Nat Commun , IF:12.121 , 2020 Jan , V11 (1) : P364 doi: 10.1038/s41467-019-14226-7
Auxin-dependent control of a plasmodesmal regulator creates a negative feedback loop modulating lateral root emergence.
Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19711, USA.; Institut fur Physiologie und Biotechnologie der Pflanzen, Universitat Hohenheim, Emil-Wolff-Strasse 23, 70593, Stuttgart, Germany.; Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK.; Zentrum fur Molekularbiologie der Pflanzen, Universitat Tubingen, Auf der Morgenstelle 32, 72076, Tubingen, Germany.; Gene Editing Institute, Christina Health Care System, Newark, DE, 19711, USA.; Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.; Department of Biological Sciences, University of Delaware, Newark, DE, 19711, USA.; Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19711, USA. lee@dbi.udel.edu.; Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA. lee@dbi.udel.edu.; Department of Biological Sciences, University of Delaware, Newark, DE, 19711, USA. lee@dbi.udel.edu.
Lateral roots originate from initial cells deep within the main root and must emerge through several overlying layers. Lateral root emergence requires the outgrowth of the new primordium (LRP) to coincide with the timely separation of overlying root cells, a developmental program coordinated by the hormone auxin. Here, we report that in Arabidopsis thaliana roots, auxin controls the spatiotemporal expression of the plasmodesmal regulator PDLP5 in cells overlying LRP, creating a negative feedback loop. PDLP5, which functions to restrict the cell-to-cell movement of signals via plasmodesmata, is induced by auxin in cells overlying LRP in a progressive manner. PDLP5 localizes to plasmodesmata in these cells and negatively impacts organ emergence as well as overall root branching. We present a model, incorporating the spatiotemporal expression of PDLP5 in LRP-overlying cells into known auxin-regulated LRP-overlying cell separation pathways, and speculate how PDLP5 may function to negatively regulate the lateral root emergence process.
PMID: 31953391
Nat Commun , IF:12.121 , 2020 Jan , V11 (1) : P218 doi: 10.1038/s41467-019-13927-3
Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed.
Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK. Zaigham.Shahzad@glasgow.ac.uk.; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK.; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK. Anna.Amtmann@glasgow.ac.uk.
Maintaining the right balance between plasticity and robustness in biological systems is important to allow adaptation while maintaining essential functions. Developmental plasticity of plant root systems has been the subject of intensive research, but the mechanisms underpinning robustness remain unclear. Here, we show that potassium deficiency inhibits lateral root organogenesis by delaying early stages in the formation of lateral root primordia. However, the severity of the symptoms arising from this perturbation varies within a natural population of Arabidopsis and is associated with the genetic variation in CLSY1, a key component of the RNA-directed DNA-methylation machinery. Mechanistically, CLSY1 mediates the transcriptional repression of a negative regulator of root branching, IAA27, and promotes lateral root development when the auxin-dependent proteolysis pathway fails. Our study identifies DNA-methylation-mediated transcriptional repression as a backup system for post-translational protein degradation which ensures robust development and performance of plants in a challenging environment.
PMID: 31924796
Nat Commun , IF:12.121 , 2020 Jan , V11 (1) : P76 doi: 10.1038/s41467-019-13729-7
Polar recruitment of RLD by LAZY1-like protein during gravity signaling in root branch angle control.
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.; FAFU-UCR Joint Center, Fujian Provincial Key Laboratory of Haixia Applied Plant System Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.; Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.; Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0101, Japan.; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.; Division of Plant Environmental Responses, National Institute for Basic Biology, Myodaiji, Okazaki, 444-8556, Japan.; Laboratory of Biological Diversity, National Institute for Basic Biology, Myodaiji, Okazaki, 444-8556, Japan.; Bioimage Informatics Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Myodaiji, Okazaki, 444-8585, Japan.; Department of Bioinformatics, Ritsumeikan University, Kusatsu, 525-8577, Japan.; Division of Plant Environmental Responses, National Institute for Basic Biology, Myodaiji, Okazaki, 444-8556, Japan. mimorita@nibb.ac.jp.
In many plant species, roots maintain specific growth angles relative to the direction of gravity, known as gravitropic set point angles (GSAs). These contribute to the efficient acquisition of water and nutrients. AtLAZY1/LAZY1-LIKE (LZY) genes are involved in GSA control by regulating auxin flow toward the direction of gravity in Arabidopsis. Here, we demonstrate that RCC1-like domain (RLD) proteins, identified as LZY interactors, are essential regulators of polar auxin transport. We show that interaction of the CCL domain of LZY with the BRX domain of RLD is important for the recruitment of RLD from the cytoplasm to the plasma membrane by LZY. A structural analysis reveals the mode of the interaction as an intermolecular beta-sheet in addition to the structure of the BRX domain. Our results offer a molecular framework in which gravity signal first emerges as polarized LZY3 localization in gravity-sensing cells, followed by polar RLD1 localization and PIN3 relocalization to modulate auxin flow.
PMID: 31900388
Dev Cell , IF:10.092 , 2020 Jan , V52 (2) : P223-235.e5 doi: 10.1016/j.devcel.2019.11.015
Plasma Membrane Domain Patterning and Self-Reinforcing Polarity in Arabidopsis.
Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.; Institute of Experimental Botany, Czech Acad Sci, Rozvojova 263, 165 02 Praha 6, Czech Republic.; Plant Systems Biology, Technical University of Munich, 85354 Freising, Germany.; Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland. Electronic address: christian.hardtke@unil.ch.
Cell polarity is a key feature in the development of multicellular organisms. For instance, asymmetrically localized plasma-membrane-integral PIN-FORMED (PIN) proteins direct transcellular fluxes of the phytohormone auxin that govern plant development. Fine-tuned auxin flux is important for root protophloem sieve element differentiation and requires the interacting plasma-membrane-associated BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX) proteins. We observed "donut-like" polar PIN localization in developing sieve elements that depends on complementary, "muffin-like" polar localization of BRX and PAX. Plasma membrane association and polarity of PAX, and indirectly BRX, largely depends on phosphatidylinositol-4,5-bisphosphate. Consistently, mutants in phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) display protophloem differentiation defects similar to brx mutants. The same PIP5Ks are in complex with BRX and display "muffin-like" polar localization. Our data suggest that the BRX-PAX module recruits PIP5Ks to reinforce PAX polarity and thereby the polarity of all three proteins, which is required to maintain a local PIN minimum.
PMID: 31866202
EMBO J , IF:9.889 , 2020 Jan , V39 (2) : Pe101928 doi: 10.15252/embj.2019101928
UV-B photoreceptor UVR8 interacts with MYB73/MYB77 to regulate auxin responses and lateral root development.
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, Shanghai, China.; University of Chinese Academy of Sciences, Shanghai, China.; The Joint Center for Infection and Immunity between Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, China.
The UV-B photoreceptor UVR8 mediates multiple UV-B responses in plants, but the function of UVR8 in regulating root development has not previously been investigated. Here, we show that UV-B light inhibits Arabidopsis lateral root growth in a UVR8-dependent manner. Monomeric UVR8 inhibits auxin responses in a tissue-autonomous manner and thereby regulates lateral root growth. Genome-wide gene expression analysis demonstrated that auxin and UV-B irradiation antagonistically regulate auxin-regulated gene expression. We further show that UVR8 physically interacts with MYB73/MYB77 (MYB DOMAIN PROTEIN 73/77) in a UV-B-dependent manner. UVR8 inhibits lateral root development via regulation of MYB73/MYB77. When activated by UV-B light, UVR8 localizes to the nucleus and inhibits the DNA-binding activities of MYB73/MYB77 and directly represses the transcription of their target auxin-responsive genes. Our results demonstrate that UV-B light and UVR8 are critical for both shoot morphogenesis and root development. The UV-B-dependent interaction of UVR8 and MYB73/MYB77 serves as an important module that integrates light and auxin signaling and represents a new UVR8 signaling mechanism in plants.
PMID: 31777974
EMBO J , IF:9.889 , 2020 Jan , V39 (1) : Pe101515 doi: 10.15252/embj.2019101515
Non-canonical AUX/IAA protein IAA33 competes with canonical AUX/IAA repressor IAA5 to negatively regulate auxin signaling.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China.; College of Life Sciences, Liaocheng University, Liaocheng, Shandong, China.; Department of Biochemistry, University of Missouri, Columbia, MO, USA.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; VIB Center for Plant Systems Biology, Ghent, Belgium.; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China.
The phytohormone auxin controls plant growth and development via TIR1-dependent protein degradation of canonical AUX/IAA proteins, which normally repress the activity of auxin response transcription factors (ARFs). IAA33 is a non-canonical AUX/IAA protein lacking a TIR1-binding domain, and its role in auxin signaling and plant development is not well understood. Here, we show that IAA33 maintains root distal stem cell identity and negatively regulates auxin signaling by interacting with ARF10 and ARF16. IAA33 competes with the canonical AUX/IAA repressor IAA5 for binding to ARF10/16 to protect them from IAA5-mediated inhibition. In contrast to auxin-dependent degradation of canonical AUX/IAA proteins, auxin stabilizes IAA33 protein via MITOGEN-ACTIVATED PROTEIN KINASE 14 (MPK14) and does not affect IAA33 gene expression. Taken together, this study provides insight into the molecular functions of non-canonical AUX/IAA proteins in auxin signaling transduction.
PMID: 31617603
Autophagy , IF:9.77 , 2020 Jan , V16 (1) : P123-139 doi: 10.1080/15548627.2019.1598753
Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis.
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China.
Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. In Arabidopsis thaliana, the core machinery of autophagy is well defined, but its transcriptional regulation is largely unknown. The ATG8 (autophagy-related 8) protein plays central roles in decorating autophagosomes and binding to specific cargo receptors to recruit cargo to autophagosomes. We propose that the transcriptional control of ATG8 genes is important during the formation of autophagosomes and therefore contributes to survival during stress. Here, we describe a yeast one-hybrid (Y1H) screen for transcription factors (TFs) that regulate ATG8 gene expression in Arabidopsis, using the promoters of 4 ATG8 genes. We identified a total of 225 TFs from 35 families that bind these promoters. The TF-ATG8 promoter interactions revealed a wide array of diverse TF families for different promoters, as well as enrichment for families of TFs that bound to specific fragments. These TFs are not only involved in plant developmental processes but also in the response to environmental stresses. TGA9 (TGACG (TGA) motif-binding protein 9)/AT1G08320 was confirmed as a positive regulator of autophagy. TGA9 overexpression activated autophagy under both control and stress conditions and transcriptionally up-regulated expression of ATG8B, ATG8E and additional ATG genes via binding to their promoters. Our results provide a comprehensive resource of TFs that regulate ATG8 gene expression and lay a foundation for understanding the transcriptional regulation of plant autophagy.Abbreviations: ABRC: Arabidopsis biological resource center; AP2-EREBP: APETALA2/Ethylene-responsive element binding protein; ARF: auxin response factor; ATF4: activating transcription factor 4; ATG: autophagy-related; ChIP: chromatin immunoprecipitation; DAP-seq: DNA affinity purification sequencing; FOXO: forkhead box O; GFP: green fluorescent protein; GO: gene ontologies; HB: homeobox; LD: long-day; LUC: firefly luciferase; MAP1LC3: microtubule associated protein 1 light chain 3; MDC: monodansylcadaverine; 3-MA: 3-methyladenine; OE: overexpressing; PCD: programmed cell death; qPCR: quantitative polymerase chain reaction; REN: renilla luciferase; RT: room temperature; SD: standard deviation; TF: transcription factor; TFEB: transcription factor EB; TGA: TGACG motif; TOR: target of rapamycin; TSS: transcription start site; WT: wild-type; Y1H: yeast one-hybrid.
PMID: 30909785
Plant Cell , IF:9.618 , 2020 Jan , V32 (1) : P100-122 doi: 10.1105/tpc.19.00431
An Improved Recombineering Toolset for Plants.
Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695.; Department of Biology, Stanford University, Stanford, California 94305.; Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708.; Instituto de Biologia Molecular y Celular de Plantas (IBMCP), Universidad Politecnica de Valencia (UPV)-Consejo Superior de Investigaciones Cientificas (CSIC), 46022 Valencia, Spain.; Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695 jmalonso@ncsu.edu.
Gene functional studies often rely on the expression of a gene of interest as transcriptional and translational fusions with specialized tags. Ideally, this is done in the native chromosomal contexts to avoid potential misexpression artifacts. Although recent improvements in genome editing have made it possible to directly modify the target genes in their native chromosomal locations, classical transgenesis is still the preferred experimental approach chosen in most gene tagging studies because of its time efficiency and accessibility. We have developed a recombineering-based tagging system that brings together the convenience of the classical transgenic approaches and the high degree of confidence in the results obtained by direct chromosomal tagging using genome-editing strategies. These simple, scalable, customizable recombineering toolsets and protocols allow a variety of genetic modifications to be generated. In addition, we developed a highly efficient recombinase-mediated cassette exchange system to facilitate the transfer of the desired sequences from a bacterial artificial chromosome clone to a transformation-compatible binary vector, expanding the use of the recombineering approaches beyond Arabidopsis (Arabidopsis thaliana). We demonstrated the utility of this system by generating more than 250 whole-gene translational fusions and 123 Arabidopsis transgenic lines corresponding to 62 auxin-related genes and characterizing the translational reporter expression patterns for 14 auxin biosynthesis genes.
PMID: 31666295
Plant Cell , IF:9.618 , 2020 Jan , V32 (1) : P226-241 doi: 10.1105/tpc.19.00378
AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration.
