecular switches. Drought is a major abiotic stress that limits cotton yield and fiber quality. In this study, virus-induced gene silencing (VIGS) technology was used to analyze the biological function of GhROP3 in cotton drought stress tolerance. Meanwhile, we used yeast two-hybrid and bimolecular fluorescence complementation assays to examine the interaction between GhROP3 and GhGGB. GhROP3 has a high expression level in cotton true leaves and roots, and responds to drought, high salt, cold, heat stress, and exogenous abscisic acid (ABA) and auxin (IAA) treatments. Silencing GhROP3 improved the drought tolerance of cotton. The water loss rates (WLR) of detached leaves significantly reduced in silenced plants. Also, the relative water content (RWC) and total contents of chlorophyll (Chl) and proline (Pro) of leaves after drought stress and the activities of three antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) significantly increased, whereas the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA) significantly reduced. In the leaves of silenced plants, the expression of genes related to ABA synthesis and its related pathway was significantly upregulated, and the expression of decomposition-related GhCYP707A gene and genes related to IAA synthesis and its related pathways was significantly downregulated. It indicated that GhROP3 was a negative regulator of cotton response to drought by participating in the negative regulation of the ABA signaling pathway and the positive regulation of the IAA signaling pathway. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhROP3 protein interacted with the GhGGB protein in vivo and in vitro. This study provided a theoretical basis for the in-depth investigation of the drought resistance-related molecular mechanism of the GhROP3 gene and the biological function of the GhGGB gene.
PMID: 35736735
Life (Basel) , IF:3.817 , 2022 Jun , V12 (6) doi: 10.3390/life12060921
Transcriptome and Metabolome Analysis of Upland Cotton (Gossypium hirsutum) Seed Pretreatment with MgSO4 in Response to Salinity Stress.
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.; Fukang Station of Desert Ecology, Chinese Academy of Sciences, Fukang 831505, China.; College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China.
Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can withstand high salinity levels without showing signs of harm to the plant. However, the plant is more prone to salinity stress at the germination stage and a poor germination as well as poor crop stand lead to a weak productivity. It is possible to obtain a comprehensive picture of the cotton seedling germination and establishment against salt stress by examining dynamic changes in the transcriptomic and metabolomic profiles. The reported study employed a pretreatment of cotton seeds by soaking them in 0.2% Magnesium Sulphate (MgSO4) solution at room temperature for 4, 8, and 12 h. The analysis of variance based on the studied traits emergence rate, above and underground plant parts' fresh weight measured, displayed significant differences of the three treatments compared with the control. A total of 28,801 and 264 differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were discovered to code for biological processes such as response to salt stress, cellular response to salt stress, abscisic acid receptor PYR/PYL, regulation of seed growth and germination, and auxin-activated signaling pathways. A large amount of ethylene-responsive transcription factors (ERF) was identified (1235) as differentially expressed, followed by bHLH (252), WRKY (96), MYB (202), GATA (81), RABA (64), DIVARICATA (28), and MADs-box (26) in treated seedling samples. Functional enrichment analysis revealed the significant roles in the hormones and signal transduction, carbohydrates metabolism, and biosynthesis of amino acids, promoting salt stress tolerance. Our results indicated positive effects of MgSO4 at 4 h treatment on seedling germination and growth, seemingly by activating certain growth-regulating enzymes (auxins, gibberellins, jasmonates, abscisic acid, and salicylic acid) and metabolites (phenolic acids, flavonoids, and akaloids). Such pretreatment of MgSO4 on seeds would be beneficial in future cotton management under saline conditions to enhance good crop stand and productivity.
PMID: 35743952
Gene , IF:3.688 , 2022 Aug , V837 : P146692 doi: 10.1016/j.gene.2022.146692
SAUR8, a small auxin-up RNA gene in poplar, confers drought tolerance to transgenic Arabidopsis plants.
Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.; Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China. Electronic address: xiangyanahau@sina.com.
SAUR (small auxin-up RNA) is an early auxin-responsive gene. In this study, a novel SAUR gene PtSAUR8 was cloned from poplar (Populus trichocarpa), and subcellular location analysis showed that it is targeted to the nuclear membrane. In addition, PtSAUR8 overexpression in Arabidopsis improved the plant resistance to drought stress. Meanwhile, the loss of function mutant saur53 showed more drought sensitivity compared to the WT. PtSAUR8 conferred drought tolerance in transgenic Arabidopsis, as determined through phenotypic and stress-associated physiological indicator analyses, namely, root length, germination rate, relative water content, proline content, CAT content, POD content, malondialdehyde content, hydrogen peroxide content, and relative conductivity. In addition, after the 1 muM abscisic acid (ABA) treatment, the PtSAUR8-OE lines promoted stomata closure. Quantitative fluorescence analysis of related genes induced by drought mutant stress further confirmed that overexpression of PtSAUR8 can improve drought resistance in transgenic Arabidopsis lines. Therefore, PtSAUR8 may play a role in plant drought resistance through ABA-mediated pathways; thus, providing new research materials for molecular breeding of poplar resistance.
PMID: 35760288
Gene , IF:3.688 , 2022 Jul , V833 : P146592 doi: 10.1016/j.gene.2022.146592
Comparative transcriptome profiling of sweetpotato storage roots during curing-mediated wound healing.
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea; R&D Center, Genolution Inc., 63, Magokjungang 8-ro 3-gil, Gangseo-gu, Seoul 07793, Republic of Korea.; Department of Biology Education, IALS, Gyeongsang National University, Jinju 52828, Republic of Korea.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea.; Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, 199 Muan-ro, Muan-gun 58545, Republic of Korea.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea. Electronic address: sskwak@kribb.re.kr.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea. Electronic address: hskim@kribb.re.kr.
