Nucleic Acids Res , IF:16.971 , 2024 Jun , V52 (11) : P6253-6268 doi: 10.1093/nar/gkae272
Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals.
Oncology Division, CHU de Quebec-Universite Laval Research Center, Quebec, QC G1R 3S3, Canada.; Universite Laval Cancer Research Centre, Quebec, QC G1R 3S3, Canada.
MicroRNAs (miRNAs) are essential regulators of several biological processes. They are loaded onto Argonaute (AGO) proteins to achieve their repressive function, forming the microRNA-Induced Silencing Complex known as miRISC. While several AGO proteins are expressed in plants and animals, it is still unclear why specific AGOs are strictly binding miRNAs. Here, we identified the co-chaperone DNJ-12 as a new interactor of ALG-1, one of the two major miRNA-specific AGOs in Caenorhabditis elegans. DNJ-12 does not interact with ALG-2, the other major miRNA-specific AGO, and PRG-1 and RDE-1, two AGOs involved in other small RNA pathways, making it a specific actor in ALG-1-dependent miRNA-mediated gene silencing. The loss of DNJ-12 causes developmental defects associated with defective miRNA function. Using the Auxin Inducible Degron system, a powerful tool to acutely degrade proteins in specific tissues, we show that DNJ-12 depletion hampers ALG-1 interaction with HSP70, a chaperone required for miRISC loading in vitro. Moreover, DNJ-12 depletion leads to the decrease of several miRNAs and prevents their loading onto ALG-1. This study uncovers the importance of a co-chaperone for the miRNA function in vivo and provides insights to explain how different small RNAs associate with specific AGO in animals.
PMID: 38613392
Nat Plants , IF:15.793 , 2024 Jun , V10 (6) : P846-847 doi: 10.1038/s41477-024-01707-x
A family of maternally expressed auxin response factors trigger endosperm cellularization.
PMID: 38822059
Nat Plants , IF:15.793 , 2024 Jun , V10 (6) : P1018-1026 doi: 10.1038/s41477-024-01706-y
Parental conflict driven regulation of endosperm cellularization by a family of Auxin Response Factors.
Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden.; INRAE Centre Ile-de-France - Versailles-Saclay, France, Versailles-Sacley, France.; Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany. koehler@mpimp-golm.mpg.de.; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden. koehler@mpimp-golm.mpg.de.
The endosperm is a reproductive tissue supporting embryo development. In most flowering plants, the initial divisions of endosperm nuclei are not succeeded by cellularization; this process occurs only after a specific number of mitotic cycles have taken place. The timing of cellularization significantly influences seed viability and size. Previous research implicated auxin as a key factor in initiating nuclear divisions and determining the timing of cellularization. Here we uncover the involvement of a family of clustered auxin response factors (cARFs) as dosage-sensitive regulators of endosperm cellularization. cARFs, maternally expressed and paternally silenced, are shown to induce cellularization, thereby restricting seed growth. Our findings align with the predictions of the parental conflict theory, suggesting that cARFs represent major molecular targets in this conflict. We further demonstrate a recurring amplification of cARFs in the Brassicaceae, suggesting an evolutionary response to parental conflict by reinforcing maternal control over endosperm cellularization. Our study highlights that antagonistic parental control on endosperm cellularization converges on auxin biosynthesis and signalling.
PMID: 38806655
Plant Cell , IF:11.277 , 2024 Jun doi: 10.1093/plcell/koae184
NIN-LIKE PROTEIN3.2 inhibits repressor Aux/IAA14 expression and enhances root biomass in maize seedlings under low nitrogen.
State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.; State Key Laboratory of Plant Environmental Resilience, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.; State Key Laboratory of Plant Environmental Resilience, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou 310058, China.; College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.; State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China.; Center for Crop Functional Genomics and Molecular Breeding of China Agricultural University.