National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, 200032 Shanghai, P. R. China.; University of Chinese Academy of Sciences, 200032 Shanghai, P. R. China.; School of Life Sciences, Nantong University, Nantong, 226019 Jiangsu, P. R. China.; Chinese Academy of Sciences Key Laboratory of Insect Developmental and Evolutionary Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, 200032 Shanghai, P. R. China.; School of Public Health, Nantong University, Nantong, 226019 Jiangsu, P. R. China.; Fujian Agriculture and Forestry University-University of California Riverside Joint Center, Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, 350002 Fuzhou, P. R. China.; National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, 200032 Shanghai, P. R. China jwwang@sippe.ac.cn.; ShanghaiTech University, Shanghai 200031, P. R. China.
Age and wounding are two major determinants for regeneration. In plants, the root regeneration is triggered by wound-induced auxin biosynthesis. As plants age, the root regenerative capacity gradually decreases. How wounding leads to the auxin burst and how age and wound signals collaboratively regulate root regenerative capacity are poorly understood. Here, we show that the increased levels of three closely-related miR156-targeted Arabidopsis (Arabidopsis thaliana) SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, SPL2, SPL10, and SPL11, suppress root regeneration with age by inhibiting wound-induced auxin biosynthesis. Mechanistically, we find that a subset of APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factors including ABSCISIC ACID REPRESSOR1 and ERF109 is rapidly induced by wounding and serves as a proxy for wound signal to induce auxin biosynthesis. In older plants, SPL2/10/11 directly bind to the promoters of AP2/ERFs and attenuates their induction, thereby dampening auxin accumulation at the wound. Our results thus identify AP2/ERFs as a hub for integration of age and wound signal for root regeneration.
PMID: 31649122
New Phytol , IF:8.512 , 2020 Jan , V225 (2) : P848-865 doi: 10.1111/nph.16194
Photoexcited CRY1 and phyB interact directly with ARF6 and ARF8 to regulate their DNA-binding activity and auxin-induced hypocotyl elongation in Arabidopsis.
Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.; School of Life Sciences, Fudan University, Shanghai, 200438, China.; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Arabidopsis CRY1 and phyB are the primary blue and red light photoreceptors mediating blue and red light inhibition of hypocotyl elongation, respectively. Auxin is a pivotal phytohormone involved in promoting hypocotyl elongation. CRY1 and phyB interact with and stabilize auxin/indole acetic acid proteins (Aux/IAAs) to inhibit auxin signaling. The present study investigated whether photoreceptors might interact directly with Auxin Response Factors (ARFs) to regulate auxin signaling. Protein-protein interaction studies demonstrated that CRY1 and phyB interact physically with ARF6 and ARF8 through their N-terminal domains in a blue and red light-dependent manner, respectively. Moreover, the N-terminal DNA-binding domain of ARF6 and ARF8 is involved in mediating their interactions with CRY1. Genetic studies showed that ARF6 and ARF8 act partially downstream from CRY1 and PHYB to regulate hypocotyl elongation under blue and red light, respectively. Chromatin immunoprecipitation-PCR assays demonstrated that CRY1 and phyB mediate blue and red light repression of the DNA-binding activity of ARF6 and ARF6-target gene expression, respectively. Altogether, the results herein suggest that the direct repression of auxin-responsive gene expression mediated by the interactions of CRY1 and phyB with ARFs constitutes a new layer of the regulatory mechanisms by which light inhibits auxin-induced hypocotyl elongation.
PMID: 31514232
New Phytol , IF:8.512 , 2020 Jan , V225 (1) : P284-296 doi: 10.1111/nph.16150
A role for auxin signaling in the acquisition of longevity during seed maturation.
UMR 1345 Institut de Recherche en Horticulture et Semences, Agrocampus Ouest, INRA, Universite d'Angers, SFR 4207 QUASAV, Beaucouze, 49070, France.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Seed longevity, the maintenance of viability during dry storage, is a crucial factor to preserve plant genetic resources and seed vigor. Inference of a temporal gene-regulatory network of seed maturation identified auxin signaling as a putative mechanism to induce longevity-related genes. Using auxin-response sensors and tryptophan-dependent auxin biosynthesis mutants of Arabidopsis thaliana L., the role of auxin signaling in longevity was studied during seed maturation. DII and DR5 sensors demonstrated that, concomitant with the acquisition of longevity, auxin signaling input and output increased and underwent a spatiotemporal redistribution, spreading throughout the embryo. Longevity of seeds of single auxin biosynthesis mutants with altered auxin signaling activity was affected in a dose-response manner depending on the level of auxin activity. Longevity-associated genes with promoters enriched in auxin response elements and the master regulator ABSCISIC ACID INSENSITIVE3 were induced by auxin in developing embryos and deregulated in auxin biosynthesis mutants. The beneficial effect of exogenous auxin during seed maturation on seed longevity was abolished in abi3-1 mutants. These data suggest a role for auxin signaling activity in the acquisition of longevity during seed maturation.
PMID: 31461534
New Phytol , IF:8.512 , 2020 Jan , V225 (1) : P297-309 doi: 10.1111/nph.16115
Auxin abolishes SHI-RELATED SEQUENCE5-mediated inhibition of lateral root development in Arabidopsis.
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.; Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China.
Lateral roots (LRs), which form in the plant postembryonically, determine the architecture of the root system. While negative regulatory factors that inhibit LR formation and are counteracted by auxin exist in the pericycle, these factors have not been characterised. Here, we report that SHI-RELATED SEQUENCE5 (SRS5) is an intrinsic negative regulator of LR formation and that auxin signalling abolishes this inhibitory effect of SRS5. Whereas LR primordia (LRPs) and LRs were fewer and less dense in SRS5ox and Pro35S:SRS5-GFP plants than in the wild-type, they were more abundant and denser in the srs5-2 loss-of-function mutant. SRS5 inhibited LR formation by directly downregulating the expression of LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) and LBD29. Auxin repressed SRS5 expression. Auxin-mediated repression of SRS5 expression was not observed in the arf7-1 arf19-1 double mutant, likely because ARF7 and ARF19 bind to the promoter of SRS5 and inhibit its expression in response to auxin. Taken together, our data reveal that SRS5 negatively regulates LR formation by repressing the expression of LBD16 and LBD29 and that auxin releases this inhibitory effect through ARF7 and ARF19.
PMID: 31403703
New Phytol , IF:8.512 , 2020 Jan , V225 (1) : P53-69 doi: 10.1111/nph.16034
Handedness in plant cell expansion: a mutant perspective on helical growth.
Botanical Institute, Biology and Chemistry Department, University of Osnabruck, 49076, Osnabruck, Germany.
Many plant mutants are known that exhibit some degree of helical growth. This 'twisted' phenotype has arisen frequently in mutant screens of model organisms, but it is also found in cultivars of ornamental plants, including trees. The phenomenon, in many cases, is based on defects in cell expansion symmetry. Any complete model which explains the anisotropy of plant cell growth must ultimately explain how helical cell expansion comes into existence - and how it is normally avoided. While the mutations observed in model plants mainly point to the microtubule system, additional affected components involve cell wall functions, auxin transport and more. Evaluation of published data suggests a two-way mechanism underlying the helical growth phenomenon: there is, apparently, a microtubular component that determines handedness, but there is also an influence arising in the cell wall that feeds back into the cytoplasm and affects cellular handedness. This idea is supported by recent reports demonstrating the involvement of the cell wall integrity pathway. In addition, there is mounting evidence that calcium is an important relayer of signals relating to the symmetry of cell expansion. These concepts suggest experimental approaches to untangle the phenomenon of helical cell expansion in plant mutants.
PMID: 31254400
Plant Biotechnol J , IF:8.154 , 2020 Jan , V18 (1) : P155-171 doi: 10.1111/pbi.13183
Multiple GmWRI1s are redundantly involved in seed filling and nodulation by regulating plastidic glycolysis, lipid biosynthesis and hormone signalling in soybean (Glycine max).
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.; State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China.; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.; Department of Biology, University of Missouri, St. Louis, MO, USA.; Donald Danforth Plant Science Center, St. Louis, MO, USA.
It has been reported that lipid biosynthesis in plant host root cells plays critical roles in legume-fungal or -rhizobial symbioses, but little is known about its regulatory mechanism in legume-rhizobia interaction. Soybean WRINKLED1 (WRI1) a and b, with their alternative splicing (AS) products a' and b', are highly expressed in developing seeds and nodules, but their functions in soybean nodulation are not known. GmWRI1a and b differently promoted triacylglycerol (TAG) accumulation in both Arabidopsis wild-type and wri1 mutant seeds and when they ectopically expressed in the soybean hairy roots. Transcriptome analysis revealed that 15 genes containing AW boxes in their promoters were targeted by GmWRI1s, including genes involved in glycolysis, fatty acid (FA) and TAG biosynthesis. GmWRI1a, GmWRI1b and b' differentially transactivated most targeted genes. Overexpression of GmWRI1s affected phospholipid and galactolipid synthesis, soluble sugar and starch contents and led to increased nodule numbers, whereas GmWRI1 knockdown hairy roots interfered root glycolysis and lipid biosynthesis and resulted in fewer nodules. These phenomena in GmWRI1 mutants coincided with the altered expression of nodulation genes. Thus, GmWRI1-regulated starch degradation, glycolysis and lipid biosynthesis were critical for nodulation. GmWRI1 mutants also altered auxin and other hormone-related biosynthesis and hormone-related genes, by which GmWRI1s may affect nodule development. The study expands the views for pleiotropic effects of WRI1s in regulating soybean seed filling and root nodulation.
PMID: 31161718
Plant Physiol , IF:6.902 , 2020 Jan , V182 (1) : P361-377 doi: 10.1104/pp.19.00818
SnRK2 Protein Kinases and mRNA Decapping Machinery Control Root Development and Response to Salt.
Plant Cell Biology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands.; Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands.; Mass Spectrometry of Biomacromolecules, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands.; Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands.; Department of Biomolecular Medicine, Ghent University, 9000 Gent, Belgium.; VIB Center for Medical Biotechnology, 9000 Gent, Belgium.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Gent, Belgium.; VIB Center for Plant Systems Biology, 9052 Gent, Belgium.; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland.; Plant Cell Biology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands christa.testerink@wur.nl.
SNF1-RELATED PROTEIN KINASES 2 (SnRK2) are important components of early osmotic and salt stress signaling pathways in plants. The Arabidopsis (Arabidopsis thaliana) SnRK2 family comprises the abscisic acid (ABA)-activated protein kinases SnRK2.2, SnRK2.3, SnRK2.6, SnRK2.7, and SnRK2.8, and the ABA-independent subclass 1 protein kinases SnRK2.1, SnRK2.4, SnRK2.5, SnRK2.9, and SnRK2.10. ABA-independent SnRK2s act at the posttranscriptional level via phosphorylation of VARICOSE (VCS), a member of the mRNA decapping complex, that catalyzes the first step of 5'mRNA decay. Here, we identified VCS and VARICOSE RELATED (VCR) as interactors and phosphorylation targets of SnRK2.5, SnRK2.6, and SnRK2.10. All three protein kinases phosphorylated Ser-645 and Ser-1156 of VCS, whereas SnRK2.6 and SnRK2.10 also phosphorylated VCS Ser-692 and Ser-680 of VCR. We showed that subclass 1 SnRK2s, VCS, and 5' EXORIBONUCLEASE 4 (XRN4) are involved in regulating root growth under control conditions as well as modulating root system architecture in response to salt stress. Our results suggest interesting patterns of redundancy within subclass 1 SnRK2 protein kinases, with SnRK2.1, SnRK2.5, and SnRK2.9 controlling root growth under nonstress conditions and SnRK2.4 and SnRK2.10 acting mostly in response to salinity. We propose that subclass 1 SnRK2s function in root development under salt stress by affecting the transcript levels of aquaporins, as well as CYP79B2, an enzyme involved in auxin biosynthesis.
PMID: 31570508
Plant Physiol , IF:6.902 , 2020 Jan , V182 (1) : P185-203 doi: 10.1104/pp.19.00416
PcG Proteins MSI1 and BMI1 Function Upstream of miR156 to Regulate Aerial Tuber Formation in Potato.
Biology Division, Indian Institute of Science Education and Research, Pune 411008, Maharashtra, India.; Biology Division, Indian Institute of Science Education and Research, Pune 411008, Maharashtra, India akb@iiserpune.ac.in.
Polycomb Repressive Complexes (PRC1 and PRC2) regulate developmental transitions in plants. AtBMI1, a PRC1 member, represses micro RNA156 (miR156) to trigger the onset of adult phase in Arabidopsis (Arabidopsis thaliana). miR156 overexpression (OE) reduces below-ground tuber yield, but stimulates aerial tubers in potato (Solanum tuberosum ssp andigena) under short-day (SD) photoperiodic conditions. Whether PRC members could govern tuber development through photoperiod-mediated regulation of miR156 is unknown. Here, we investigated the role of two PRC proteins, StMSI1 (PRC2 member) and StBMI1-1, in potato development. In wild-type andigena plants, StMSI1 and miR156 levels increased in stolon, whereas StBMI1-1 decreased under SD conditions. StMSI1-OE and StBMI1-1-antisense (AS) lines produced pleiotropic effects, including altered leaf architecture/compounding and reduced below-ground tuber yield. Notably, these lines showed enhanced miR156 accumulation accompanied by aerial stolons and tubers from axillary nodes, similar to miR156-OE lines. Further, grafting of StMSI1-OE or StBMI1-1-AS on wild-type stock resulted in reduced root biomass and showed increased accumulation of miR156a/b and -c precursors in the roots of wild-type stocks. RNA-sequencing of axillary nodes from StMSI1-OE and StBMI1-1-AS lines revealed downregulation of auxin and brassinosteroid genes, and upregulation of cytokinin transport/signaling genes, from 1,023 differentially expressed genes shared between the two lines. Moreover, we observed downregulation of genes encoding H2A-ubiquitin ligase and StBMI1-1/3, and upregulation of Trithorax group H3K4-methyl-transferases in StMSI1-OE Chromatin immunoprecipitation-quantitative PCR confirmed H3K27me3-mediated suppression of StBMI1-1/3, and H3K4me3-mediated activation of miR156 in StMSI1-OE plants. In summary, we show that cross talk between histone modifiers regulates miR156 and alters hormonal response during aerial tuber formation in potato under SD conditions.