Sweetpotato (Ipomoea batatas L. Lam) is an economically important crop that is cultivated for its storage roots. Storage roots provide a source of valuable nutrients, processed foods, animal feeds, and pigments. Sweetpotato storage roots spoil during post-harvest handling because of wounding, which makes them more susceptible to disease-causing microorganisms. Curing to promote wound healing is a common method to control microbial spoilage during post-harvest storage. However, molecular mechanisms underlying the process of curing in sweetpotato storage roots are unknown. To better understand the biology behind curing, the transcriptome of the sweetpotato cultivar, Pungwonmi, was studied using RNA-seq. Storage roots of sweetpotato were treated at 33 degrees C (Curing) and 13 degrees C (Control) for 3 days. RNA-seq data identified 78,781 unigenes and 3,366 differentially expressed genes by over log2 fold change (FC) > 2 and <-2. During curing, DEGs encoded genes related to drought/salt stress responses, phyto-hormones (e.g., auxin, ethylene and jasmonic acid), and proteolysis, were up-regulated, whereas those related to redox state, phyto-hormones (e.g., salicylic acid and brassinosteroids), and lignin and flavonoid biosynthesis were down-regulated. Additionally, among the candidate genes, DEGs encoded genes related to proteolysis and pathogen defense, such as protease inhibitors and lipid transfer proteins, were highly up-regulated during curing and storage. This study provides a valuable resource to further understand the molecular basis of curing-mediated wound healing in sweetpotato storage roots. Moreover, genes revealed in this work could present targets for the development of sweetpotato varieties with improved post-harvest storage characteristics.
PMID: 35605748
Gene , IF:3.688 , 2022 Jun , V829 : P146494 doi: 10.1016/j.gene.2022.146494
Whole genome duplication and dispersed duplication characterize the evolution of the plant PINOID gene family across plant species.
State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.; Department of Biology, California State University East Bay, Hayward, CA, United States of America.; State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing, China.; State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China. Electronic address: ligt18@lzu.edu.cn.
PINOID is a kinase belonging to the AGCVIII family, which regulates the polar distribution of PIN proteins and plays an important role in plant geotropism. However, the origin and evolutionary history of this gene family is not fully known. In this study, we identified 79 similar sequences across 17 plant species genomes (PINOID, D6PK, PINOID2, "hypothetical kinase"). Our results show that the AGCVIII kinase family may have originated from related "Hypothetical Kinases" that come out sister to the rest of the gene family members. These kinases differentiated their functions are found in different plant classes: D6PK in moss and PINOID and PINOID2 evolving in angiosperms including the pioneer plant Amborella trichopoda. Our study investigates the evolution of PINOID kinases from a phylogenetic perspective giving us insight into how this important plant signal transduction network switch evolved to play a fundamental and important function in plant growth and development. We highlight the importance of whole genome duplications and dispersed duplications as opposed to tandem duplications in the evolution of this gene family.
PMID: 35447241
J Sci Food Agric , IF:3.638 , 2022 Jul , V102 (9) : P3644-3654 doi: 10.1002/jsfa.11711
Controlled-release urea combined with fulvic acid enhanced carbon/nitrogen metabolic processes and maize growth.
National Engineering Laboratory for Efficient Use of Soil and Fertilizer Resources, College of Resources and the Environment, Shandong Agricultural University, Taian, China.; Shandong Pengbo Biotechnology Co., Ltd, Taian, China.; Shandong Wanhao Fertilizer Co. Ltd, Jinan, China.
BACKGROUND: Controlled-release urea (CRU) or fulvic acid (FA), when applied, have been shown to increase nitrogen (N) use efficiency (NUE) or to stimulate plant growth, yet their interactive effects are not well explored. The objective of this study was to investigate the synergistic mechanisms of CRU combined with FA (CRU + FA) on maize (Zea mays L.) growth. Through the experimental design with five treatments, the N metabolism through the transcriptomic analysis of maize leaf, endogenous hormones, photosynthesis enzymes in maize leaf and root, and maize yield and NUE were evaluated. RESULTS: Compared with CRU treatment, CRU + FA treatment significantly increased auxin, nitrate reductase, and glutamate dehydrogenase in leaf by 35.4%, 43.9%, 40.8% and 19.5%, respectively, as well as, the relative content of the leaf chlorophyll and photosynthetic rate by 14.8% and 45.6%, respectively, at 12-leaf collar stage; the carbon/nitrogen (C/N) metabolic process was significantly enriched in CRU + FA treatment by 312 and 418 genes, according to transcriptome profiles of C/N metabolic in leaves from various fertilizer treated maize; maize yield and NUE of CRU + FA treatment were increased by 6.3% and 38.4%, respectively. CONCLUSIONS: These results demonstrated that CRU + FA is a viable fertilization scheme that can enhance maize growth, yield and NUE through their synergies in improving N uptake, promoting photosynthesis, increasing C/N metabolic processes, and enhancing enzyme activities. (c) 2021 Society of Chemical Industry.
PMID: 34888887
ACS Omega , IF:3.512 , 2022 Jul , V7 (27) : P23566-23575 doi: 10.1021/acsomega.2c02102
Effect of Coated Diammonium Phosphate Combined with Paecilomyces variotii Extracts on Soil Available Nutrients, Photosynthesis-Related Enzyme Activities, Endogenous Hormones, and Maize Yield.
National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China.; Shandong Pengbo Biotechnology Co., Ltd., Taian 271018, Shandong, China.; Kingenta Ecological Engineering Group Co., Ltd., Linshu 276700, Shandong, China.
Coated diammonium phosphate (CDAP) is intended to release nutrients steadily in response to the demand of crop growth. A novel biostimulant extracted from Paecilomyces variotii has been shown to regulate gene expression in nutrient transport, enhance nitrogen (N) and phosphorus (P) uptake, and improve nutrient use efficiency. The application of CDAP combined with the Paecilomyces variotii extracts (ZNC) in maize is an efficient approach for reducing waste of resources, improving nutrient supply, and maintaining production stability. The effects of CDAP combined with ZNC on photosynthesis, enzyme activities, endogenous hormone content, maize yield, and P use efficiency (PUE) were investigated in this study. In a pot experiment, CDAP and diammonium phosphate (DAP) were tested together with P levels (1.80, 1.44 g pot(-1), P2O5) and two ZNC application rates (0, 4.4 mug pot(-1)), which included the control treatment that had no P fertilizer added. Results showed that the key influencing elements of maize growth and yield were the soil available-P content, endogenous hormone content, and plant photosynthesis in this study. The combination of DAP and ZNC increased the soil available-P content and the auxin content in leaves at the key stage and hence increased the yield and PUE of maize, compared with DAP. The net photosynthetic rate of CDAP combined with ZNC was higher by 23.1% than that of CDAP alone, as well as by 32.0% than that of DAP combined with ZNC. Moreover, the combination of CDAP and ZNC increased the yield and PUE by 8.2% and 15.6 percentage points compared with DAP combined with ZNC while increasing the yield and PUE compared with CDAP. In conclusion, combining CDAP with ZNC as an environmentally friendly fertilizer could improve photosynthesis-related enzyme activity and enhance the net photosynthetic rate, resulting in an increase in maize yield and PUE significantly.