Plants generally enhance their root growth in the form of greater biomass and/or root length to boost nutrient uptake in response to short-term low nitrogen (LN). However, the underlying mechanisms of short-term LN-mediated root growth remain largely elusive. Our genome-wide association study, haplotype analysis, and phenotyping of transgenic plants showed that the crucial nitrate signaling component NIN-LIKE PROTEIN3.2 (ZmNLP3.2), a positive regulator of root biomass, is associated with natural variations in root biomass of maize (Zea mays L.) seedlings under LN. The monocot-specific gene AUXIN/INDOLE-3-ACETIC ACID14 (ZmAux/IAA14) exhibited opposite expression patterns to ZmNLP3.2 in ZmNLP3.2 knockout and overexpression lines, suggesting that ZmNLP3.2 hampers ZmAux/IAA14 transcription. Importantly, ZmAux/IAA14 knockout seedlings showed a greater root dry weight (RDW), whereas ZmAux/IAA14 overexpression reduced RDW under LN compared with wild-type plants, indicating that ZmAux/IAA14 negatively regulates the RDW of LN-grown seedlings. Moreover, in vitro and vivo assays indicated that AUXIN RESPONSE FACTOR19 (ZmARF19) binds to and transcriptionally activates ZmAux/IAA14, which was weakened by the ZmNLP3.2-ZmARF19 interaction. The zmnlp3.2 ZmAux/IAA14-OE seedlings exhibited further reduced RDW compared to ZmAux/IAA14 overexpression lines when subjected to LN treatment, corroborating the ZmNLP3.2-ZmAux/IAA14 interaction. Thus, our study reveals a ZmNLP3.2-ZmARF19-ZmAux/IAA14 module regulating root biomass in response to nitrogen limitation in maize.
PMID: 38917216
Proc Natl Acad Sci U S A , IF:11.205 , 2024 Jun , V121 (26) : Pe2321877121 doi: 10.1073/pnas.2321877121
A CUC1/auxin genetic module links cell polarity to patterned tissue growth and leaf shape diversity in crucifer plants.
Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany.; Universite Paris-Saclay, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France.; Department of Computer Science, University of Calgary, Calgary, AB T2N 1N4, Canada.
How tissue-level information encoded by fields of regulatory gene activity is translated into the patterns of cell polarity and growth that generate the diverse shapes of different species remains poorly understood. Here, we investigate this problem in the case of leaf shape differences between Arabidopsis thaliana, which has simple leaves, and its relative Cardamine hirsuta that has complex leaves divided into leaflets. We show that patterned expression of the transcription factor CUP-SHAPED COTYLEDON1 in C. hirsuta (ChCUC1) is a key determinant of leaf shape differences between the two species. Through inducible genetic perturbations, time-lapse imaging of growth, and computational modeling, we find that ChCUC1 provides instructive input into auxin-based leaf margin patterning. This input arises via transcriptional regulation of multiple auxin homeostasis components, including direct activation of WAG kinases that are known to regulate the polarity of PIN-FORMED auxin transporters. Thus, we have uncovered a mechanism that bridges biological scales by linking spatially distributed and species-specific transcription factor expression to cell-level polarity and growth, to shape diverse leaf forms.
PMID: 38905239
Curr Biol , IF:10.834 , 2024 Jun , V34 (11) : P2330-2343.e4 doi: 10.1016/j.cub.2024.04.029
Photoperiod-1 regulates the wheat inflorescence transcriptome to influence spikelet architecture and flowering time.
Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.; School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia.; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia. Electronic address: scott.boden@adelaide.edu.au.
Photoperiod insensitivity has been selected by breeders to help adapt crops to diverse environments and farming practices. In wheat, insensitive alleles of Photoperiod-1 (Ppd-1) relieve the requirement of long daylengths to flower by promoting expression of floral promoting genes early in the season; however, these alleles also limit yield by reducing the number and fertility of grain-producing florets through processes that are poorly understood. Here, we performed transcriptome analysis of the developing inflorescence using near-isogenic lines that contain either photoperiod-insensitive or null alleles of Ppd-1, during stages when spikelet number is determined and floret development initiates. We report that Ppd-1 influences the stage-specific expression of genes with roles in auxin signaling, meristem identity, and protein turnover, and analysis of differentially expressed transcripts identified bZIP and ALOG transcription factors, namely PDB1 and ALOG1, which regulate flowering time and spikelet architecture. These findings enhance our understanding of genes that regulate inflorescence development and introduce new targets for improving yield potential.