PMID: 31427464
Plant Cell Environ , IF:6.362 , 2020 Jan , V43 (1) : P143-158 doi: 10.1111/pce.13646
Halotropism requires phospholipase Dzeta1-mediated modulation of cellular polarity of auxin transport carriers.
Plant Physiology and Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098, XH, Amsterdam, The Netherlands.; Theoretical Biology, Department of Biology, Utrecht University, 3584, CH, Utrecht, The Netherlands.; Laboratory of Plant Physiology, Wageningen University & Research, 6700, AA, Wageningen, The Netherlands.
Endocytosis and relocalization of auxin carriers represent important mechanisms for adaptive plant growth and developmental responses. Both root gravitropism and halotropism have been shown to be dependent on relocalization of auxin transporters. Following their homology to mammalian phospholipase Ds (PLDs), plant PLDzeta-type enzymes are likely candidates to regulate auxin carrier endocytosis. We investigated root tropic responses for an Arabidopsis pldzeta1-KO mutant and its effect on the dynamics of two auxin transporters during salt stress, that is, PIN2 and AUX1. We found altered root growth and halotropic and gravitropic responses in the absence of PLDzeta1 and report a role for PLDzeta1 in the polar localization of PIN2. Additionally, irrespective of the genetic background, salt stress induced changes in AUX1 polarity. Utilizing our previous computational model, we found that these novel salt-induced AUX1 changes contribute to halotropic auxin asymmetry. We also report the formation of "osmotic stress-induced membrane structures." These large membrane structures are formed at the plasma membrane shortly after NaCl or sorbitol treatment and have a prolonged presence in a pldzeta1 mutant. Taken together, these results show a crucial role for PLDzeta1 in both ionic and osmotic stress-induced auxin carrier dynamics during salt stress.
PMID: 31430837
Plant J , IF:6.141 , 2020 Jan , V101 (2) : P334-351 doi: 10.1111/tpj.14545
GmMAX2-D14 and -KAI interaction-mediated SL and KAR signaling play essential roles in soybean root nodulation.
State Key Lab of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, 230036, China.; State Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430075, China.
Despite of important functions of strigolactones (SLs) and karrikins (KARs) in plant development, plant-parasite and plant-fungi interactions, their roles in soybean-rhizobia interaction remain elusive. SL/KAR signaling genes GmMAX2a, GmD14s, and GmKAIs are activated by rhizobia infection. GmMAX2a restored atmax2 root hair defects and soybean root hairs were changed in GmMAX2a overexpression (GmMAX2a-OE) or knockdown (GmMAX2a-KD) mutants. GmMAX2a-KD gave fewer, whereas GmMAX2a-OE produced more nodules than GUS hairy roots. Mutation of GmMAX2a in its KD or OE transgenic hairy roots affected the rhizobia infection-induced increases in early nodulation gene expression. Both mutant hairy roots also displayed the altered auxin, jasmonate and abscisic acid levels, as further verified by transcriptomic analyses of their synthetic genes. Overexpression of an auxin synthetic gene GmYUC2a also affected SL and KAR signaling genes. GmMAX2a physically interacted with SL/KAR receptors GmD14s, GmKAIs, and GmD14Ls with different binding affinities, depending on variations in the critical amino acids, forming active D14/KAI-SCF(MAX2) complexes. The knockdown mutant roots of the nodule-specifically expressing GmKAIs and GmD14Ls gave fewer nodules, with altered expression of several early nodulation genes. The expression levels of GmKAIs, and GmD14Ls were markedly changed in GmMAX2a mutant roots, so did their target repressor genes GmD53s and GmSMAX1s. Thus, SL and KAR signaling were involved in soybean-rhizobia interaction and nodulation partly through interactions with hormones, and this may explain the different effects of MXA2 orthologs on legume determinate and indeterminate nodulation. The study provides fresh insights into the roles of GmMAX2-mediated SL/KAR signaling in soybean root hair and nodule formation.
PMID: 31559658
Plant J , IF:6.141 , 2020 Jan , V101 (1) : P87-100 doi: 10.1111/tpj.14520
Auxin signaling modulates LATERAL ROOT PRIMORDIUM1 (LRP1) expression during lateral root development in Arabidopsis.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.; Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.
Auxin signaling mediated by various auxin/indole-3-acetic acid (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs) regulate lateral root (LR) development by controlling the expression of downstream genes. LATERAL ROOT PRIMORDIUM1 (LRP1), a member of the SHORT INTERNODES/STYLISH (SHI/STY) family, was identified as an auxin-inducible gene. The precise developmental role and molecular regulation of LRP1 in root development remain to be understood. Here we show that LRP1 is expressed in all stages of LR development, besides the primary root. The expression of LRP1 is regulated by histone deacetylation in an auxin-dependent manner. Our genetic interaction studies showed that LRP1 acts downstream of auxin responsive Aux/IAAs-ARFs modules during LR development. We showed that auxin-mediated induction of LRP1 is lost in emerging LRs of slr-1 and arf7arf19 mutants roots. NPA treatment studies showed that LRP1 acts after LR founder cell specification and asymmetric division during LR development. Overexpression of LRP1 (LRP1 OE) showed an increased number of LR primordia (LRP) at stages I, IV and V, resulting in reduced emerged LR density, which suggests that it is involved in LRP development. Interestingly, LRP1-induced expression of YUC4, which is involved in auxin biosynthesis, contributes to the increased accumulation of endogenous auxin in LRP1 OE roots. LRP1 interacts with SHI, STY1, SRS3, SRS6 and SRS7 proteins of the SHI/STY family, indicating their possible redundant role during root development. Our results suggested that auxin and histone deacetylation affect LRP1 expression and it acts downstream of LR forming auxin response modules to negatively regulate LRP development by modulating auxin homeostasis in Arabidopsis thaliana.
PMID: 31483536
J Exp Bot , IF:5.908 , 2020 Jan , V71 (1) : P219-233 doi: 10.1093/jxb/erz443
Enzymes contributing to the hydrogen peroxide signal dynamics that regulate wall labyrinth formation in transfer cells.
School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia.; School of Life Sciences, Henan University, Kaifeng, Henan, China.; International Joint Center for Biomedical Innovation, Henan University, Kaifeng, Henan, China.; Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, China.
Transfer cells are characterized by an amplified plasma membrane area supported on a wall labyrinth composed of a uniform wall layer (UWL) from which wall ingrowth (WI) papillae arise. Adaxial epidermal cells of developing Vicia faba cotyledons, when placed in culture, undergo a rapid (hours) trans-differentiation to a functional epidermal transfer cell (ETC) phenotype. The trans-differentiation event is controlled by a signalling cascade comprising auxin, ethylene, apoplasmic reactive oxygen species (apoROS), and cytosolic Ca2+. Apoplasmic hydrogen peroxide (apoH2O2) was confirmed as the apoROS regulating UWL and WI papillae formation. Informed by an ETC-specific transcriptome, a pharmacological approach identified a temporally changing cohort of H2O2 biosynthetic enzymes. The cohort contained a respiratory burst oxidase homologue, polyamine oxidase, copper amine oxidase, and a suite of class III peroxidases. Collectively these generated two consecutive bursts in apoH2O2 production. Spatial organization of biosynthetic/catabolic enzymes was deduced from responses to pharmacologically blocking their activities on the cellular and subcellular distribution of apoH2O2. The findings were consistent with catalase activity constraining the apoH2O2 signal to the outer periclinal wall of the ETCs. Strategic positioning of class III peroxidases in this outer domain shaped subcellular apoH2O2 signatures that differed during assembly of the UWL and WI papillae.
PMID: 31587068
J Exp Bot , IF:5.908 , 2020 Jan , V71 (1) : P168-177 doi: 10.1093/jxb/erz429
LAZY3 plays a pivotal role in positive root gravitropism in Lotus japonicus.
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.; University of Chinese Academy of Sciences, Beijing, China.; Kazusa DNA Research Institute, Chiba, Japan.
LAZY1 family genes play important roles in both shoot and root gravitropism in plants. Here we report a Lotus japonicus mutant that displays negative gravitropic response in primary and lateral roots. Map-based cloning identified the mutant gene LAZY3 as a functional ortholog of the LAZY1 gene. Mutation of the LAZY3 gene reduced rootward polar auxin transport (PAT) in the primary root, which was also insensitive to the PAT inhibitor N-1-naphthylphthalamic acid. Moreover, immunolocalization of enhanced green fluorescent protein-tagged LAZY3 in L. japonicus exhibited polar localization of LAZY3 on the plasma membrane in root stele cells. We therefore suggest that the polar localization of LAZY3 in stele cells might be required for PAT in L. japonicus root. LAZY3 transcripts displayed asymmetric distribution at the root tip within hours of gravistimulation, while overexpression of LAZY3 under a constitutive promoter in lazy3 plants rescued the gravitropic response in roots. These data indicate that root gravitropism depends on the presence of LAZY3 but not on its asymmetric expression in root tips. Expression of other LAZY genes in a lazy3 background did not rescue the growth direction of roots, suggesting that the LAZY3 gene plays a distinct role in root gravitropism in L. japonicus.
PMID: 31559427
Ying Yong Sheng Tai Xue Bao , IF:5.84 , 2020 Jan , V31 (1) : P189-198 doi: 10.13287/j.1001-9332.202001.026
[Effects of exogenous plant hormones on physiological characteristics and yield of sweet potato under drought stress].
College of Resources and Environmental Science, Qingdao Agricultural University, Qingdao 266109, Shandong, China.
To explore the alleviation effect of spraying phytohormone on physiological characteristics and yield of sweet potato under drought stress in different periods, and to determine the best period of spraying external plant hormones, the effects on endogenous hormone content, photosynthetic fluorescence characteristics and yield of sweet potato were examined by spraying 6-benzylaminopurine (6-BA), alpha-naphthylacetic acid (NAA) and abscisic acid (ABA) respectively under drought stress after transplanting for 20 days (early stage), 60 days (middle stage) and 100 days (later stage) under artificial water control. The results showed that compared with spraying water, exogenous phytohormones significantly increased the yield of sweet potato under drought stress, among which 6-BA had the highest effect, followed by NAA and ABA. The effect of spraying in early stage was better than that in middle and late stages. Exogenous phytohormones significantly increased photosynthetic and chlorophyll fluorescence parameters of sweet potato leaves under drought stress at different stages, alleviated the decrease in eatin ribonucleoside (ZR) and auxin (IAA) caused by drought. Stepwise regression analysis showed that endogenous hormones and photosynthetic characteristics were key factors affecting yield of sweet potato. Results of path analysis showed that spraying exogenous plant hormone affected sweet potato yield by changing net photosynthetic rate (Pn), IAA, ZR, maximal photochemical efficiency and photochemical performance index under drought stress at early stage. Therefore, spraying 6-BA could regulate the content of endogenous hormones and improve photosynthetic characteristics of sweet potato at the early growth stage, and thus effectively alleviate the loss of yield caused by drought stress.
PMID: 31957396
J Integr Plant Biol , IF:4.885 , 2020 Jan doi: 10.1111/jipb.12905
Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid.
College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China.; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China.; Industrial Crop Research Institute, Shanxi Academy of Agricultural Sciences, Fenyang, 032200, China.; Department of Steering Committee, Yunnan Agricultural University, Kunming, 650201, China.; Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.; Mengzi Seed Management Station, Mengzi, 661199, China.; Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.; College of Horticulture and Landscape, Southwest Forestry University, Kunming, 650224, China.
Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole-3-acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2-15 mumol/L) and 1-naphthalenacetic acid (NAA) (10-20 mumol/L). Moreover, the roots of the JA signaling-defective coi1-18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild-type Nipponbare and miR393b-overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross-talk between JA signaling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants.
PMID: 31912615
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (2) doi: 10.3390/ijms21020441
Molecular Mechanism of Vegetative Growth Advantage in Allotriploid Populus.
Beijing Advanced Innovation Center for Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China.; Beijing Academy of Forestry and Pomology Sciences No. 12 A Rui Wang Fen, Fragrance Hills Haidian District, Beijing 100093, China.; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China.; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China.
Allotriploid poplar has a prominent vegetative growth advantage that impacts dramatically on lumber yield. The growth regulation is complex which involves abundant genes, metabolic and signaling pathways, while the information about the functional control process is very little. We used high-throughput sequencing and physiological index measurement to obtain a global overview of differences between allotriploid and diploid Populus. The genes related to plant growth advantage show a higher expression compared to diploid, and most of them are revolved around hormones, photosynthesis and product accumulation. Thus, allotriploid Populus showed more efficient photosynthesis, carbon fixation, sucrose and starch synthesis, and metabolism as well as augmented biosynthesis of auxin, cytokinin, and gibberellin. These data enable the connection of metabolic processes, signaling pathways, and specific gene activity, which will underpin the development of network models to elucidate the process of triploid Populus advantage growth.