PMID: 35847329
Phytochem Anal , IF:3.373 , 2022 Jun doi: 10.1002/pca.3135
Development of approach for flavonoid profiling of biotechnological raw materials Iris sibirica L. by HPLC with high-resolution tandem mass spectrometry.
Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia.; Saint Petersburg Scientific Research Institute of Vaccines and Serums and the Enterprise for the Production of Bacterial Preparations, Saint Petersburg, Russia.
INTRODUCTION: Iris L. are promising in medicine due to the biological activity of extracts. Iris sibirica L. is spread in Russia but its phytochemical composition has not been studied in detail though it is included in the Red Book. For this reason, I. sibirica L. biotechnology is in high demand. One of the key points in biotechnology is the regulation of plant metabolism using phytohormones. Obtaining of chromatographic metabolite profiles allows to control this process. OBJECTIVE: The aim of this study was to develop an approach for effective control of biotechnological raw materials of I. sibirica L. by flavonoid profiles using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and to investigate the influence of phytohormones in nutrient media on content of flavonoids. METHODOLOGY: Iris sibirica L. regenerated plants were grown on Murashige-Skoog media with 6-benzylaminopurine (6-BAP) and alpha-naphtylacetic acid (NAA) additives. To optimise extraction conditions, the design of the experiment was used. Profiles of polyphenols were obtained by HPLC-MS/MS in the positive and negative ionisation modes. RESULTS: The process for efficient extraction from leaves of I. sibirica L. were developed. The factors influencing the extraction efficiency of flavonoids have been determined. A total of 36 compounds were identified by HPLC-MS/MS. Among them isoflavones and their glycosides are the main classes. Addition of an auxin-like hormone increased the non-polar flavonoid levels, but decreased the polar ones. The variation in concentration of cytokinin (6-BAP) affected almost all of the analytes. CONCLUSION: The methodology for effective control of I. sibirica L. raw plant material biotechnology was developed by analysing obtained chromatographic polyphenol profiles.
PMID: 35680077
Protoplasma , IF:3.356 , 2022 Jul , V259 (4) : P835-854 doi: 10.1007/s00709-021-01705-2
Plant growth-promoting and non-promoting rhizobacteria from avocado trees differentially emit volatiles that influence growth of Arabidopsis thaliana.
Red de Biodiversidad y Sistematica, Instituto de Ecologia A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico.; Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-Leon, 36821, Irapuato, Guanajuato, Mexico.; Red de Estudios Moleculares Avanzados, Cluster BioMimic(R), Instituto de Ecologia A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico.; Red de Biodiversidad y Sistematica, Instituto de Ecologia A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico. gloria.carrion@inecol.mx.; Red de Estudios Moleculares Avanzados, Cluster BioMimic(R), Instituto de Ecologia A.C., Carretera Antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico. randy.ortiz@inecol.mx.
Microbial volatile organic compounds (mVOCs) play important roles in inter- and intra-kingdom interactions, and they are also important as signal molecules in physiological processes acting either as plant growth-promoting or negatively modulating plant development. We investigated the effects of mVOCs emitted by PGPR vs non-PGPR from avocado trees (Persea americana) on growth of Arabidopsis thaliana seedlings. Chemical diversity of mVOCs was determined by SPME-GC-MS; selected compounds were screened in dose-response experiments in A. thaliana transgenic lines. We found that plant growth parameters were affected depending on inoculum concentration. Twenty-six compounds were identified in PGPR and non-PGPR with eight of them not previously reported. The VOCs signatures were differential between those groups. 4-methyl-2-pentanone, 1-nonanol, 2-phenyl-2-propanol and ethyl isovalerate modified primary root architecture influencing the expression of auxin- and JA-responsive genes, and cell division. Lateral root formation was regulated by 4-methyl-2-pentanone, 3-methyl-1-butanol, 1-nonanol and ethyl isovalerate suggesting a participation via JA signalling. Our study revealed the differential emission of volatiles by PGPR vs non-PGPR from avocado trees and provides a general view about the mechanisms by which those volatiles influence plant growth and development. Rhizobacteria strains and mVOCs here reported are promising for improvement the growth and productivity of avocado crop.
PMID: 34529144
PLoS One , IF:3.24 , 2022 , V17 (6) : Pe0269984 doi: 10.1371/journal.pone.0269984
PIF-independent regulation of growth by an evening complex in the liverwort Marchantia polymorpha.
Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden.; Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre of Plant Biology in Uppsala, Uppsala, Sweden.; Physiological Botany, Department of Organismal Biology, Uppsala University, The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden.
Previous studies in the liverwort Marchantia polymorpha have shown that the putative evening complex (EC) genes LUX ARRHYTHMO (LUX) and ELF4-LIKE (EFL) have a function in the liverwort circadian clock. Here, we studied the growth phenotypes of MpLUX and MpEFL loss-of-function mutants, to establish if PHYTOCHROME-INTERACTING FACTOR (PIF) and auxin act downstream of the M. polymorpha EC in a growth-related pathway similar to the one described for the flowering plant Arabidopsis. We examined growth rates and cell properties of loss-of-function mutants, analyzed protein-protein interactions and performed gene expression studies using reporter genes. Obtained data indicate that an EC can form in M. polymorpha and that this EC regulates growth of the thallus. Altered auxin levels in Mplux mutants could explain some of the phenotypes related to an increased thallus surface area. However, because MpPIF is not regulated by the EC, and because Mppif mutants do not show reduced growth, the growth phenotype of EC-mutants is likely not mediated via MpPIF. In Arabidopsis, the circadian clock regulates elongation growth via PIF and auxin, but this is likely not an evolutionarily conserved growth mechanism in land plants. Previous inventories of orthologs to Arabidopsis clock genes in various plant lineages showed that there is high levels of structural differences between clocks of different plant lineages. Here, we conclude that there is also variation in the output pathways used by the different plant clocks to control growth and development.