PMID: 38781956
J Hazard Mater , IF:10.588 , 2024 Jul , V473 : P134719 doi: 10.1016/j.jhazmat.2024.134719
NtARF11 positively regulates cadmium tolerance in tobacco by inhibiting expression of the nitrate transporter NtNRT1.1.
State Key Laboratory of Tobacco Cultivation, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China. Electronic address: jiahongfang@126.com.; State Key Laboratory of Tobacco Cultivation, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.; State Key Laboratory of Tobacco Cultivation, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.; State Key Laboratory of Tobacco Cultivation, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China. Electronic address: shf_email2011@126.com.; State Key Laboratory of Tobacco Cultivation, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China. Electronic address: ycszp@henau.edu.cn.
Heavy metal cadmium (Cd) is widespread in contaminated soil and an important factor limiting plant growth. NO(3)(-) (nitrate) affects Cd uptake and thus changes Cd tolerance in plants; however, the underlying molecular regulatory mechanisms have not yet been elucidated. Here, we analyzed a novel gene, NtARF11 (auxin response factor), which regulates Cd tolerance in tobacco via the NO(3)(-) uptake pathway, through experiments with NtARF11-knockout and NtARF11-overexpression transgenic tobacco lines. NtARF11 was highly expressed under Cd stress in tobacco plants. Under Cd stress, overexpression of NtARF11 enhanced Cd tolerance in tobacco compared to that in wild-type tobacco, as shown by the low Cd concentration, high chlorophyll concentration, and low accumulation of reactive oxygen species in NtARF11-overexpressing tobacco. Moreover, low NO(3)(-) concentrations were observed in NtARF11-overexpressing tobacco plants. Further analyses revealed direct binding of NtARF11 to the promoter of the nitrate transporter NtNRT1.1, thereby negatively regulating its expression in tobacco. Notably, NtNRT1.1 knockout reduced NO(3)(-) uptake, which resulted in low Cd concentrations in tobacco. Altogether, these results demonstrate that the NtARF11-NtNRT1.1 module functions as a positive regulator of Cd tolerance by reducing the Cd uptake in tobacco, providing new insights for improving Cd tolerance of plants through genetic engineering.
PMID: 38797073
J Hazard Mater , IF:10.588 , 2024 Jul , V473 : P134587 doi: 10.1016/j.jhazmat.2024.134587
Suppression of OsSAUR2 gene expression immobilizes soil arsenic bioavailability by modulating root exudation and rhizosphere microbial assembly in rice.
The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China.; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China. Electronic address: liuqp@zafu.edu.cn.
One of the factors influencing the behavior of arsenic (As) in environment is microbial-mediated As transformation. However, the detailed regulatory role of gene expression on the changes of root exudation, rhizosphere microorganisms, and soil As occurrence forms remains unclear. In this study, we evidence that loss-of-function of OsSAUR2 gene, a member of the SMALL AUXIN-UP RNA family in rice, results in significantly higher As uptake in roots but greatly lower As accumulation in grains via affecting the expression of OsLsi1, OsLsi2 in roots and OsABCC1 in stems. Further, the alteration of OsSAUR2 expression extensively affects the metabolomic of root exudation, and thereby leading to the variations in the composition of rhizosphere microbial communities in rice. The microbial community in the rhizosphere of Ossaur2 plants strongly immobilizes the occurrence forms of As in soil. Interestingly, Homovanillic acid (HA) and 3-Coumaric acid (CA), two differential metabolites screened from root exudation, can facilitate soil iron reduction, enhance As bioavailability, and stimulate As uptake and accumulation in rice. These findings add our further understanding in the relationship of OsSAUR2 expression with the release of root exudation and rhizosphere microbial assembly under As stress in rice, and provide potential rice genetic resources and root exudation in phytoremediation of As-contaminated paddy soil.