PMID: 32284503
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (2) doi: 10.3390/ijms21020673
Glycerol-Induced Powdery Mildew Resistance in Wheat by Regulating Plant Fatty Acid Metabolism, Plant Hormones Cross-Talk, and Pathogenesis-Related Genes.
Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.; Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, Haifa 3498838, Israel.; Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
Our previous study indicated that glycerol application induced resistance to powdery mildew (Bgt) in wheat by regulating two important signal molecules, glycerol-3-phosphate (G3P) and oleic acid (OA18:1). Transcriptome analysis of wheat leaves treated by glycerol and inoculated with Bgt was performed to identify the activated immune response pathways. We identified a set of differentially expressed transcripts (e.g., TaGLI1, TaACT1, and TaSSI2) involved in glycerol and fatty acid metabolism that were upregulated in response to Bgt infection and might contribute to G3P and OA18:1 accumulation. Gene Ontology (GO) enrichment analysis revealed GO terms induced by glycerol, such as response to jasmonic acid (JA), defense response to bacterium, lipid oxidation, and growth. In addition, glycerol application induced genes (e.g., LOX, AOS, and OPRs) involved in the metabolism pathway of linolenic and alpha-linolenic acid, which are precursor molecules of JA biosynthesis. Glycerol induced JA and salicylic acid (SA) levels, while glycerol reduced the auxin (IAA) level in wheat. Glycerol treatment also induced pathogenesis related (PR) genes, including PR-1, PR-3, PR-10, callose synthase, PRMS, RPM1, peroxidase, HSP70, HSP90, etc. These results indicate that glycerol treatment regulates fatty acid metabolism and hormones cross-talk and induces the expression of PR genes that together contribute to Bgt resistance in wheat.
PMID: 31968554
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (1) doi: 10.3390/ijms21010321
Histone Deacetylase (HDAC) Gene Family in Allotetraploid Cotton and Its Diploid Progenitors: In Silico Identification, Molecular Characterization, and Gene Expression Analysis under Multiple Abiotic Stresses, DNA Damage and Phytohormone Treatments.
School of Life Sciences, Tsinghua University, Beijing 100084, China.; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan.; Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON N6A5B8, Canada.; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.; Forage & Range Research, United States Department of Agriculture, Agricultural Research Service, Logan, UT 84322, USA.
Histone deacetylases (HDACs) play a significant role in a plant's development and response to various environmental stimuli by regulating the gene transcription. However, HDACs remain unidentified in cotton. In this study, a total of 29 HDACs were identified in allotetraploid Gossypium hirsutum, while 15 and 13 HDACs were identified in Gossypium arboretum and Gossypium raimondii, respectively. Gossypium HDACs were classified into three groups (reduced potassium dependency 3 (RPD3)/HDA1, HD2-like, and Sir2-like (SRT) based on their sequences, and Gossypium HDACs within each subgroup shared a similar gene structure, conserved catalytic domains and motifs. Further analysis revealed that Gossypium HDACs were under a strong purifying selection and were unevenly distributed on their chromosomes. Gene expression data revealed that G. hirsutum HDACs were differentially expressed in various vegetative and reproductive tissues, as well as at different developmental stages of cotton fiber. Furthermore, some G. hirsutum HDACs were co-localized with quantitative trait loci (QTLs) and single-nucleotide polymorphism (SNPs) of fiber-related traits, indicating their function in fiber-related traits. We also showed that G. hirsutum HDACs were differentially regulated in response to plant hormones (abscisic acid (ABA) and auxin), DNA damage agent (methyl methanesulfonate (MMS)), and abiotic stresses (cold, salt, heavy metals and drought), indicating the functional diversity and specification of HDACs in response to developmental and environmental cues. In brief, our results provide fundamental information regarding G. hirsutum HDACs and highlight their potential functions in cotton growth, fiber development and stress adaptations, which will be helpful for devising innovative strategies for the improvement of cotton fiber and stress tolerance.
PMID: 31947720
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (2) doi: 10.3390/ijms21020453
Full-Length Transcriptome Analysis of the ABCB, PIN/PIN-LIKES, and AUX/LAX Families Involved in Somatic Embryogenesis of Lilium pumilum DC. Fisch.
Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.; National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Horticulture Department, Shenyang Agricultural University, Shenyang 110866, China.
Plant cell totipotency is one of the 25 major topics in current scientific research, and somatic embryos are good experimental material for studying cell totipotency. Polar auxin transport plays an important regulatory role in somatic embryogenesis (SE). However, little is known about the auxin transport genes and their regulatory mechanisms in Lilium SE. In this study, we applied single-molecule real-time (SMRT) sequencing to Lilium pumilum DC. Fisch. for the first time and obtained a total of 119,649 transcripts, of which 14 encoded auxin transport genes. Correlation analyses between somatic embryo induction and gene expression under different treatments revealed that auxin transport genes, especially ATP-binding cassette (ABC) transporter B family member 21 (ABCB21) and PIN-FORMED (PIN) LIKES 7 (PILS7), may be key players in SE, and the necessary duration of picloram (PIC) treatment to induce SE is as short as 3 days. Our research provides valuable genetic information on Lilium pumilum, elucidating the candidate auxin transport genes involved in SE and their influencing factors. This study lays a foundation for elucidating the regulatory mechanism of auxin transport in SE.
PMID: 31936841
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (2) doi: 10.3390/ijms21020454
Overexpression of Rice Expansin7 (Osexpa7) Confers Enhanced Tolerance to Salt Stress in Rice.
Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Jungangro, Anseong-si, Gyeonggi-do 17579, Korea.; Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.; Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
Expansins are key regulators of cell-wall extension and are also involved in the abiotic stress response. In this study, we evaluated the function of OsEXPA7 involved in salt stress tolerance. Phenotypic analysis showed that OsEXPA7 overexpression remarkably enhanced tolerance to salt stress. OsEXPA7 was highly expressed in the shoot apical meristem, root, and the leaf sheath. Promoter activity of OsEXPA7:GUS was mainly observed in vascular tissues of roots and leaves. Morphological analysis revealed structural alterations in the root and leaf vasculature of OsEXPA7 overexpressing (OX) lines. OsEXPA7 overexpression resulted in decreased sodium ion (Na(+)) and accumulated potassium ion (K(+)) in the leaves and roots. Under salt stress, higher antioxidant activity was also observed in the OsEXPA7-OX lines, as indicated by lower reactive oxygen species (ROS) accumulation and increased antioxidant activity, when compared with the wild-type (WT) plants. In addition, transcriptional analysis using RNA-seq and RT-PCR revealed that genes involved in cation exchange, auxin signaling, cell-wall modification, and transcription were differentially expressed between the OX and WT lines. Notably, salt overly sensitive 1, which is a sodium transporter, was highly upregulated in the OX lines. These results suggest that OsEXPA7 plays an important role in increasing salt stress tolerance by coordinating sodium transport, ROS scavenging, and cell-wall loosening.
PMID: 31936829
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (1) doi: 10.3390/ijms21010305
Crosstalk with Jasmonic Acid Integrates Multiple Responses in Plant Development.
School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea.; Department of Environmental Health Science, Konkuk University, Seoul 05029, Korea.; The National Academy of Sciences, Seoul 06579, Korea.
To date, extensive studies have identified many classes of hormones in plants and revealed the specific, nonredundant signaling pathways for each hormone. However, plant hormone functions largely overlap in many aspects of plant development and environmental responses, suggesting that studying the crosstalk among plant hormones is key to understanding hormonal responses in plants. The phytohormone jasmonic acid (JA) is deeply involved in the regulation of plant responses to biotic and abiotic stresses. In addition, a growing number of studies suggest that JA plays an essential role in the modulation of plant growth and development under stress conditions, and crosstalk between JA and other phytohormones involved in growth and development, such as gibberellic acid (GA), cytokinin, and auxin modulate various developmental processes. This review summarizes recent findings of JA crosstalk in the modulation of plant growth and development, focusing on JA-GA, JA-cytokinin, and JA-auxin crosstalk. The molecular mechanisms underlying this crosstalk are also discussed.
PMID: 31906415
Microorganisms , IF:4.152 , 2020 Jan , V8 (2) doi: 10.3390/microorganisms8020156
A MATE Transporter is Involved in Pathogenicity and IAA Homeostasis in the Hyperplastic Plant Pathogen Pseudomonas savastanoi pv. nerii.
Dipartimento di Scienze e Tecnologie Agrarie, Alimentari Ambientali e Forestali, Laboratorio di Patologia Vegetale Molecolare, Universita degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino (Firenze), Italy.; Next Genomics srl, Via Madonna del Piano, 6, 50019 Sesto Fiorentino (Firenze), Italy.
During the last years, many evidences have been accumulating about the phytohormone indole-3-acetic acid (IAA) as a multifaceted compound in the microbial world, with IAA playing a role as a bacterial intra and intercellular signaling molecule or as an effector during pathogenic or beneficial plant-bacteria interactions. However, pretty much nothing is known on the mechanisms that bacteria use to modulate IAA homeostasis, in particular on IAA active transport systems. Here, by an approach combining in silico three-dimensional (3D) structural modeling and docking, mutagenesis, quantitative gene expression analysis, and HPLC FLD auxin quantitative detection, for the first time a bacterial multidrug and toxic compound extrusion (MATE) transporter was demonstrated to be involved in the efflux of IAA, as well as of its conjugate IAA-Lysine, in the plant pathogenic hyperplastic bacterium Pseudomonas savastanoi pv. nerii strain Psn23. Furthermore, according to the role proved to be played by Psn23 MatE in the development of plant disease, and to the presence of Psn23 MatE homologs in all the genomospecies of the P. syringae complex, this membrane transporter could likely represent a promising target for the design of novel and selective anti-infective molecules for plant disease control.
PMID: 31979049
Physiol Plant , IF:4.148 , 2020 Jan , V168 (1) : P88-97 doi: 10.1111/ppl.12970
Molecular functional analysis of auxin/indole-3-acetic acid proteins (Aux/IAAs) in plant disease resistance in cassava.
Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
Auxin/indole-3-acetic acid proteins (Aux/IAAs) play important roles in auxin signaling pathways, with extensive involvement in plant development and plant response to abiotic and biotic stresses. Manihot esculenta (Cassava) is one of the most important biomass energy crops in tropical regions; however, the information about Aux/IAA proteins remain limited in cassava. In this study, 37 MeAux/IAA gene family members were identified in cassava and a phylogenetic analysis was performed. The transcript levels of MeAux/IAAs were commonly regulated by the pathogen Xanthomonas axonopodis pv manihotis (Xam), and some of them were specifically localized to the nucleus. Moreover, the overexpression of MeAux/IAAs confers an improved disease resistance against Xam in Nicotiana benthamiana, while MeAux/IAAs-silenced plants show disease sensitivity against Xam in cassava, as evidenced by the leaf phenotype and leaf bacterial population. Consistent with the disease resistance, MeAux/IAAs regulated the transcript levels of PATHOGENESIS-RELATED GENES (MePRs), reactive oxygen species accumulation and callose development in the plants' defense response. Taken together, gene profile and functional analysis identified several MeAux/IAAs as novel members in plant disease resistance, providing important information for further utilization of MeAux/IAAs.
PMID: 30950065
Physiol Plant , IF:4.148 , 2020 Jan , V168 (1) : P205-217 doi: 10.1111/ppl.12944
Comprehensive dynamic transcriptome analysis at two seed germination stages in maize (Zea mays L.).
College of Agronomy, Henan University of Science and Technology, Luoyang, 471003, China.; College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.; Henan Academy of Agricultural Science/Henan Provincial Key Laboratory of Maize Biology, Cereal Institute, Zhengzhou, 450002, China.
Seed germination, as an integral stage of crop production, directly affects Zea mays (maize) yield and grain quality. However, the molecular mechanisms of seed germination remain unclear in maize. We performed comparative transcriptome analysis of two maize inbred lines, Yu82 and Yu537A, at two stages of seed germination. Expression profile analysis during seed germination revealed that a total of 3381 and 4560 differentially expressed genes (DEGs) were identified in Yu82 and Yu537A at the two stages. Transcription factors were detected from several families, such as the bZIP, ERF, WRKY, MYB and bHLH families, which indicated that these transcription factor families might be involved in driving seed germination in maize. Prominent DEGs were submitted for KEGG enrichment analysis, which included plant hormones, amino acid mechanism, nutrient reservoir, metabolic pathways and ribosome. Of these pathways, genes associated with plant hormones, especially gibberellins, abscisic acid and auxin may be important for early germination in Yu82. In addition, DEGs involved in amino acid mechanism showed significantly higher expression levels in Yu82 than in Yu537A, which indicated that energy supply from soluble sugars and amino acid metabolism may contribute to early germination in Yu82. This results provide novel insights into transcriptional changes and gene interactions in maize during seed germination.
PMID: 30767243
Physiol Plant , IF:4.148 , 2020 Jan , V168 (1) : P174-187 doi: 10.1111/ppl.12933
Overexpressing broccoli tryptophan biosynthetic genes BoTSB1 and BoTSB2 promotes biosynthesis of IAA and indole glucosinolates.