PMID: 35709169
Pathog Dis , IF:3.166 , 2022 Jul doi: 10.1093/femspd/ftac029
3-indoleacetonitrile attenuates biofilm formation and enhances sensitivity to imipenem in Acinetobacter baumannii.
Department of Biotechnology, South Campus, Basic Medical Science (Block I), Panjab University, Sector 25, Chandigarh, India.; Department of Microbiology, South Campus, Basic Medical Science (Block I), Panjab University, Sector 25, Chandigarh, India.
Acinetobacter baumannii poses a global danger due to its ability to resist most of the currently available antimicrobial agents. Furthermore, the rise of carbapenem-resistant A. baumannii isolates has limited the treatment options available. In the present study, plant auxin 3-indoleacetonitrile was found to inhibit biofilm formation and motility of A. baumannii at sub-lethal concentration. Mechanistically, 3-indoleacetonitrile inhibited the synthesis of the quorum sensing signal 3-OH-C12-HSL by downregulating the expression of the abaI autoinducer synthase gene. 3-indoleacetonitrile was found to reduce MIC of A. baumannii ATCC 17 978 against imipenem, ofloxacin, ciprofloxacin, tobramycin, and levofloxacin, and significantly decreased persistence against imipenem. Inhibition of efflux pumps by down-regulating genes expression may be responsible for enhanced sensitivity and low persistence. 3-indoleacetonitrile reduced the resistance to imipenem in carbapenem-resistant A. baumannii isolates by down-regulating the expression of OXA beta-lactamases (blaoxa-51 and blaoxa-23), outer membrane protein carO and transporter protein adeB. These findings demonstrate the therapeutic potential of 3-indoleacetonitrile which could be explored as an adjuvant with antibiotics for controlling A. baumannii infections.
PMID: 35867872
Funct Plant Biol , IF:3.101 , 2022 Jul , V49 (8) : P742-758 doi: 10.1071/FP21315
DELAY OF GERMINATION 1 (DOG1) regulates dormancy in dimorphic seeds of Xanthium strumarium.
Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.; Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; and Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.; Department of Agronomy, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.; Agricultural and Natural Resources College, University of Tehran, Tehran, Iran.; Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
Seed dormancy ensures plant survival but many mechanisms remain unclear. A high-throughput RNA-seq analysis investigated the mechanisms involved in the establishment of dormancy in dimorphic seeds of Xanthium strumarium (L.) developing in one single burr. Results showed that DOG1 , the main dormancy gene in Arabidopsis thaliana L., was over-represented in the dormant seed leading to the formation of two seeds with different cell wall properties. Less expression of DME /EMB1649 , UBP26 , EMF2, MOM, SNL2, and AGO4 in the non-dormant seed was observed, which function in the chromatin remodelling of dormancy-associated genes through DNA methylation. However, higher levels of ATXR7 /SDG25, ELF6 , and JMJ16/PKDM7D in the non-dormant seed that act at the level of histone demethylation and activate germination were found. Dramatically lower expression in the splicing factors SUA, PWI , and FY in non-dormant seed may indicate that variation in RNA splicing for ABA sensitivity and transcriptional elongation control of DOG1 is of importance for inducing seed dormancy. Seed size and germination may be influenced by respiratory factors, and alterations in ABA content and auxin distribution and responses. TOR (a serine/threonine-protein kinase) is likely at the centre of a regulatory hub controlling seed metabolism, maturation, and germination. Over-representation of the respiration-associated genes (ACO3 , PEPC3 , and D2HGDH ) was detected in non-dormant seed, suggesting differential energy supplies in the two seeds. Degradation of ABA biosynthesis and/or proper auxin signalling in the large seed may control germinability, and suppression of endoreduplication in the small seed may be a mechanism for cell differentiation and cell size determination.
PMID: 35569923
Plant Direct , IF:3.038 , 2022 Jun , V6 (6) : Pe414 doi: 10.1002/pld3.414
The rolB-transgenic Nicotiana tabacum plants exhibit upregulated ARF7 and ARF19 gene expression.
Department of Genetics University of Calcutta Kolkata West Bengal India.; Division of Plant Biology Bose Institute Kolkata West Bengal India.; Department of Botany University of Calcutta Kolkata West Bengal India.
Agrobacterium rhizogenes root oncogenic locus B (rolB) is known to induce hairy roots along with triggering several physiological and morphological changes when present as a transgene. However, it is still unknown how this gene triggers these changes within the plant system. In this study, the effect of rolB in-planta, when present as a transgene, was assessed on the gene expression levels of auxin response factors (ARFs)-transcription factors which are key players in auxin-mediated responses. The goal was to uncover Auxin/ARF-driven transcriptional networks potentially active and working selectively, if any, in rolB transgenic background, which might potentially be associated with hairy root development. Hence, the approach involved establishing rolB-transgenic Nicotiana tabacum plants, selecting ARFs (NtARFs) for context-relevance using bioinformatics followed by gene expression profiling. It was observed that out of the chosen NtARFs, NtARF7 and NtARF19 exhibited a consistent pattern of gene upregulation across organ types. In order to understand the significance of these selective gene upregulation, ontology-based transcriptional network maps of the differentially and nondifferentially expressed ARFs were constructed, guided by co-expression databases. The network maps suggested that NtARF7-NtARF19 might have major deterministic, underappreciated roles to play in root development in a rolB-transgenic background-as observed by higher number of "root-related" biological processes present as nodes compared to network maps for similarly constructed other non-differentially expressed ARFs. Based on the inferences drawn, it is hypothesized that rolB, when present as a transgene, might drive hairy root development by selective induction of NtARF7 and NtARF19, suggesting a functional link between the two, leading to the specialized and characteristic rolB-associated traits.
PMID: 35774625
PeerJ , IF:2.984 , 2022 , V10 : Pe13798 doi: 10.7717/peerj.13798
Identification and characterization of auxin response factor (ARF) family members involved in fig (Ficus carica L.) fruit development.
College of Horticulture, China Agricultural University, Beijing, Beijing, China.; State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, Beijing, China.