PMID: 38772107
New Phytol , IF:10.151 , 2024 Jun , V242 (6) : P2746-2762 doi: 10.1111/nph.19766
A lateral organ boundaries domain transcription factor acts downstream of the auxin response factor 2 to control nodulation and root architecture in Medicago truncatula.
Instituto de Biotecnologia y Biologia Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Cientifico y Tecnologico-La Plata, Consejo Nacional de Investigaciones Cientificas y Tecnicas, 1900, La Plata, Argentina.; Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France.; Laboratoire des Interactions Plantes-Microorganismes, Universite de Toulouse, INRAE, CNRS, 31326, Castanet-Tolosan, France.; Instituto de Agrobiotecnologia del Litoral, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
Legume plants develop two types of root postembryonic organs, lateral roots and symbiotic nodules, using shared regulatory components. The module composed by the microRNA390, the Trans-Acting SIRNA3 (TAS3) RNA and the Auxin Response Factors (ARF)2, ARF3, and ARF4 (miR390/TAS3/ARFs) mediates the control of both lateral roots and symbiotic nodules in legumes. Here, a transcriptomic approach identified a member of the Lateral Organ Boundaries Domain (LBD) family of transcription factors in Medicago truncatula, designated MtLBD17/29a, which is regulated by the miR390/TAS3/ARFs module. ChIP-PCR experiments evidenced that MtARF2 binds to an Auxin Response Element present in the MtLBD17/29a promoter. MtLBD17/29a is expressed in root meristems, lateral root primordia, and noninfected cells of symbiotic nodules. Knockdown of MtLBD17/29a reduced the length of primary and lateral roots and enhanced lateral root formation, whereas overexpression of MtLBD17/29a produced the opposite phenotype. Interestingly, both knockdown and overexpression of MtLBD17/29a reduced nodule number and infection events and impaired the induction of the symbiotic genes Nodulation Signaling Pathway (NSP) 1 and 2. Our results demonstrate that MtLBD17/29a is regulated by the miR390/TAS3/ARFs module and a direct target of MtARF2, revealing a new lateral root regulatory hub recruited by legumes to act in the root nodule symbiotic program.
PMID: 38666352
New Phytol , IF:10.151 , 2024 Jun , V242 (5) : P2059-2076 doi: 10.1111/nph.19737
Genome-wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and cross talk.
Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA.; Statistics Department, Oregon State University, Corvallis, OR, 97331, USA.; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA.
Wide variation in amenability to transformation and regeneration (TR) among many plant species and genotypes presents a challenge to the use of genetic engineering in research and breeding. To help understand the causes of this variation, we performed association mapping and network analysis using a population of 1204 wild trees of Populus trichocarpa (black cottonwood). To enable precise and high-throughput phenotyping of callus and shoot TR, we developed a computer vision system that cross-referenced complementary red, green, and blue (RGB) and fluorescent-hyperspectral images. We performed association mapping using single-marker and combined variant methods, followed by statistical tests for epistasis and integration of published multi-omic datasets to identify likely regulatory hubs. We report 409 candidate genes implicated by associations within 5 kb of coding sequences, and epistasis tests implicated 81 of these candidate genes as regulators of one another. Gene ontology terms related to protein-protein interactions and transcriptional regulation are overrepresented, among others. In addition to auxin and cytokinin pathways long established as critical to TR, our results highlight the importance of stress and wounding pathways. Potential regulatory hubs of signaling within and across these pathways include GROWTH REGULATORY FACTOR 1 (GRF1), PHOSPHATIDYLINOSITOL 4-KINASE beta1 (PI-4Kbeta1), and OBF-BINDING PROTEIN 1 (OBP1).