College of Life Sciences, Northeast Agricultural University, Harbin, China.
Tryptophan is one of the amino acids that cannot be produced in humans and has to be acquired primarily from plants. In Arabidopsis thaliana (Arabidopsis), the tryptophan synthase beta subunit (TSB) genes have been found to catalyze the biosynthesis of tryptophan. Here, we report the isolation and characterization of two TSB genes from Brassica oleracea (broccoli), designated BoTSB1 and BoTSB2. Overexpressing BoTSB1 or BoTSB2 in Arabidopsis resulted in higher tryptophan content and the accumulation of indole-3-acetic acid (IAA) and indole glucosinolates in rosette leaves. Therefore, the transgenic plants showed a series of high auxin phenotypes, including long hypocotyls, large plants and a high number of lateral roots. The spatial expression of BoTSB1 and BoTSB2 was detected by quantitative real-time PCR in broccoli and by expressing the beta-glucuronidase reporter gene (GUS) controlled by the promoters of the two genes in Arabidopsis. BoTSB1 was abundantly expressed in vascular tissue of shoots and inflorescences. Compared to BoTSB1, BoTSB2 was expressed at a very low level in shoots but at a higher level in roots. We further investigated the expression response of the two genes to several hormone and stress treatments. Both genes were induced by methyl jasmonate (MeJA), salicylic acid (SA), gibberellic acid (GA), Flg22 (a conserved 22-amino acid peptide derived from bacterial flagellin), wounding, low temperature and NaCl and were repressed by IAA. Our study enhances the understanding of tryptophan biosynthesis and its regulation in broccoli and Arabidopsis. In addition, we provide evidence that TSB genes can potentially be a good tool to breed plants with high biomass and high nutrition.
PMID: 30706476
Ann Bot , IF:4.005 , 2020 Jan , V125 (1) : P119-130 doi: 10.1093/aob/mcz154
Heterogeneous phosphate supply influences maize lateral root proliferation by regulating auxin redistribution.
Department of Plant Nutrition, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Key Laboratory of Plant Nutrition, Ministry of Agriculture, Beijing , P. R. China.; Ecological Science Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
BACKGROUND AND AIMS: Roots take up phosphorus (P) as inorganic phosphate (Pi). Enhanced root proliferation in Pi-rich patches enables plants to capture the unevenly distributed Pi, but the underlying control of root proliferation remains largely unknown. Here, the role of auxin in this response was investigated in maize (Zea mays). METHODS: A split-root, hydroponics system was employed to investigate root responses to Pi supply, with one (heterogeneous) or both (homogeneous) sides receiving 0 or 500 mum Pi. KEY RESULTS: Maize roots proliferated in Pi-rich media, particularly with heterogeneous Pi supply. The second-order lateral root number was 3-fold greater in roots of plants receiving a heterogeneous Pi supply than in roots of plants with a homogeneous Pi supply. Root proliferation in a heterogeneous Pi supply was inhibited by the auxin transporter inhibitor 1-N-naphthylphthalamic acid (NPA). The proliferation of lateral roots was accompanied by an enhanced auxin response in the apical meristem and vascular tissues at the root tip, as demonstrated in a DR5::RFP marker line. CONCLUSIONS: It is concluded that the response of maize root morphology to a heterogeneous Pi supply is modulated by local signals of Pi availability and systemic signals of plant P nutritional status, and is mediated by auxin redistribution.
PMID: 31560368
Sci Rep , IF:3.998 , 2020 Jan , V10 (1) : P897 doi: 10.1038/s41598-020-57717-0
Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum.
Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.; Division of Plant Physiology, Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India.; Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.; Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India. rita.genomics@gmail.com.
Sorghum is a self-pollinated crop with multiple economic uses as cereal, forage, and biofuel feedstock. Hybrid breeding is a cornerstone for sorghum improvement strategies that currently relies on cytoplasmic male sterile lines. To engineer genic male sterility, it is imperative to examine the genetic components regulating anther/pollen development in sorghum. To this end, we have performed transcriptomic analysis from three temporal stages of developing anthers that correspond to meiotic, microspore and mature pollen stages. A total of 5286 genes were differentially regulated among the three anther stages with 890 of them exhibiting anther-preferential expression. Differentially expressed genes could be clubbed into seven distinct developmental trajectories using K-means clustering. Pathway mapping revealed that genes involved in cell cycle, DNA repair, regulation of transcription, brassinosteroid and auxin biosynthesis/signalling exhibit peak expression in meiotic anthers, while those regulating abiotic stress, carbohydrate metabolism, and transport were enriched in microspore stage. Conversely, genes associated with protein degradation, post-translational modifications, cell wall biosynthesis/modifications, abscisic acid, ethylene, cytokinin and jasmonic acid biosynthesis/signalling were highly expressed in mature pollen stage. High concurrence in transcriptional dynamics and cis-regulatory elements of differentially expressed genes in rice and sorghum confirmed conserved developmental pathways regulating anther development across species. Comprehensive literature survey in conjunction with orthology analysis and anther-preferential accumulation enabled shortlisting of 21 prospective candidates for in-depth characterization and engineering male fertility in sorghum.
PMID: 31964983
Sci Rep , IF:3.998 , 2020 Jan , V10 (1) : P679 doi: 10.1038/s41598-019-57161-9
The dynamic response of the Arabidopsis root metabolome to auxin and ethylene is not predicted by changes in the transcriptome.
Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America.; Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States of America.; Department of Biology and Center for Molecular Signaling, Wake Forest University, Winston-Salem, North Carolina, United States of America.; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America. winkel@vt.edu.
While the effects of phytohormones on plant gene expression have been well characterized, comparatively little is known about how hormones influence metabolite profiles. This study examined the effects of elevated auxin and ethylene on the metabolome of Arabidopsis roots using a high-resolution 24 h time course, conducted in parallel to time-matched transcriptomic analyses. Mass spectrometry using orthogonal UPLC separation strategies (reversed phase and HILIC) in both positive and negative ionization modes was used to maximize identification of metabolites with altered levels. The findings show that the root metabolome responds rapidly to hormone stimulus and that compounds belonging to the same class of metabolites exhibit similar changes. The responses were dominated by changes in phenylpropanoid, glucosinolate, and fatty acid metabolism, although the nature and timing of the response was unique for each hormone. These alterations in the metabolome were not directly predicted by the corresponding transcriptome data, suggesting that post-transcriptional events such as changes in enzyme activity and/or transport processes drove the observed changes in the metabolome. These findings underscore the need to better understand the biochemical mechanisms underlying the temporal reconfiguration of plant metabolism, especially in relation to the hormone-metabolome interface and its subsequent physiological and morphological effects.
PMID: 31959762
Sci Rep , IF:3.998 , 2020 Jan , V10 (1) : P449 doi: 10.1038/s41598-019-57219-8
Transcriptome analyses revealed molecular responses of Cynanchum auriculatum leaves to saline stress.
Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Province, 224045, P.R. China.; Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Province, 224045, P.R. China. syzwcd@126.com.; Shenzhen GenProMetab Biotechnology Company Limited., Shenzhen, Guangdong Province, 51800, P.R. China. zhanggen1988@163.com.
Cynanchum auriculatum is a traditional herbal medicine in China and can grow in saline soils. However, little is known in relation to the underlying molecular mechanisms. In the present study, C. auriculatum seedlings were exposed to 3.75 per thousand and 7.5 per thousand salinity. Next, transcriptome profiles of leaves were compared. Transcriptome sequencing showed 35,593 and 58,046 differentially expressed genes (DEGs) in treatments with 3.75 per thousand and 7.5 per thousand, compared with the control, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these DEGs enriched various defense-related biological pathways, including ROS scavenging, ion transportation, lipid metabolism and plant hormone signaling. Further analyses suggested that C. auriculatum up-regulated Na(+)/H(+) exchanger and V-type proton ATPase to avoid accumulation of Na(+). The flavonoid and phenylpropanoids biosynthesis pathways were activated, which might increase antioxidant capacity in response to saline stress. The auxin and ethylene signaling pathways were upregulated in response to saline treatments, both of which are important plant hormones. Overall, these results raised new insights to further investigate molecular mechanisms underlying resistance of C. auriculatum to saline stress.
PMID: 31949203
Sci Rep , IF:3.998 , 2020 Jan , V10 (1) : P373 doi: 10.1038/s41598-019-57232-x
A Comprehensive Transcriptome-Wide Identification and Screening of WRKY Gene Family Engaged in Abiotic Stress in Glycyrrhiza glabra.
Plant Biotechnology Department, Council for Scientific Research-Indian Institute of Integrative Medicine, Canal Road, Jammu, India.; Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India.; Plant Biotechnology Department, Council for Scientific Research-Indian Institute of Integrative Medicine, Canal Road, Jammu, India. suphlabg@gmail.com.
The study reports 147 full-length WRKY genes based on the transcriptome analysis of Glycyrrhiza genus (G. glabra and G. uralensis). Additional motifs in G. glabra included DivIVA (GgWRKY20) and SerS Superfamily (GgWRKY21) at the C-terminal, and Coat family motifs (GgWRKY55) at the N-terminal of the proteins, while Exo70 exo cyst complex subunit of 338 amino acid (GuWRKY9) was present at the N-terminal of G. uralensis only. Plant Zn cluster super-family domain (17 WRKYs) and bZIP domain (2 WRKYs) were common between the two species. Based on the number of WRKY domains, sequence alignment and phylogenesis, the study identified GuWRKY27 comprising of 3 WRKY domains in G. uralensis and a new subgroup-IIf (10 members), having novel zinc finger pattern (C-X4-C-X22-HXH) in G. glabra. Multiple WRKY binding domains (1-11) were identified in the promoter regions of the GgWRKY genes indicating strong interacting network between the WRKY proteins. Tissue-specific expression of 25 GgWRKYs, under normal and treated conditions, revealed 11 of the 18 induction factor triggered response corroborating to response observed in AtWRKYs. The study identified auxin-responsive GgWRKY 55 & GgWRKY38; GA3 responsive GgWRKYs15&59 in roots and GgWRKYs8, 20, 38, 57 &58 in the shoots of the treated plant. GgWRKYs induced under various stresses included GgWRKY33 (cold), GgWRKY4 (senescence), GgWRKYs2, 28 & 33 (salinity) and GgWRKY40 (wounding). Overall, 23 GgWRKYs responded to abiotic stress, and 17 WRKYs were induced by hormonal signals. Of them 13 WRKYs responded to both suggesting inter-connection between hormone signalling and stress response. The present study will help in understanding the transcriptional reprogramming, protein-protein interaction and cross-regulation during stress and other physiological processes in the plant.
PMID: 31941983
Rice (N Y) , IF:3.912 , 2020 Jan , V13 (1) : P2 doi: 10.1186/s12284-019-0364-0
OsFPFL4 is Involved in the Root and Flower Development by Affecting Auxin Levels and ROS Accumulation in Rice (Oryza sativa).
Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China.; Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China. huangjunli@cqu.edu.cn.
BACKGROUND: FPF1 (flowering-promoting factor 1) is one of the important family involved in the genetic control of flowering time in plant. Until now, limited knowledge concerning FPF1 family in rice has been understood. RESULTS: As a homologue of AtFPF1, FPF1-like protein 4 of rice (OsFPFL4) is expressed in various tissues of plants. The functions of OsFPFL4 in rice were investigated by the reverse genetics approaches. Plants overexpressing OsFPFL4 have shorter primary root, more lateral roots and adventitious roots than wild type; however, RNA interference (RNAi) of OsFPFL4 significantly inhibits the growth of root system, and also delays the flowering time in rice. Interestingly, increased or repressed expression of OsFPFL4 leads to shrunken anthers and abnormal pollen grains. It is well recognized that auxin plays important roles in plant root and flower development, and the root elongation is also regulated by reactive oxygen species (ROS) homeostasis. Here, our results show that rice plants overexpressing OsFPFL4 accumulate more auxin in the shoot and root, whereas RNAi lines have less auxin than wild type. As expected, the transcript levels of genes responsible for auxin biosynthesis and polar transport are altered in these OsFPFL4 transgenic plants. As to ROS, slightly higher ROS levels were detected in overexpression root and inflorescence than the counterparts of wild type; however, the ROS levels were significantly increased in the RNAi lines, due to increased expression of ROS-producers and reduced expression of ROS-scavengers. CONCLUSION: Our results reveal that OsFPFL4 is involved in modulating the root and flower development by affecting auxin and ROS homeostasis in rice plants. OsFPFL4 controls auxin accumulation via affecting auxin biosynthesis and transport, and also modulates ROS homeostasis by balancing ROS producing and scavenging. Thus, auxin-mediated ROS production might play a role in regulating redox status, which controls plant root and flower development.
PMID: 31912314
Viruses , IF:3.816 , 2020 Jan , V12 (1) doi: 10.3390/v12010076
Comparative Transcriptome Analysis Provides Molecular Insights into the Interaction of Beet necrotic yellow vein virus and Beet soil-borne mosaic virus with Their Host Sugar Beet.
Department of Plant Biology, Uppsala BioCenter SLU, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, 75007 Uppsala, Sweden.; Genome Research of Industrial Microorganisms, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.; Department of Plant Protection, School of Agriculture, University of Zanjan, Zanjan 45371-38791, Iran.; Department of Phytopathology, Institute of Sugar Beet Research, 37079 Gottingen, Germany.