The auxin response factor (ARF) combines with AuxREs cis-acting elements in response to auxin to regulate plant development. To date, no comprehensive analysis of ARF genes expressed during fruit development has been conducted for common fig (Ficus carica L.). In this study, members of the FcARF gene family were screened, identified in the fig genome database and their features characterized using bioinformatics. Twenty FcARF genes were clustered into three classes, with almost similar highly conserved DBD (B3-like DNA binding domain), AUX/IAA (auxin/indole-3-acetic acid gene family) and MR domain structure among class members. Analysis of amino acid species in MR domain revealed 10 potential transcription activators and 10 transcription inhibitors, and 17 FcARF members were predicted to be located in the nucleus. DNA sequence analysis showed that the ARF gene family consisted of 4-25 exons, and the promoter region contained 16 cis-acting elements involved in stress response, hormone response and flavonoid biosynthesis. ARF genes were expressed in most tissues of fig, especially flower and peel. Transcriptomics analysis results showed that FcARF2, FcARF11 and FcARF12, belonging to class-Ia, were stably and highly expressed in the early development stage of flower and peel of 'Purple peel' fig. However, their expression levels decreased after maturity. Expression of class-Ic member FcARF3 conformed to the regularity of fig fruit development. These four potential transcription inhibitors may regulate fruit growth and development of 'Purple Peel' fig. This study provides comprehensive information on the fig ARF gene family, including gene structure, chromosome position, phylogenetic relationship and expression pattern. Our work provides a foundation for further research on auxin-mediated fig fruit development.
PMID: 35898939
PeerJ , IF:2.984 , 2022 , V10 : Pe13710 doi: 10.7717/peerj.13710
ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17.
College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China.; School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China.
Background: The auxin indole-3-acetic acid (IAA) is a type of endogenous plant hormone with a low concentration in plants, but it plays an important role in their growth and development. The AUX/IAA gene family was found to be an early sensitive auxin gene with a complicated way of regulating growth and development in plants. The regulation of root growth and development by AUX/IAA family genes has been reported in Arabidopsis, rice and maize. Results: In this study, subcellular localization indicated that ZmIAA1-ZmIAA6 primarily played a role in the nucleus. A thermogram analysis showed that AUX/IAA genes were highly expressed in the roots, which was also confirmed by the maize tissue expression patterns. In maize overexpressing ZmIAA5, the length of the main root, the number of lateral roots, and the stalk height at the seedling stage were significantly increased compared with those of the wild type, while the EMS mutant zmiaa5 was significantly reduced. The total number of roots and the dry weight of maize overexpressing ZmIAA5 at the mature stage were also significantly increased compared with those of the wild type, while those of the mutant zmiaa5 was significantly reduced. Yeast one-hybrid experiments showed that ZmTCP15/16/17 could specifically bind to the ZmIAA5 promoter region. Bimolecular fluorescence complementation and yeast two-hybridization indicated an interaction between ZmIAA5 and ZmARF5. Conclusions: Taken together, the results of this study indicate that ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17.
PMID: 35855434
J Environ Qual , IF:2.751 , 2022 Jul doi: 10.1002/jeq2.20394
Using the pesticide toxicity index to show the potential ecosystem benefits of on-farm biobeds.
Department of Soil Science, University of Manitoba, Ellis Building, 13 Freedman Crescent, Winnipeg, MB, R3T2N2, Canada.; Deceased July 12, 2020, Previous address: Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J4B1, Canada.
The influent and effluent of two single-cell biobeds (Province of Alberta, Canada) and two dual cell-biobeds (Province of Saskatchewan, Canada) were monitored during a number of growing seasons. A total of fifty-nine unique pesticide active ingredients were detected, with all biobed influent samples (n = 54) and 93% of effluent samples (n = 54) containing pesticide mixtures. About one-half of the effluent samples in both single- (56%) and dual-cell (45%) biobeds contained active ingredients that have GUS values greater than 2.8 and so were more likely to move through the biomatrix materials into effluent. The Pesticide Toxicity Index (PTI) calculated for aquatic indicator species (i.e., vascular and non-vascular plants, invertebrates and fish) was always larger for influent samples (e.g., median PTI > 500 for invertebrates in dual-cell biobed) than effluent samples (i.e., median PTI < 1). As such, this study demonstrates the potential ecosystem benefits of the broad adoption of on-farm biobeds in the Canadian Prairies for recycling tank rinsate as part of strategies to accelerate a green economy. Although biobeds were highly effective in reducing the concentrations for pesticides with a wide range of Koc and half-lives values, the biobed effectiveness was relatively poor for herbicides clopyralid, diclofop, fluroxypyr and imazethapyr. Clopyralid (3.02), fluroxypyr (3.70) and imazethapyr (3.90) all have relatively high GUS values (> 2.8) and are thus more likely to be detected in effluent than active ingredients with smaller GUS values. This suggests that further improvements in biosystem design need to be made for optimizing the recycling of these pesticides. This article is protected by copyright. All rights reserved.
PMID: 35838005
Arch Microbiol , IF:2.552 , 2022 Jul , V204 (7) : P443 doi: 10.1007/s00203-022-03072-9
Transcriptomic analysis reveals the mechanism of host growth promotion by endophytic fungus of Rumex gmelinii Turcz.
College of Pharmacy, Heilongjiang University of Traditional Chinese Medicine, Harbin, China. 598808726@qq.com.; College of Pharmacy, Heilongjiang University of Traditional Chinese Medicine, Harbin, China.
Rumex gmelinii Turcz. (RGT) is a medicinal plant of the genus Rumex, family Polygonaceae. Our research group isolated an endophytic fungus, Plectosphaerella cucumerina (Strain J-G) from RGT, which could significantly promote host growth when co-cultured with host seedlings. In this study, we used transcriptome analysis and verification experiments to explore the molecular mechanisms underlying this growth-promoting effect. We found that, during co-culture with Strain J-G, the expression of genes encoding key enzymes in amino acid metabolism and carbohydrate synthesis and metabolism were up-regulated in RGT tissue culture seedlings, providing additional substrate and energy for plant growth. In addition, the expression of genes encoding the responser of RGT seedlings to hormones, including auxin and cytokinin, were significantly enhanced, promoting plant growth and development. Furthermore, RGT seedling defense systems were mobilized by Strain J-G; therefore, more secondary metabolites and substances involved in stress resistance were produced, ensuring normal plant growth and metabolism. The research showed Strain J-G significantly promote the accumulation of biomass and effective components of RGT, which provide basis for its application. This research also provides a reference method for the study of growth-promoting mechanism of endophytic fungi.