PMID: 38650352
New Phytol , IF:10.151 , 2024 Jun , V242 (5) : P1996-2010 doi: 10.1111/nph.19728
Ethylene controls three-dimensional growth involving reduced auxin levels in the moss Physcomitrium patens.
College of Life Sciences, Capital Normal University, Beijing, 100048, China.; Institute of Radiation Technology, Beijing Academy of Science and Technology, Beijing, 100050, China.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
The conquest of land by plants was concomitant with, and possibly enabled by, the evolution of three-dimensional (3D) growth. The moss Physcomitrium patens provides a model system for elucidating molecular mechanisms in the initiation of 3D growth. Here, we investigate whether the phytohormone ethylene, which is believed to have been a signal before land plant emergence, plays a role in 3D growth regulation in P. patens. We report ethylene controls 3D gametophore formation, based on results from exogenously applied ethylene and genetic manipulation of PpEIN2, which is a central component in the ethylene signaling pathway. Overexpression (OE) of PpEIN2 activates ethylene responses and leads to earlier formation of gametophores with fewer gametophores produced thereafter, phenocopying ethylene-treated wild-type. Conversely, Ppein2 knockout mutants, which are ethylene insensitive, show initially delayed gametophore formation with more gametophores produced later. Furthermore, pharmacological and biochemical analyses reveal auxin levels are decreased in the OE lines but increased in the knockout mutants. Our results suggest that evolutionarily, ethylene and auxin molecular networks were recruited to build the plant body plan in ancestral land plants. This might have played a role in enabling ancient plants to acclimate to the continental surfaces of the planet.
PMID: 38571393
Plant Biotechnol J , IF:9.803 , 2024 Jul , V22 (7) : P2054-2074 doi: 10.1111/pbi.14325
CaIAA2-CaARF9 module mediates the trade-off between pepper growth and immunity.
Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China.; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China.; Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.; Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.
To challenge the invasion of various pathogens, plants re-direct their resources from plant growth to an innate immune defence system. However, the underlying mechanism that coordinates the induction of the host immune response and the suppression of plant growth remains unclear. Here we demonstrate that an auxin response factor, CaARF9, has dual roles in enhancing the immune resistance to Ralstonia solanacearum infection and in retarding plant growth by repressing the expression of its target genes as exemplified by Casmc4, CaLBD37, CaAPK1b and CaRROP1. The expression of these target genes not only stimulates plant growth but also negatively impacts pepper resistance to R. solanacearum. Under normal conditions, the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 is active when promoter-bound CaARF9 is complexed with CaIAA2. Under R. solanacearum infection, however, degradation of CaIAA2 is triggered by SA and JA-mediated signalling defence by the ubiquitin-proteasome system, which enables CaARF9 in the absence of CaIAA2 to repress the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 and, in turn, impeding plant growth while facilitating plant defence to R. solanacearum infection. Our findings uncover an exquisite mechanism underlying the trade-off between plant growth and immunity mediated by the transcriptional repressor CaARF9 and its deactivation when complexed with CaIAA2.
PMID: 38450864
Plant Biotechnol J , IF:9.803 , 2024 Jun , V22 (6) : P1636-1648 doi: 10.1111/pbi.14292
Homoeologous exchanges contribute to branch angle variations in rapeseed: Insights from transcriptome, QTL-seq and gene functional analysis.
Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.; National Key Laboratory of Crop Genetic Improvement/National Center of Rapeseed Improvement/Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
Branch angle (BA) is a critical morphological trait that significantly influences planting density, light interception and ultimately yield in plants. Despite its importance, the regulatory mechanism governing BA in rapeseed remains poorly understood. In this study, we generated 109 transcriptome data sets for 37 rapeseed accessions with divergent BA phenotypes. Relative to adaxial branch segments, abaxial segments accumulated higher levels of auxin and exhibited lower expression of six TCP1 homologues and one GA20ox3. A co-expression network analysis identified two modules highly correlated with BA. The modules contained homologues to known BA control genes, such as FUL, YUCCA6, TCP1 and SGR3. Notably, a homoeologous exchange (HE), occurring at the telomeres of A09, was prevalent in large BA accessions, while an A02-C02 HE was common in small BA accessions. In their corresponding regions, these HEs explained the formation of hub gene hotspots in the two modules. QTL-seq analysis confirmed that the presence of a large A07-C06 HE (~8.1 Mb) was also associated with a small BA phenotype, and BnaA07.WRKY40.b within it was predicted as candidate gene. Overexpressing BnaA07.WRKY40.b in rapeseed increased BA by up to 20 degrees , while RNAi- and CRISPR-mediated mutants (BnaA07.WRKY40.b and BnaC06.WRKY40.b) exhibited decreased BA by up to 11.4 degrees . BnaA07.WRKY40.b was exclusively localized to the nucleus and exhibited strong expression correlations with many genes related to gravitropism and plant architecture. Taken together, our study highlights the influence of HEs on rapeseed plant architecture and confirms the role of WRKY40 homologues as novel regulators of BA.
PMID: 38308663
EMBO Rep , IF:8.807 , 2024 Jun , V25 (6) : P2571-2591 doi: 10.1038/s44319-024-00142-5
NBR1-mediated selective autophagy of ARF7 modulates root branching.
Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.; Centro de Biotecnologia y Genomica de Plantas (Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC (INIA/CSIC)). Campus de Montegancedo, Pozuelo de Alarcon, 28223, Madrid, Spain.; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, 08193, Spain.; Consejo Superior de Investigaciones Cientificas (CSIC), Barcelona, 08001, Spain.; Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark. Eleazar.rodriguez@bio.ku.dk.
Auxin dictates root architecture via the Auxin Response Factor (ARF) family of transcription factors, which control lateral root (LR) formation. In Arabidopsis, ARF7 regulates the specification of prebranch sites (PBS) generating LRs through gene expression oscillations and plays a pivotal role during LR initiation. Despite the importance of ARF7 in this process, there is a surprising lack of knowledge about how ARF7 turnover is regulated and how this impacts root architecture. Here, we show that ARF7 accumulates in autophagy mutants and is degraded through NBR1-dependent selective autophagy. We demonstrate that the previously reported rhythmic changes to ARF7 abundance in roots are modulated via autophagy and might occur in other tissues. In addition, we show that the level of co-localization between ARF7 and autophagy markers oscillates and can be modulated by auxin to trigger ARF7 turnover. Furthermore, we observe that autophagy impairment prevents ARF7 oscillation and reduces both PBS establishment and LR formation. In conclusion, we report a novel role for autophagy during development, namely by enacting auxin-induced selective degradation of ARF7 to optimize periodic root branching.
PMID: 38684906
Plant Physiol , IF:8.34 , 2024 Jun doi: 10.1093/plphys/kiae346
Filling the gaps on root hair development under salt stress and phosphate starvation using current evidence coupled with a meta-analysis approach.
ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago, Chile.; Centro de Biotecnologia Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.; Centro de Genomica y Bioinformatica, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, Santiago, Chile.; Fundacion Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina.
Population expansion is a global issue, especially for food production. Meanwhile, global climate change is damaging our soils, making it difficult for crops to thrive and lowering both production and quality. Poor nutrition and salinity stress affect plant growth and development. Although the impact of individual plant stresses has been studied for decades, the real stress scenario is more complex due to the exposure to multiple stresses at the same time. Here we investigate using existing evidence and a meta-analysis approach to determine molecular linkages between two contemporaneous abiotic stimuli, phosphate (Pi) deficiency and salinity, on a single plant cell model, the root hairs (RHs), which is the first plant cell exposed to them. Understanding how these two stresses work molecularly in RHs may help us build super-adaptable crops and sustainable agriculture in the face of global climate change.