Beet necrotic yellow vein virus (BNYVV) and Beet soil-borne mosaic virus (BSBMV) are closely related species, but disease development induced in their host sugar beet displays striking differences. Beet necrotic yellow vein virus induces excessive lateral root (LR) formation, whereas BSBMV-infected roots appear asymptomatic. A comparative transcriptome analysis was performed to elucidate transcriptomic changes associated with disease development. Many differentially expressed genes (DEGs) were specific either to BNYVV or BSBMV, although both viruses shared a high number of DEGs. Auxin biosynthesis pathways displayed a stronger activation by BNYVV compared to BSBMV-infected plants. Several genes regulated by auxin signalling and required for LR formation were exclusively altered by BNYVV. Both viruses reprogrammed the transcriptional network, but a large number of transcription factors involved in plant defence were upregulated in BNYVV-infected plants. A strong activation of pathogenesis-related proteins by both viruses suggests a salicylic acid or jasmonic acid mediated-defence response, but the data also indicate that both viruses counteract the SA-mediated defence. The ethylene signal transduction pathway was strongly downregulated which probably increases the susceptibility of sugar beet to Benyvirus infection. Our study provides a deeper insight into the interaction of BNYVV and BSBMV with the economically important crop sugar beet.
PMID: 31936258
BMC Genomics , IF:3.594 , 2020 Jan , V21 (1) : P62 doi: 10.1186/s12864-020-6469-4
Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour.
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. laizx01@163.com.; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. buliang84@163.com.
BACKGROUND: The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors that regulate diverse developmental processes and stress responses in plants. They have been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.), which is an important tropical/subtropical evergreen fruit tree that produces a variety of bioactive compounds with rich nutritional and medicinal value. We conducted a genome-wide analysis of the AP2/ERF superfamily and its roles in somatic embryogenesis (SE) and developmental processes in longan. RESULTS: A genome-wide survey of the AP2/ERF superfamily was carried out to discover its evolution and function in longan. We identified 125 longan AP2/ERF genes and classified them into the ERF (101 members), AP2 (19 members), RAV (four members) families, and one Soloist. The AP2 and Soloist genes contained one to ten introns, whereas 87 genes in the ERF and RAV families had no introns. Hormone signaling molecules such as methyl jasmonate (MeJA), abscisic acid (ABA), gibberellin, auxin, and salicylic acid (SA), and stress response cis-acting element low-temperature (55) and defense (49) boxes also were identified. We detected diverse single nucleotide polymorphisms (SNPs) between the 'Hong He Zi' (HHZ) and 'SI JI MI' (SJM) cultivars. The number of insertions and deletions (InDels) was far fewer than SNPs. The AP2 family members exhibited more alternative splicing (AS) events in different developmental processes of longan than members of the other families. Expression pattern analysis revealed that some AP2/ERF members regulated early SE and developmental processes in longan seed, root, and flower, and responded to exogenous hormones such as MeJA, SA, and ABA, and 2,4-D, a synthetic auxin. Protein interaction predictions indicated that the Baby Boom (BBM) transcription factor, which was up-regulated at the transcriptional level in early SE, may interact with the LALF/AGL15 network. CONCLUSIONS: The comprehensive analysis of molecular evolution and expression patterns suggested that the AP2/ERF superfamily may plays an important role in longan, especially in early SE, and in seed, root, flower, and young fruit. This systematic analysis provides a foundation for further functional characterization of the AP2/ERF superfamily with the aim of longan improvement.
PMID: 31959122
BMC Genomics , IF:3.594 , 2020 Jan , V21 (1) : P4 doi: 10.1186/s12864-019-6393-7
Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour.
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300, Toulouse, France.; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. buliang84@163.com.; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. laizx01@163.com.
BACKGROUND: Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). RESULTS: RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. CONCLUSION: This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.
PMID: 31898486
Plant Sci , IF:3.591 , 2020 Jan , V290 : P110294 doi: 10.1016/j.plantsci.2019.110294
The role of auxin transporters and receptors in adventitious rooting of Arabidopsis thaliana pre-etiolated flooded seedlings.
Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), CP 15005, Porto Alegre, RS, 91501-970, Brazil.; Department of Plant Developmental Genetics, Institute of Biology Leiden, Sylvius Laboratory, Sylviusweg 72, 2333 CB, Leiden, the Netherlands. Electronic address: r.offringa@biology.leidenuniv.nl.; Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), CP 15005, Porto Alegre, RS, 91501-970, Brazil. Electronic address: fettneto@cbiot.ufrgs.br.
Adventitious roots (ARs) form from above-ground organs, and auxins are major regulators of AR development. TIR1/AFB F-box proteins act as well-established auxin receptors. Auxin transport involves the PINFORMED (PIN) auxin efflux carriers and AUXIN RESISTANT 1/LIKE AUX1 (AUX1/LAX1) influx carriers. To further elucidate the basis of AR development, we investigated the participation of these proteins and phosphorylation of PINs during adventitious rooting in hypocotyls of pre-etiolated flooded Arabidopsis thaliana seedlings. Mutant and GUS localization studies indicated that AFB2 is important in AR development. AUX1 loss-of-function reduced AR numbers, which could not be reversed by exogenous auxin. Single mutations in LAX1, LAX2 and LAX3 had no negative impact on AR development and the first and last mutations even promoted it. Double and triple mutants of AUX1, LAX1, LAX2 and LAX3 significantly reduced rooting, which was reversed by exogenous auxin. AUX1 was essential in AR establishment, with LAX3 apparently acting in conjunction. Proper phosphorylation of PINs by PID, WAG1 and WAG2 and auxin transport direction were equally essential for AR establishment. PIN1, AUX1 and AFB2 (overexpression) and LAX1, LAX3, PIN4 and PIN7 (downregulation) emerged as potential targets for genetic manipulation aiming at improving AR development.
PMID: 31779904
Plant Sci , IF:3.591 , 2020 Jan , V290 : P110196 doi: 10.1016/j.plantsci.2019.110196
Ethephon-regulated maize internode elongation associated with modulating auxin and gibberellin signal to alter cell wall biosynthesis and modification.
Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.; College of Crop Science, Fujian Agriculture and Forestry University, Fujian, 350002, China.; Engineering Research Center of Plant Growth Regulator, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China. Electronic address: zmc1214@163.com.
Ethephon efficiently regulates plant growth to modulate the maize (Zea mays L.) stalk strength and yield potential, yet there is little information on how ethylene governs a specific cellular response for altering internode elongation. Here, the internode elongation kinetics, cell morphological and physiological properties and transcript expression patterns were investigated in the ethephon-treated elongating internode. Ethephon decreased the internode elongation rate, shortened the effective elongation duration, and advanced the growth process. Ethephon regulated the expression patterns of expansin and secondary cell wall-associated cellulose synthase genes to alter cell size. Moreover, ethephon increased the activities and transcripts level of phenylalanine ammonia-lyase and peroxidase, which contributed to lignin accumulation. Otherwise, ethephon-boosted ethylene evolution activated ethylene signal and increased ZmGA2ox3 and ZmGA2ox10 transcript levels while down-regulating ZmPIN1a, ZmPIN4 and ZmGA3ox1 transcript levels, which led to lower accumulation of gibberellins and auxin. In addition, transcriptome profiles confirmed previous results and identified several transcription factors that are involved in the ethephon-modulated transcriptional regulation of cell wall biosynthesis and modification and responses to ethylene, gibberellins and auxin. These results indicated that ethylene-modulated auxin and gibberellins signaling mediated the transcriptional operation of cell wall modification to regulate cell elongation in the ethephon-treated maize internode.
PMID: 31779899
Plant Sci , IF:3.591 , 2020 Jan , V290 : P110318 doi: 10.1016/j.plantsci.2019.110318
An S-domain receptor-like kinase, OsESG1, regulates early crown root development and drought resistance in rice.
Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China.; Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China. Electronic address: yaofy@163.com.; Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China. Electronic address: wheiliu@163.com.
Plant receptor-like kinase (RLKs) are serine/threonine protein kinases that play fundamental roles in development, innate immunity, and abiotic stress response. Here, we identified an S-domain receptor-like kinase OsESG1 from rice (Oryza sativa), and identified its involvement in early crown root (CR) development and drought response. The OsESG1 kinase domain possessed auto-phosphorylation activity and was able to phosphorylate MBP and His proteins. OsESG1 was expressed ubiquitously in all tissues that were examined, with relatively higher expression in the embryo. And it could be induced to express by treating with PEG, NaCl and ABA. Transgenic plants carrying anti-sense (AS) OsESG1 were generated by knockdown of OsESG1 expression. At the early seedling stage, AS lines had fewer CRs and shorter shoot compared with wild type (WT) plants. IAA flux and the genes' expressions of the auxin responsive and efflux carrier were infected in the AS lines. These results indicated that auxin signaling and polar auxin transport (PAT) were disrupted. The AS lines were more sensitive to osmotic stress compared to WT, and showed excessive accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), lower activities of antioxidant enzymes, and impaired expressions of stress-related genes under PEG treatment. Results above suggested that OsESG1 may regulate CR initiation and development by controlling auxin response and distribution, and participate in stress response by regulating the activities of antioxidants and expressions of stress-regulated genes.
PMID: 31779898
Plant Sci , IF:3.591 , 2020 Jan , V290 : P110328 doi: 10.1016/j.plantsci.2019.110328
The pH of the leaf apoplast is critical for the formation of Pseudomonas syringae-induced lesions on leaves of the common bean (Phaseolus vulgaris).
Division of Controlled Environment Horticulture, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin, Albrecht-Thaer-Weg 1, 14195 Berlin, Germany. Electronic address: geilfusc@hu-berlin.de.; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. Electronic address: wangli@wbgcas.cn.; College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.; China College of Resources and Environmental Sciences, Agricultural University of Hebei, Hebei, China.
Inoculating a virulent strain of Pseudomonas syringae pv. phaseolicola (Pph) into the leaf of common bean (Phaseolus vulgaris) causes the leaf apoplast to alkalinize. Whether or not this apoplastic pH event facilitates virulence of Pph in interaction with common bean is unclear. For elucidating this topic, (i) Pph colonization of the common bean leaf apoplast, (ii) the formation of bacterial lesions, and (iii) apoplastic sucrose concentration were investigated in relation to the apoplastic leaf pH. For this, the Pph-induced leaf apoplastic alkalinization was attenuated by spray application of either a synthetic auxin or an acidic pH buffer. Apoplastic pH was quantified in planta via microscopy-based pH imaging. Apoplastic washing fluids were extracted to quantify both colonization of bacteria in leaf apoplast and the concentration of apoplastic sucrose. Results reveal that the apoplastic alkalinization facilitated bacterial colonization of the apoplast. Number of colony forming units and area of bacterial lesions were reduced when Pph-induced apoplastic alkalinization was attenuated by foliar application of a synthetic auxin or acidic pH buffer. Application of both agents attenuated the Pph-induced increase of sucrose in the leaf apoplast, which is nutrient for bacteria. Data demonstrate that the Pph-mediated leaf apoplastic alkalinisation favours bacterial colonization.
PMID: 31779895
BMC Plant Biol , IF:3.497 , 2020 Jan , V20 (1) : P41 doi: 10.1186/s12870-020-2251-7
A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening.
Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA. cramer@unr.edu.; Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.; UMR Ecophysiology and Grape Functional Genomics, Institut des Sciences de la Vigne et du Vin, University of Bordeaux, Villenave d'Ornon, France.
BACKGROUND: Grape berry ripening is influenced by climate, the main component of the "terroir" of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. RESULTS: To better understand the effect of "place" on transcript abundance during the late stages of berry ripening, Cabernet Sauvignon berries grown in Bordeaux and Reno were compared at similar sugar levels (19 to 26 degrees Brix (total soluble solids)). Day temperatures were warmer and night temperatures were cooler in Reno. degrees Brix was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-Seq analysis identified 5528 differentially expressed genes between Bordeaux and Reno grape skins at 22 degrees Brix. Weighted Gene Coexpression Network Analysis for all expressed transcripts for all four degrees Brix levels measured indicated that the majority (75%) of transcript expression differed significantly between the two locations. Top gene ontology categories for the common transcript sets were translation, photosynthesis, DNA metabolism and catabolism. Top gene ontology categories for the differentially expressed genes at 22 degrees Brix involved response to stimulus, biosynthesis and response to stress. Some differentially expressed genes encoded terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. Bordeaux berries had higher transcript abundance with differentially expressed genes associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with differentially expressed genes involved in water deprivation, cold response, ABA signaling and iron homeostasis. CONCLUSIONS: Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-Seq analysis identified a smaller (25% of total) common core set of ripening genes that appear not to depend on rootstock, vineyard management, plant age, soil and climatic conditions. Much of the gene expression differed between the two locations and could be associated with multiple differences in environmental conditions that may have affected the berries in the two locations; some of these genes may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result.
PMID: 31992236
BMC Plant Biol , IF:3.497 , 2020 Jan , V20 (1) : P30 doi: 10.1186/s12870-020-2241-9
Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.).
Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.; Tobacco Breeding Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China.; School of Plant Sciences and Bio5 Institute, The University of Arizona, Tucson, AZ, 85721, USA.; Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.; Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China. sung@vip.henu.edu.cn.; Tobacco Breeding Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China. bwwang76@hotmail.com.