PMID: 35776209
Biointerphases , IF:2.456 , 2022 Jun , V17 (3) : P031006 doi: 10.1116/6.0001949
Mass spectral imaging showing the plant growth-promoting rhizobacteria's effect on the Brachypodium awn.
State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354.; Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354.; Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354.; Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830.
The plant growth-promoting rhizobacteria (PGPR) on the host plant surface play a key role in biological control and pathogenic response in plant functions and growth. However, it is difficult to elucidate the PGPR effect on plants. Such information is important in biomass production and conversion. Brachypodium distachyon (Brachypodium), a genomics model for bioenergy and native grasses, was selected as a C3 plant model; and the Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.) were chosen as representative PGPR strains. The PGPRs were introduced to the Brachypodium seed's awn prior to germination, and their possible effects on the seeding and growth were studied using different modes of time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements, including a high mass-resolution spectral collection and delayed image extraction. We observed key plant metabolic products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and auxin indole-3-acetic acid in the Brachypodium awns. Furthermore, principal component analysis and two-dimensional imaging analysis reveal that the Brachypodium awns are sensitive to the PGPR, leading to chemical composition and morphology changes on the awn surface. Our results show that ToF-SIMS can be an effective tool to probe cell-to-cell interactions at the biointerface. This work provides a new approach to studying the PGPR effects on awn and shows its potential for the research of plant growth in the future.
PMID: 35738921
J Microbiol Biotechnol , IF:2.351 , 2022 Jul , V32 (7) : P862-868 doi: 10.4014/jmb.2205.05016
Effect of Scenedesmus sp. CHK0059 on Strawberry Microbiota Community.
Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea.; Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea.; Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea.
Microalgae are photosynthetic cyanobacteria and eukaryotic microorganisms, mainly living in the water. In agriculture, numerous studies have been conducted to utilize microalgae as a biostimulant resource. Scenedesmus has been known to be one such microalga that can promote plant growth by secretion of auxin or cytokinin hormone analogs. However, no research has been performed on the effect of microalgae treatment on plant microbiota communities. This study was conducted to investigate the mode of action of microalgae as biostimulants in a plant microbiota perspective by using Scenedesmus sp. CHK0059 (also known as species Chlorella fusca), which has been well documented as a biostimulant for strawberries. The strawberry cultivar Keumsil was bred with Seolhyang and Maehyang as the parent cultivars. Using these three cultivars, microbiota communities were evaluated for changes in structural composition according to the CHK0059 treatment. CHK0059-treated Seolhyang, and CHK0059-untreated Maehyang were similar in microbial diversity in the endosphere. From a microbiota community perspective, the diversity change showed that CHK0059 was affected by the characteristics of the host. Conversely, when CHK0059 treatment was applied, populations of Streptomyces and Actinospica were observed in the crown endosphere.
PMID: 35880478
J Nat Med , IF:2.343 , 2022 Jun doi: 10.1007/s11418-022-01631-4
The ability of callus tissues induced from three Allium plants to accumulate health-beneficial natural products, S-alk(en)ylcysteine sulfoxides.
Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan. naokoy@faculty.chiba-u.jp.; Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan. naokoy@faculty.chiba-u.jp.; School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan.; Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan.; Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
S-Alk(en)ylcysteine sulfoxides (CSOs), such as methiin, alliin, and isoalliin, are health-beneficial natural products biosynthesized in the genus Allium. Here, we report the induction of multiple callus tissue lines from three Allium vegetables, onion (A. cepa), Welsh onion (A. fistulosum), and Chinese chive (A. tuberosum), and their ability to accumulate CSOs. Callus tissues were initiated and maintained in the presence of picloram and 2-isopentenyladenine as auxin and cytokinin, respectively. For all plant species tested, the callus tissues almost exclusively accumulated methiin as CSO, while the intact plants contained a substantial amount of isoalliin together with methiin. These results suggest that the cellular developmental conditions and the regulatory mechanisms required for the biosynthesis of methiin are different from those of alliin and isoalliin. The methiin content in the callus tissues of onion and Welsh onion was much higher compared to that in the intact plants, and its cellular concentration could be estimated as 1.9-21.7 mM. The activity of alliinase that degrades CSOs in the callus tissues was much lower than that of the intact plants for onion and Welsh onion, but at similar levels as in the intact plants for Chinese chive. Our findings that the callus tissues of onion and Welsh onion showed high methiin content and low alliinase activity highlighted their potential as a plant-based system for methiin production.
PMID: 35691991
Mol Biol Rep , IF:2.316 , 2022 Jul doi: 10.1007/s11033-022-07731-4
PheGRF4e initiated auxin signaling during moso bamboo shoot development.
Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China. gaojian@icbr.ac.cn.
BACKGROUND: As a ubiquitous acid-regulating protein family in eukaryotes, general regulatory factors (GRFs) are active in various life activities of plants. However, detailed investigations of the GRFs gene family in moso bamboo are scarce. METHODS AND RESULTS: Genome-wide characteristics of the GRF gene family in moso bamboo were analyzed using the moso bamboo genome. GRF phylogeny, gene structure, conserved domains, cis-element promoters, and gene expression were systematically analyzed. A total of 20 GRF gene family members were identified in the moso bamboo genome. These genes were divided into epsilon and non-epsilon groups. qRT-PCR (real-time quantitative reverse transcription polymerase chain reaction) showed that PheGRF genes responded to auxin and gibberellin treatment. To further study PheGRF gene functions, a yeast two-hybrid experiment was performed and verified by a bimolecular fluorescence complementation experiment. The results showed that PheGRF4e could interact with PheIAA30 (auxin/indole-3-acetic acid, an Aux/IAA family gene), and both were found to act mainly on the root tip meristem and vascular bundle cells of developing shoots by in situ hybridization assay. CONCLUSIONS: This study revealed that PheGRF genes were involved in hormone response during moso bamboo shoot development, and the possible regulatory functions of PheGRF genes were enriched by the fact that PheGRF4e initiated auxin signaling by binding to PheIAA30.