PMID: 38918899
Plant Physiol , IF:8.34 , 2024 Jun doi: 10.1093/plphys/kiae334
Of attachment and connection: Auxin signaling in the cambium promotes successful plant grafting.
Assistant Features Editor, Plant Physiology, American Society of Plant Biologists.; Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines.
PMID: 38865436
Plant Physiol , IF:8.34 , 2024 Jun doi: 10.1093/plphys/kiae322
TRANSPARENT TESTA GLABRA1 Regulates High-Intensity Blue Light-Induced Phototropism by Reducing CRYPTOCHROME1 Levels.
State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.; College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, Henan, China.
The asymmetrical distribution of auxin supports high intensity blue light (HBL)-mediated phototropism. Flavonoids, secondary metabolites induced by blue light and TRANSPARENT TESTA GLABRA1 (TTG1), alter auxin transport. However, the role of TTG1 in HBL-induced phototropism in Arabidopsis (Arabidopsis thaliana) remains unclear. We found that TTG1 regulates HBL-mediated phototropism. HBL-induced degradation of CRYPTOCHROME 1 (CRY1) was repressed in ttg1-1, and depletion of CRY1 rescued the phototropic defects of the ttg1-1 mutant. Moreover, overexpression of CRY1 in a cry1 mutant background led to phototropic defects in response to HBL. These results indicated that CRY1 is involved in the regulation of TTG1-mediated phototropism in response to HBL. Further investigation showed that TTG1 physically interacts with CRY1 via its N-terminus and that the added TTG1 promotes the dimerization of CRY1. The interaction between TTG1 and CRY1 may promote HBL-mediated degradation of CRY1. TTG1 also physically interacted with blue light inhibitor of cryptochrome 1 (BIC1) and Light-Response Bric-a-Brack/Tramtrack/Broad 2 (LRB2), and these interactions either inhibited or promoted their interaction with CRY1. Exogenous gibberellins (GA) and auxins, two key plant hormones that crosstalk with CRY1, may confer the recovery of phototropic defects in the ttg1-1 mutant and CRY1-overexpressing plants. Our results revealed that TTG1 participates in the regulation of HBL-induced phototropism by modulating CRY1 levels, which are coordinated with GA or IAA signaling.
PMID: 38833579
Plant Physiol , IF:8.34 , 2024 May doi: 10.1093/plphys/kiae301
A network comprising ELONGATED HYPOCOTYL5, microRNA397b, and auxin-associated factors regulates root hair growth in Arabidopsis.
CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.; CSIR- Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP) P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow-226 015, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
ELONGATED HYPOCOTYL 5 (HY5) is a major light-associated transcription factor involved in plant growth and development. In Arabidopsis (Arabidopsis thaliana), the role of HY5 is very well-defined in regulating primary root growth and lateral root formation; however, information regarding its role in root hair development is still lacking, and little is known about the genetic pathways regulating this process. In this study, we investigated the role of HY5 and its associated components in root hair development. Detailed analysis of root hair phenotype in wild-type (WT) and light signaling mutants in light and dark conditions revealed the importance of light-dependent HY5-mediated root hair initiation. Altered auxin levels in the root apex of the hy5 mutant and interaction of HY5 with promoters of root hair developmental genes were responsible for differential expression of root hair developmental genes and phenotype in the hy5 mutant. The partial complementation of root hair in the hy5 mutant after external supplementation of auxin and regaining of root hair in PIN-FORMED 2 (pin2) and PIN-FORMED 2 (pin3) mutants after grafting suggested that the auxin-mediated root hair development pathway requires HY5. Furthermore, miR397b overexpression (miR397bOX) and CRISPR/Cas9-based mutants (miR397bCR) indicated miR397b targets genes encoding Reduced Residual Arabinose (RRA1/RRA2), which in turn regulate root hair growth. The regulation of the miR397b- (RRA1/RRA2) module by HY5 demonstrated its indirect role by targeting root hair cell wall genes. Together, this study demonstrated that HY5 controls root hair development by integrating auxin signalling and other miRNA-mediated pathways.