BACKGROUND: Nicotiana tabacum is an important economic crop. Topping, a common agricultural practice employed with flue-cured tobacco, is designed to increase leaf nicotine contents by increasing nicotine biosynthesis in roots. Many genes are found to be differentially expressed in response to topping, particularly genes involved in nicotine biosynthesis, but comprehensive analyses of early transcriptional responses induced by topping are not yet available. To develop a detailed understanding of the mechanisms regulating nicotine biosynthesis after topping, we have sequenced the transcriptomes of Nicotiana tabacum roots at seven time points following topping. RESULTS: Differential expression analysis revealed that 4830 genes responded to topping across all time points. Amongst these, nine gene families involved in nicotine biosynthesis and two gene families involved in nicotine transport showed significant changes during the immediate 24 h period following topping. No obvious preference to the parental species was detected in the differentially expressed genes (DEGs). Significant changes in transcript levels of nine genes involved in nicotine biosynthesis and phytohormone signal transduction were validated by qRT-PCR assays. 549 genes encoding transcription factors (TFs), found to exhibit significant changes in gene expression after topping, formed 15 clusters based on similarities of their transcript level time-course profiles. 336 DEGs involved in phytohormone signal transduction, including genes functionally related to the phytohormones jasmonic acid, abscisic acid, auxin, ethylene, and gibberellin, were identified at the earliest time point after topping. CONCLUSIONS: Our research provides the first detailed analysis of the early transcriptional responses to topping in N. tabacum, and identifies excellent candidates for further detailed studies concerning the regulation of nicotine biosynthesis in tobacco roots.
PMID: 31959100
BMC Plant Biol , IF:3.497 , 2020 Jan , V20 (1) : P3 doi: 10.1186/s12870-019-2217-9
Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato.
Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda. barastere@gmail.com.; Institut des Sciences Agronomiques du Burundi, Avenue de la Cathedrale - B.P. 795, Bujumbura, Burundi. barastere@gmail.com.; Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996-4560, USA.; Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda.; International Potato Center (CIP), Avenida La Molina 1895, La Molina Apartado Postal, 1558, Lima, Peru.; International Livestock Research Institute, ILRI Campus, Naivasha Rd, Nairobi, 30709-00100, Kenya.; International Potato Center (CIP), Regional office sub-Sahara Africa, P.O. Box 25171-00603, Nairobi, Kenya.; International Potato Center (CIP), Plot 47, Ntinda II Road, P.O. Box 22274, Kampala, Uganda.
BACKGROUND: Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking. RESULTS: Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 x 10(- 7)), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence. CONCLUSION: Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.
PMID: 31898489
Planta , IF:3.39 , 2020 Jan , V251 (2) : P43 doi: 10.1007/s00425-019-03335-8
Systematic identification of genes associated with plant growth-defense tradeoffs under JA signaling in Arabidopsis.
State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China.; State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China. fanzj@nankai.edu.cn.
MAIN CONCLUSION: Co-expression and regulatory networks yield important insights into the growth-defense tradeoffs mechanism under jasmonic acid (JA) signals in Arabidopsis. Elevated defense is commonly associated with growth inhibition. However, a comprehensive atlas of the genes associated with the plant growth-defense tradeoffs under JA signaling is lacking. To gain an insight into the dynamic architecture of growth-defense tradeoffs, a coexpression network analysis was employed on publicly available high-resolution transcriptomes of Arabidopsis treated with coronatine (COR), a mimic of jasmonoyl-l-isoleucine. The genes involved in JA-mediated growth-defense tradeoffs were systematically revealed. Promoter enrichment analysis revealed the core regulatory module in which the genes underwent rapid activation, sustained upregulation after COR treatment, and mediated the growth-defense tradeoffs. Several transcription factors (TFs), including RAP2.6L, MYB44, WRKY40, and WRKY18, were identified as instantly activated components associated with pathogen and insect resistance. JA might rapidly activate RAV1 and KAN1 to repress brassinosteroid (BR) response genes, upregulate KAN1, the C2H2 TF families ZF2, ZF3, ZAT6, and STZ/ZAT10 to repress the biosynthesis, transport, and signaling of auxin to arrest growth. Independent datasets and preserved analyses validated the reproducibility of the results. Our study provided a comprehensive snapshot of genes that respond to JA signals and provided valuable resources for functional studies on the genetic modification of breeding population that exhibit robust growth and defense simultaneously.
PMID: 31907627
Funct Integr Genomics , IF:3.058 , 2020 Jan , V20 (1) : P133-149 doi: 10.1007/s10142-019-00701-3
A role of age-dependent DNA methylation reprogramming in regulating the regeneration capacity of Boea hygrometrica leaves.
Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. deng@ibcas.ac.cn.
Plants can regenerate new individuals under appropriate culture conditions. Although the molecular basis of shoot regeneration has steadily been unraveled, the role of age-dependent DNA methylation status in the regulation of explant regeneration remains practically unknown. Here, we established an effective auxin/cytokinin-induced shoot regeneration system for the resurrection plant Boea hygrometrica via direct organogenesis and observed that regeneration was postponed with increasing age of donor plants. Global transcriptome analysis revealed significant upregulation of genes required for hormone signaling and phenylpropanoid biosynthesis and downregulation of photosynthetic genes during regeneration. Transcriptional changes in the positive/negative regulators and cell wall-related proteins involved in plant regeneration, such as ELONGATED HYPOCOTYL5 (HY5), LATERAL ORGAN BOUNDARIES DOMAIN, SHOOT-MERISTEMLESS, and WUSCHEL, were associated with the regeneration process. Comparison of DNA methylation profiling between leaves from young seedlings (YL) and mature plants (ML) revealed increased asymmetrical methylation in ML, which was predominantly distributed in promoter regions of genes, such as HY5 and a member of ABA-responsive element (ABRE) binding protein/ABRE binding factor, as well as genes encoding glycine-rich cell wall structural protein, CENTRORADIALIS-like protein, and beta-glucosidase 40-like essential for shoot meristem and cell wall architecture. Their opposite transcription response in ML explants during regeneration compared with those from YL demonstrated the putative involvement of DNA methylation in regeneration. Moreover, a significant lower expression of DNA glycosylase-lyase required for DNA demethylation in ML was coincident with its postponed regeneration compared with those in YL. Taken together, our results suggest a role of promoter demethylation in B. hygrometrica regeneration.
PMID: 31414312
Environ Sci Pollut Res Int , IF:3.056 , 2020 Jan , V27 (1) : P380-390 doi: 10.1007/s11356-019-06760-0
Identification and expression analysis of conserved microRNAs during short and prolonged chromium stress in rice (Oryza sativa).
Amity Institute of Biotechnology, Amity University, Sector-125, Noida, U.P, 201313, India. sdubey1@amity.edu.; Transcriptome Laboratory, Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P, 201307, India.; Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.; Transcriptome Laboratory, Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P, 201307, India. vibha.rani@jiit.ac.in.
MicroRNAs (miRNAs) are one of the most critical epigenetic regulators of gene expression which modulate a spectrum of development and defence response processes in plants. Chromium (Cr) contamination in rice imposes a serious concern to human health as rice is used as staple food throughout the world. Although several studies have established the differential response of miRNAs in rice during heavy metal (arsenic, cadmium) and heat or cold stress, no report is available about the response of miRNAs during Cr stress. In the present study, we identified 512 and 568 known miRNAs from Cr treated and untreated samples, respectively. Expression analysis revealed that 13 conserved miRNAs (miR156, miR159, miR160, miR166, miR169, miR171, miR396, miR397, miR408, miR444, miR1883, miR2877, miR5072) depicted preferential up- or down-regulation (> 4-fold change; P value < 0.05). Target gene prediction of differentially expressed miRNAs and their functional annotation suggested the important role of miRNAs in defence and detoxification of Cr though ATP-binding cassette transporters (ABC transporters), transcription factors, heat shock proteins, auxin response, and metal ion transport. Real-time PCR analysis validated the differential expression of selected miRNAs and their putative target genes. In conclusion, our study identifies and predicts miRNA-mediated regulation of signalling pathway in rice during Cr stress.
PMID: 31792790
Environ Sci Pollut Res Int , IF:3.056 , 2020 Jan , V27 (2) : P2287-2300 doi: 10.1007/s11356-019-06959-1
Biochemical and molecular characterization of arsenic response from Azospirillum brasilense Cd, a bacterial strain used as plant inoculant.
Departamento de Biologia Molecular, FCEFQyN, Universidad Nacional de Rio Cuarto (UNRC), Ruta Nacional 36 Km 601, 5800, Rio Cuarto, Cordoba, Argentina. marianavezza@gmail.com.; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina. marianavezza@gmail.com.; Departamento de Biologia Molecular, FCEFQyN, Universidad Nacional de Rio Cuarto (UNRC), Ruta Nacional 36 Km 601, 5800, Rio Cuarto, Cordoba, Argentina.; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina.
Azospirillum brasilense Cd is a bacterial strain widely used as an inoculant of several crops due to its plant growth promoting properties. However, its beneficial effects depend on its viability and functionality under adverse environmental conditions, including the presence of arsenic (As) in agricultural soils. Therefore, the aim of this work was to evaluate the response of A. brasilense Cd to arsenate (AsV) and arsenite (AsIII). This bacterium was tolerant to As concentrations frequently found in soils. Moreover, properties related to roots colonization (motility, biofilm, and exopolymers) and plant growth promotion (auxin, siderophore production, and N2 fixation) were not significantly affected by the metalloid. In order to deepen the understanding on As responses of A. brasilense Cd, As resistance genes were sequenced and characterized for the first time in this work. These genes could mediate the redox As transformation and its extrusion outside the cell, so they could have direct association with the As tolerance observed. In addition, its As oxidation/reduction capacity could contribute to change the AsV/AsIII ratio in the environment. In conclusion, the results allowed to elucidate the As response of A. brasilense Cd and generate interest for its potential use in polluted environments.
PMID: 31776908
J Plant Physiol , IF:3.013 , 2020 Jan , V244 : P153049 doi: 10.1016/j.jplph.2019.153049
Downregulation of three novel candidate genes is important for freezing tolerance of field and laboratory cold acclimated barley.
Department of Plant Physiology, University of Agriculture, Podluzna 3, 30-239, Krakow, Poland. Electronic address: bednarczyk.an@gmail.com.; Department of Plant Physiology, University of Agriculture, Podluzna 3, 30-239, Krakow, Poland. Electronic address: rrrapacz@cyf-kr.edu.pl.
Diversity arrays technology (DArT) marker sequences for barley were used for identifying new potential candidate genes for freezing tolerance (FT). We used quantitative trait loci (QTL) genetic linkage maps for FT and photosynthetic acclimation to cold for six- and two-row barley populations, and a set of 20 DArT markers obtained using the association mapping of parameters for photosynthetic acclimation to low temperatures in barley for the bioinformatics analyses. Several nucleotide and amino acid sequence, annotation databases and associated algorithms were used to identify the similarities of six of the marker sequences to potential genes involved in plant low temperature response. Gene ontology (GO) annotations based on similarities to database sequences were assigned to these marker sequences, and indicated potential involvement in signal transduction pathways in response to stress factors and epigenetic processes, as well as auxin transport mechanisms. Furthermore, relative gene expressions for three of six of new identified genes (Hv.ATPase, Hv.DDM1, and Hv.BIG) were assessed within four barley genotypes of different FT. A physiological assessment of FT was conducted based on plant survival rates in two field-laboratory and one laboratory experiments. The results suggested that plant survival rate after freezing but not the degree of freezing-induced leaf damage between the tested accessions can be correlated with the degree of low-temperature downregulation of the studied candidate genes, which encoded proteins involved in the control of plant growth and development. Additionally, candidate genes for qRT-PCR suitable for the analysis of cold acclimation response in barley were suggested after validation.
PMID: 31760347
J Microbiol , IF:2.845 , 2020 Jan , V58 (1) : P24-29 doi: 10.1007/s12275-020-9346-6
Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds.
Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.; Department of Bioactive Materials, Chonbuk National University, Jeonju, 54896, Republic of Korea.; Research Institute of Biotechnology Breeding, Asia Seed Co., Icheon, 17414, Republic of Korea.; Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea. kimsw@kribb.re.kr.; Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea. jiyoung1@kribb.re.kr.
Strain ATSA2(T) was isolated from surface-sterilized kimchi cabbage (Brassica rapa subsp. pekinensis) seeds and represents a novel bacterium based on the polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ATSA2(T) formed a lineage within genus Saccharibacillus and was most closely to Saccharibacillus deserti WLG055(T) (98.1%) and Saccharibacillus qing-shengii H6(T) (97.9%). The whole-genome of ATSA2(T) comprised a 5,619,468 bp of circular chromosome with 58.4% G + C content. The DNA-DNA relatedness values between strain ATSA2(T) and its closely related type strains S. deserti WLJ055 and S. qingshengii H6(T) were 26.0% and 24.0%, respectively. Multiple gene clusters associated with plant growth promotion activities (stress response, nitrogen and phosphorus metabolism, and auxin biosynthesis) were annotated in the genome. Strain ATSA2(T) was Gram-positive, endospore-forming, facultatively anaerobic, and rod-shaped It grew at 15-37 degrees C (optimum 25 degrees C), pH 6.0-10.0 (optimum pH 8.0), and in the presence of 0-5% (w/v) NaCl (optimum 1%). The major cellular fatty acids (> 10%) of strain ATSA2(T) were anteiso-C15:0 and C16:0. MK-7 was the major isoprenoid quinone. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, and three unknown glycolipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxo-nomic features, strain ATSA2(T) is proposed to represent a novel species of genus Saccharibacillus, for which the name is Saccharibacillus brassicae sp. nov. The type strain is ATSA2(T) (KCTC 43072(T) = CCTCC AB 2019223(T)).