PMID: 35867290
Mol Biol Rep , IF:2.316 , 2022 Jul doi: 10.1007/s11033-022-07712-7
Determination of genotoxic damages of picloram and dicamba with comet assay in Allium cepa rooted in tissue culture and distilled water.
Faculty of Gazi Education, Department of Biology Education, Gazi University, Ankara, Turkey. cigdemozel@gazi.edu.tr.; Science Faculty, Department of Biology, Gazi University, Ankara, Turkey.; Vocational School of Technical Sciences, Amasya University, Amasya, Turkey.; Faculty of Gazi Education, Department of Biology Education, Gazi University, Ankara, Turkey.
BACKGROUND: Many genotoxicity tests allow us to understand the mechanism of damages on genetic material occurring in living organisms against various physical and chemical agents. One of them is the Comet test. The current study aimed to evaluate genotoxic caused by picloram and dicamba to root meristems of Allium cepa utilizing comet assay. METHODS: Two different protocols were used for rooting and auxin/pesticide application. (i) A. cepa bulbs were rooted in MS medium and then treated with Murashige and Skoog (MS) medium (control) and 0.67, 1.34, 2.01, 2.68, 3.35, 4.02, and 8.04 mg/L of picloram and dicamba using aseptic tissue culture techniques. (ii) A. cepa bulbs were then rooted in bidistilled water and treated with 0 (control), 0.67, 1.34, 2.01, 2.68, 3.35, 4.02, and 8.04 mg/L of picloram and dicamba in distilled water. The A. cepa root tip cells in both treatment groups were examined using comet test to find the possible DNA damaging effects of picloram and dicamba. RESULTS: The results obtained at all the concentrations were statistically compared with their control groups. Almost at all the concentrations of Picloram and dicamba increased comet tail intensity (%) and tail moment in roots treated in MS medium. Two highest concentrations revealed toxic effect. On the other hand, DNA damaging effect of both auxins was only noted on the highest (> 4.02 mg/L) in roots treated in distilled water. CONCLUSIONS: This study approve and confirm genotoxic effects of how growth regulators on plants. These findings give an evidence of DNA damage in A. cepa. Therefore, both picloram and dicamba should only be used in appropriate and recommended concentrations in agriculture to conserve ecosystem and to pose minimum threat to life.
PMID: 35804213
Antonie Van Leeuwenhoek , IF:2.271 , 2022 Jul , V115 (7) : P921-932 doi: 10.1007/s10482-022-01745-5
Potential role of rhizobia to enhance chickpea-growth and yield in low fertility-soils of Tunisia.
Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), BP.901, 2050, Hammam-Lif, Tunisia. samir_benromdhane@yahoo.com.; LSTM, UMR 113 IRD/CIRAD/SupAgro/Universite de Montpellier, Campus International de Baillarguet, Montpellier, France.; Department of Plant and Soil Sciences, University of Delaware, Newark, USA.; Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), BP.901, 2050, Hammam-Lif, Tunisia.
Plant growth-promoting rhizobacteria are bacteria that improve plant growth and reduce plant pathogen damages. In this study, 100 nodule bacteria were isolated from chickpea, screened for their plant growth-promoting (PGP) traits and then characterised by PCR-RFLP of 16 S rDNA. Results showed that most of the slow-growing isolates fixed nitrogen but those exhibiting fast-growth did not. Fourteen isolates solubilized inorganic phosphorus, 16 strains produced siderophores, and 17 strains produced indole acetic acid. Co-culture experiments identified three strains having an inhibitory effect against Fusarium oxysporum, the primary pathogenic fungus for chickpea in Tunisia. Rhizobia with PGP traits were assigned to Mesorhizobium ciceri, Mesorhizobium mediterraneum, Sinorhizobium meliloti and Agrobacterium tumefaciens. We noted that PGP activities were differentially distributed between M. ciceri and M. mediterraneum. The region of Mateur in northern Tunisia, with clay-silty soil, was the origin of 53% of PGP isolates. Interestingly, we found that S. meliloti and A. tumefaciens strains did not behave as parasitic nodule-bacteria but as PGP rhizobacteria useful for chickpea nutrition and health. In fact, S. meliloti strains could solubilize phosphorus, produce siderophore and auxin. The A. tumefaciens strains could perform the previous PGP traits and inhibit pathogen growth also. Finally, one candidate strain of M. ciceri (LL10)-selected for its highest symbiotic nitrogen fixation and phosphorus solubilization-was used for field experiment. The LL10 inoculation increased grain yield more than three-fold. These finding showed the potential role of rhizobia to be used as biofertilizers and biopesticides, representing low-cost and environment-friendly inputs for sustainable agriculture.
PMID: 35639296
Plant Signal Behav , IF:2.247 , 2022 Jun : P2095143 doi: 10.1080/15592324.2022.2095143
Chemically defined elicitors activate priming in tomato seedlings.
Department of Research and Development, Zero Gravity Solutions, Inc., Boca Raton, FL, USA.
Tomato (Solanum lycopersicum L.) is an important crop that possesses about 35,000 genes. The treatment of plants with elicitors or pathogen attacks causes a cascade of defense reactions. We investigated tomato responses to the BamFX(TM) solution containing Zn and Cu elicitors and report the results of comparative transcriptome analysis of tomato seeds treated with Zn and Cu elicitors. The seeds were treated with optimum concentrations of Bam-FX solutions and subjected to cold methanolic extraction methods to obtain the secondary metabolites produced within them at different time intervals post-Bam-FX treatment. The metabolite mixture was analyzed using gas chromatography-mass spectrometry (GCMS). In transcriptome sequencing, GO and KEGG analyses revealed that the majority of the DEGs in BamFx-treated tomato was associated with primary and secondary metabolism, plant hormone signal transduction, TF regulation, transport, and responses to stimuli.The secondary metabolites found in the BamFX treated tomato seedlings - Esters of Fumaric acid, Succinic acid etc. The transcript levels of most auxin transporter-encoding genes changed significantly in the BamFX-treated seedlings (e.g., Solyc01g007010.3, a RING-type E3 ubiquitin transferase). The gene Solyc07g061720.3 for Gibberellin 2-oxidase and the Phorbol-ester/DAG-type domain-containing protein (Solyc02g068680.1) associated with the intracellular signaling genes were found upregulated in the BamFx-treated seeds. The time-dependent effect of the BamFX (1:500 for 60 min) was found to be regulating Abscisic acid signaling pathway genes (Solyc09g015380.1). This study identified many candidate genes for future functional analyses and laid a theoretical foundation for an improved understanding of the molecular mechanisms involved in the BamFx treatment of tomatoes to improve stress resistance.
PMID: 35770510
Biosci Biotechnol Biochem , IF:2.043 , 2022 Jun , V86 (7) : P824-831 doi: 10.1093/bbb/zbac070
Facilitation of auxin biosynthesis and metabolism by salt stress in rice plants.
Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
To investigate the effects of salt stress on the auxin in rice plants, we analyzed indole-3-acetic acid (IAA) and its metabolites in hydroponically grown rice plant seedlings (Oryza sativa cv. Nipponbare) and in the culture medium using LC-ESI/MS/MS. We found that the IAA level in the culture medium was increased 39-fold due to salt stress treatment, while those in the shoots and roots were increased by less than 2-fold. The culture medium also contained high amounts of oxidized metabolites such as OxIAA, DiOxIAA, DiOxIAA-Glu, and DiOxIAA-Asp. The total amount of IAA and its metabolites in the shoots, roots, and culture medium was significantly increased with salt treatment. A salt stress-responsive increase in the IAA metabolites was observed in 9 tested cultivars of rice. The results indicate that salt stress facilitates the metabolic turnover of IAA in rice plants and may open new insight into the role of auxin.
PMID: 35580591
Evol Bioinform Online , IF:1.625 , 2022 , V18 : P11769343221106795 doi: 10.1177/11769343221106795
In Silico Identification and Characterization of B12D Family Proteins in Viridiplantae.
Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-kharj, Saudi Arabia.
B12D family proteins are transmembrane proteins that contain the B12D domain involved in membrane trafficking. Plants comprise several members of the B12D family, but these members' numbers and specific functions are not determined. This study aims to identify and characterize the members of B12D protein family in plants. Phytozome database was retrieved for B12D proteins from 14 species. The total 66 B12D proteins were analyzed in silico for gene structure, motifs, gene expression, duplication events, and phylogenetics. In general, B12D proteins are between 86 and 98 aa in length, have 2 or 3 exons, and comprise a single transmembrane helix. Motif prediction and multiple sequence alignment show strong conservation among B12D proteins of 11 flowering plants species. Despite that, the phylogenetic tree revealed a distinct cluster of 16 B12D proteins that have high conservation across flowering plants. Motif prediction revealed 41 aa motif conserved in 58 of the analyzed B12D proteins similar to the bZIP motif, confirming that in the predicted biological process and molecular function, B12D proteins are DNA-binding proteins. Cis-regulatory elements screening in putative B12D promoters found various responsive elements for light, abscisic acid, methyl jasmonate, cytokinin, drought, and heat. Despite that, there is specific elements for cold stress, cell cycle, circadian, auxin, salicylic acid, and gibberellic acid in the promoter of a few B12D genes indicating for functional diversification for B12D family members. The digital expression shows that B12D genes of Glycine max have similar expression patterns consistent with their clustering in the phylogenetic tree. However, the expression of B12D genes of Hordeum vulgure appears inconsistent with their clustering in the tree. Despite the strong conservation of the B12D proteins of Viridiplantae, gene association analysis, promoter analysis, and digital expression indicate different roles for the members of the B12D family during plant developmental stages.
PMID: 35721582
Zhongguo Zhong Yao Za Zhi , 2022 Jul , V47 (14) : P3749-3755 doi: 10.19540/j.cnki.cjcmm.20220416.102
[Winter pruning boosts growth and yield of Lonicera japonica by regulating plant hormone content].
Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences) Ji'nan 250014, China School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences) Ji'nan 250014, China.; State Key Laboratory Breeding Base of Dao-di Herbs, National Rresource Center for Chinese Materia Medica,China Academy of Chinese Medical Sciences Beijing 100700, China.
Lonicera japonica is a ubiquitous medicinal species in China.Winter pruning has long been used to improve its quality and yield, but the mechanism is rarely studied.Therefore, in this study, the growth phenotypes of L.japonica processed with different pruning methods were observed and the yield-and quality-boosting mechanism of pruning was analyzed.Specifically, the young shoots of the three-year old L.japonica were cut to different degrees(heavy pruning, mild pruning, and no pruning, respectively) in winter in 2020 and 2021, respectively, and the growth phenotypes, hormone content, and gene expression of the lateral buds at the sprouting stage and young shoots at the anthesis stage in the next year were analyzed.The result showed that the length, flower bud number, internode length, and node number of young shoots in the next year were in the order of heavy pruning>mild pruning>no pruning.The content of auxin and zeatin in apical buds of young shoots at the anthesis stage was the highest in the heavy pruning group, followed by the mild pruning group, and coming in the third was the no pruning group.The content of auxin and zeatin in lateral buds at the sprouting stage was in the order of no pruning>mild pruning>heavy pruning.Transcriptome analysis of the lateral buds at sprouting stage yielded the differentially expressed genes related to auxin and cytokinin, such as Lj1A1163T36, Lj3A719T115, Lj7C657T7, Lj9C505T15, and Lj9A505T70.In conclusion, the growth phenotypes of young shoots of L.japonica processed with different pruning methods in winter were related to the difference in hormone content in the apical buds.Therefore, winter pruning influenced the content of auxin and cytokinin in new shoots of L.japonica and further regulated the expression of hormone-related genes, thereby promoting shoot growth and increasing the yield of L.japonica.
PMID: 35850831
Plant Commun , 2022 Jun : P100351 doi: 10.1016/j.xplc.2022.100351
Natural variation in the transcription factor REPLUMLESS contributes to both disease resistance and plant growth in Arabidopsis.
School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: deng@pku.edu.cn.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: heguangming@pku.edu.cn.
When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, frequently incurring growth penalties. This phenomenon is known as the growth-defense tradeoff and is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes require further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly upregulated in rpl mutants, leading to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. RPL also repressed flavonol synthesis by directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.
PMID: 35752937