PMID: 31768939
Plants (Basel) , IF:2.762 , 2020 Jan , V9 (2) doi: 10.3390/plants9020166
Role of the Cytokinin-Activated Type-B Response Regulators in Hormone Crosstalk.
Dartmouth College, Department of Biological Sciences, Hanover, NH 03755, USA.
Cytokinin is an important phytohormone that employs a multistep phosphorelay to transduce the signal from receptors to the nucleus, culminating in activation of type-B response regulators which function as transcription factors. Recent chromatin immunoprecipitation-sequencing (ChIP-seq) studies have identified targets of type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs) and integrated these into the cytokinin-activated transcriptional network. Primary targets of the type-B ARRs are enriched for genes involved in hormonal regulation, emphasizing the extensive crosstalk that can occur between cytokinin, auxin, abscisic acid, brassinosteroids, gibberellic acid, ethylene, jasmonic acid, and salicylic acid. Examination of hormone-related targets reveals multiple regulatory points including biosynthesis, degradation/inactivation, transport, and signal transduction. Here, we consider this early response to cytokinin in terms of the hormones involved, points of regulatory crosstalk, and physiological significance.
PMID: 32019090
J Plant Res , IF:2.185 , 2020 Jan , V133 (1) : P73-94 doi: 10.1007/s10265-019-01156-0
Hormonal and transcriptional analyses of fruit development and ripening in different varieties of black pepper (Piper nigrum).
Department of Research and Quality Development, Malaysian Pepper Board, Lot 1115, Jalan Utama, Pending Industrial Area, 93450, Kuching, Sarawak, Malaysia. cykhew@mpb.gov.my.; Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Jalan Simpang Tiga, 93350, Kuching, Sarawak, Malaysia. cykhew@mpb.gov.my.; Group of Environmental Response Systems, Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046, Japan.; Institute of Biological Sciences, Faculty of Science and Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia.; Department of Research and Quality Development, Malaysian Pepper Board, Lot 1115, Jalan Utama, Pending Industrial Area, 93450, Kuching, Sarawak, Malaysia.; Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Jalan Simpang Tiga, 93350, Kuching, Sarawak, Malaysia.
Black pepper (Piper nigrum L.) is one of the most popular and oldest spices in the world with culinary uses and various pharmacological properties. In order to satisfy the growing worldwide demand for black pepper, improved productivity of pepper is highly desirable. A primary constraint in black pepper production is the non-synchronous nature of flower development and non-uniform fruit ripening within a spike. The uneven ripening of pepper berries results in a high labour requirement for selective harvesting contributes to low productivity and affects the quality of the pepper products. In Malaysia, there are a few recommended varieties for black pepper planting, each having some limitations in addition to the useful characteristics. Therefore, a comparative study of different black pepper varieties will provide a better understanding of the mechanisms regulates fruit development and ripening. Plant hormones are known to influence the fruit development process and their roles in black pepper flower and fruit development were inferred based on the probe-based gene expression analysis and the quantification of the multiple plant hormones using high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS). In this study, jasmonic acid and salicylic acid were found to play roles in flowering and fruit setting, whereas auxin, gibberellin and cytokinins are important for fruit growth. Abscisic acid has positive role in fruit maturation and ripening in the development process. Distinct pattern of plant hormones related gene expression profiles with the hormones accumulation profiles suggested a complex network of regulation is involved in the signaling process and crosstalk between plant hormones was another layer of regulation in the black pepper fruit development mechanisms. The current study provides clues to help in elucidating the timing of the action of each specific plant hormone during fruit development and ripening which could be applied to enhance our ability to control the ripening process, leading to improving procedures for the production and post-harvest handling of pepper fruits.
PMID: 31853665
J Plant Res , IF:2.185 , 2020 Jan , V133 (1) : P3-14 doi: 10.1007/s10265-019-01153-3
Molecular mechanisms mediating root hydrotropism: what we have observed since the rediscovery of hydrotropism.
Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, 990-8560, Japan. miyazawa@sci.kj.yamagata-u.ac.jp.; Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
Roots display directional growth toward moisture in response to a water potential gradient. Root hydrotropism is thought to facilitate plant adaptation to continuously changing water availability. Hydrotropism has not been as extensively studied as gravitropism. However, comparisons of hydrotropic and gravitropic responses identified mechanisms that are unique to hydrotropism. Regulatory mechanisms underlying the hydrotropic response appear to differ among different species. We recently performed molecular and genetic analyses of root hydrotropism in Arabidopsis thaliana. In this review, we summarize the current knowledge of specific mechanisms mediating root hydrotropism in several plant species.
PMID: 31797131
Plant Biol (Stuttg) , IF:2.167 , 2020 Jan , V22 (1) : P3-12 doi: 10.1111/plb.13052
De novo transcriptome characterisation of two auxin-related genes associated with plant growth habit in Astragalus adsurgens Pall.
Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, China.; College of Pratacultural Science, Gansu Agricultural University, Lanzhou, China.; Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China.
Astragalus adsurgens Pall., a perennial legume native to China, is commonly used as a forage crop. And it has great value for sustainable development of grasslands in arid and semi arid regions. However, to date, little is known regarding the A. adsurgens genome, and no studies have determined whether it would be possible to improve the germplasm of A. adsurgens through genetic modification. In this study, we used an RNA-seq protocol to generate a de novo transcriptome including 151,516 unigenes of A. adsurgens. We compared the transcriptomes of A. adsurgens having different growth habits (prostrate/erect) and identified 14,133 single nucleotide polymorphism sites (SNP) in 8,139 unigenes. Differential expression gene (DEG) analysis suggested that 10,982 unigenes were up-regulated in the prostrate plant relative to the erect plant, while 10,607 unigenes were down-regulated. Of the 21,589 DEG, Unigene72782_All (LAX4) and CL12494.Contig3_All (TIR1), an auxin transporter gene and an auxin transport inhibitor gene, respectively, were predicted to influence the growth habit of A. adsurgens, which were verified by qRT-PCR in these phenotypes. These results suggest that auxin transport was more active in the prostrate plant than in the erect plant, resulting in asymmetric distribution of auxin that affects the growth habit of A. adsurgens. Overall, this study may provide a basis for future research on key genes in A. adsurgens and may deepen our understanding of the molecular mechanisms regulating plant growth habit.
PMID: 31571396
Plant Biol (Stuttg) , IF:2.167 , 2020 Jan , V22 (1) : P129-133 doi: 10.1111/plb.13040
Active BR signalling adjusts the subcellular localisation of BES1/HSP90 complex formation.
Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece.; Department of Cell Biology Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University Olomouc, Slechtitelu 27, Olomouc, 783 71, Czech Republic.
Heat shock proteins 90 (HSP90) are essential and play critical roles in the adaptation of organisms to diverse stimuli. In plants, HSP90 are involved in auxin, jasmonate and brassinosteroid (BR) signalling pathways. The BR-promoted activation of the BES1 transcription factor regulates BR-responsive genes. Using genetic, physiological, fluorescence live cell imaging, molecular and biochemical approaches, such as phenotypic analysis, co-immunoprecipitation assay, yeast-two hybrid and Bimolecular fluorescence complementation (BiFC), we studied complex formation between BES1 and HSP90 under control conditions and active BR signalling. Further, we determined the effect of the pharmacological inhibition of HSP90 ATPase activity on hypocotyl elongation of bes1-D mutant. We determined that HSP90 interact with BES1 in the nucleus and in the cytoplasm. During active BR signalling, nuclear complexes were absent while cytoplasmic HSP90/BES1 complexes were prominent. Our results showed that the hypocotyl length of bes1-D mutants was highly reduced when HSP90 was challenged by the geldanamycin (GDA) inhibitor of the ATPase activity of HSP90. Active BR signalling could not rescue the GDA effect on the hypocotyl elongation of bes1-D. Our results reveal that the constitutively active BES1 in the bes1-D mutant is hypersensitive to GDA. The interaction of HSP90 with BES1 argues that HSP90 facilitate the nuclear metastable conformation of BES1 to regulate BR-dependent gene expression, and our data show that HSP90 assist in the compartmentalised cycle of BES1 during active BR signalling.
PMID: 31469500
J Radiat Res , IF:1.95 , 2020 Jan , V61 (1) : P44-57 doi: 10.1093/jrr/rrz075
Transcriptome sequencing reveals hotspot mutation regions and dwarfing mechanisms in wheat mutants induced by gamma-ray irradiation and EMS.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
Induced mutation is an important approach for creating novel plant germplasms. The introduction of dwarf or semi-dwarf genes into wheat has led to great advancements in yield improvement. In this study, four elite dwarf wheat mutants, named dm1-dm4, induced from gamma-ray irradiation or ethyl methanesulfonate (EMS) mutagenesis, were used to identify transcriptome variations and dwarfing mechanisms. The results showed that the hotspot regions of mutations distributed on the chromosomes were consistent among the four mutant lines and these regions were mainly located around the 50, 360 and 400 Mb positions of chromosome 1A and the distal regions of chromosomes 2A and 2BL. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that 'protein processing in endoplasmic reticulum' was the most common significantly enriched pathway based on the differentially expressed genes (DEGs) between wildtype (WT) and the mutants. Notably, 18 out of 20 genes involved in this process encode heat shock proteins (HSPs). The results implied that HSPs might participate in wheat dwarfism response and function in the dwarfism process through protein folding and/or degradation. Moreover, seven genes in dm4 involved in modulating auxin levels were down-regulated and dm4 was more sensitive to auxin treatment compared with WT, indicating the important roles of auxin in regulation of dwarf phenotype in dm4. This study not only identified transcriptome sequence variation induced by physical and chemical mutagenesis but also revealed potential dwarfing mechanisms in the wheat mutant lines.
PMID: 31825082
Bull Math Biol , IF:1.812 , 2020 Jan , V82 (2) : P17 doi: 10.1007/s11538-019-00685-y
Mathematical Modelling of Auxin Transport in Plant Tissues: Flux Meets Signalling and Growth.
Department of Mathematics, Fulton Building, University of Dundee, Dundee, DD1 4HN, UK.; Department of Mathematics, Colin Maclaurin Building, Heriot-Watt University, Edinburgh, EH14 4AS, UK. m.ptashnyk@hw.ac.uk.
Plant hormone auxin has critical roles in plant growth, dependent on its heterogeneous distribution in plant tissues. Exactly how auxin transport and developmental processes such as growth coordinate to achieve the precise patterns of auxin observed experimentally is not well understood. Here we use mathematical modelling to examine the interplay between auxin dynamics and growth and their contribution to formation of patterns in auxin distribution in plant tissues. Mathematical models describing the auxin-related signalling pathway, PIN and AUX1 dynamics, auxin transport, and cell growth in plant tissues are derived. A key assumption of our models is the regulation of PIN proteins by the auxin-responsive ARF-Aux/IAA signalling pathway, with upregulation of PIN biosynthesis by ARFs. Models are analysed and solved numerically to examine the long-time behaviour and auxin distribution. Changes in auxin-related signalling processes are shown to be able to trigger transition between passage- and spot-type patterns in auxin distribution. The model was also shown to be able to generate isolated cells with oscillatory dynamics in levels of components of the auxin signalling pathway which could explain oscillations in levels of ARF targets that have been observed experimentally. Cell growth was shown to have influence on PIN polarisation and determination of auxin distribution patterns. Numerical simulation results indicate that auxin-related signalling processes can explain the different patterns in auxin distributions observed in plant tissues, whereas the interplay between auxin transport and growth can explain the 'reverse-fountain' pattern in auxin distribution observed at plant root tips.
PMID: 31970524
Pak J Biol Sci , 2020 Jan , V23 (1) : P35-44 doi: 10.3923/pjbs.2020.35.44
Zinc Nutrition and its Activated Roles on Growth, Inflorescences Attributes and Some Physiological Parameters of Tagetes erecta L. Plants.
BACKGROUND AND OBJECTIVE: There are scarcity scientific reports on the response of medicinal plants to zinc nutrition, despite its remarkable role in growth, cell division, photosynthesis and tryptophan formation, which is involved auxin (IAA) synthesis. Therefore, further studies are required to understand the effects of zinc on one of these important plants, marigold plant. MATERIALS AND METHODS: For this, a greenhouse experiment was conducted to evaluate the promoting impacts of zinc-nutrition (0, 50, 75, 100 mg L-1) on marigold growth, plant height, branch number, herb and root fresh mass (FM), herb and root dry mass (DM), flowering attributes, inflorescence number/plant (IN), inflorescence diameter (ID), inflorescence (IW) weight (fresh and dry), days to first bud emergence, leaf relative water content (RWC) as well as some physiological responses, pigments, total carbohydrate, N, P, K, Zn contents of marigold plants. RESULTS: The results indicated that zinc-fertilizer at 100 mg L-1 was the superior treatment in improving the previous parameters relative to the other levels and control. Supplying Zn significantly enhanced growth parameters, flower attributes, RWC as well as nutrient contents of marigold leaves. Chlorophyll, carotenoids content and carbohydrates (%) were enhanced due to suppling Zn. Zn treatments raised the contents of N, P, K and Zn in leaves relative to unfertilized ones. A comparison of the usage treatments showed that the higher dose of Zn was better than the lower one or control but insignificant differences were observed between this treatment and the intermediate one (75 mg L-1) for some studies parameters. CONCLUSION: The obtained results suggest that exogenous application of Zn could be essentially for the nutrition program of marigold plants to provide plants by the optimum dose of Zn-fertilizer for improving the growth and, quantity and quality of inflorescence parameters.
PMID: 31930881