PMID: 38820143
Plant Physiol , IF:8.34 , 2024 Jun , V195 (3) : P2443-2455 doi: 10.1093/plphys/kiae216
B-Box transcription factor BBX28 requires CONSTITUTIVE PHOTOMORPHOGENESIS1 to induce shade-avoidance response in Arabidopsis thaliana.
Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (FEVA), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Facultad de Agronomia, Universidad de Buenos Aires (UBA), Av. San Martin 4453, C1417DSE Ciudad Autonoma de Buenos Aires, Argentina.; Fundacion Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, 1405 Buenos Aires, Argentina.
Shade avoidance syndrome is an important adaptive strategy. Under shade, major transcriptional rearrangements underlie the reallocation of resources to elongate vegetative structures and redefine the plant architecture to compete for photosynthesis. BBX28 is a B-box transcription factor involved in seedling de-etiolation and flowering in Arabidopsis (Arabidopsis thaliana), but its function in shade-avoidance response is completely unknown. Here, we studied the function of BBX28 using two mutant and two transgenic lines of Arabidopsis exposed to white light and simulated shade conditions. We found that BBX28 promotes hypocotyl growth under shade through the phytochrome system by perceiving the reduction of red photons but not the reduction of photosynthetically active radiation or blue photons. We demonstrated that hypocotyl growth under shade is sustained by the protein accumulation of BBX28 in the nuclei in a CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1)-dependent manner at the end of the photoperiod. BBX28 up-regulates the expression of transcription factor- and auxin-related genes, thereby promoting hypocotyl growth under prolonged shade. Overall, our results suggest the role of BBX28 in COP1 signaling to sustain the shade-avoidance response and extend the well-known participation of other members of BBX transcription factors for fine-tuning plant growth under shade.
PMID: 38620015
Plant Physiol , IF:8.34 , 2024 Jun , V195 (3) : P1757-1758 doi: 10.1093/plphys/kiae194
The underground tango: How ethylene and auxin interact to regulate cereal root angle.
Assistant Features Editor, Plant Physiology, American Society of Plant Biologists.; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.; Plant Environmental Signalling and Development, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany.
PMID: 38558264
Plant Physiol , IF:8.34 , 2024 Jun , V195 (3) : P2032-2052 doi: 10.1093/plphys/kiae183
Auxin resistant 2 and short hypocotyl 2 regulate cotton fiber initiation and elongation.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China.; College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.; College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.; Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
Auxin, a pivotal regulator of diverse plant growth processes, remains central to development. The auxin-responsive genes auxin/indole-3-acetic acids (AUX/IAAs) are indispensable for auxin signal transduction, which is achieved through intricate interactions with auxin response factors (ARFs). Despite this, the potential of AUX/IAAs to govern the development of the most fundamental biological unit, the single cell, remains unclear. In this study, we harnessed cotton (Gossypium hirsutum) fiber, a classic model for plant single-cell investigation, to determine the complexities of AUX/IAAs. Our research identified 2 pivotal AUX/IAAs, auxin resistant 2 (GhAXR2) and short hypocotyl 2 (GhSHY2), which exhibit opposite control over fiber development. Notably, suppressing GhAXR2 reduced fiber elongation, while silencing GhSHY2 fostered enhanced fiber elongation. Investigating the mechanistic intricacies, we identified specific interactions between GhAXR2 and GhSHY2 with distinct ARFs. GhAXR2's interaction with GhARF6-1 and GhARF23-2 promoted fiber cell development through direct binding to the AuxRE cis-element in the constitutive triple response 1 promoter, resulting in transcriptional inhibition. In contrast, the interaction of GhSHY2 with GhARF7-1 and GhARF19-1 exerted a negative regulatory effect, inhibiting fiber cell growth by activating the transcription of xyloglucan endotransglucosylase/hydrolase 9 and cinnamate-4-hydroxylase. Thus, our study reveals the intricate regulatory networks surrounding GhAXR2 and GhSHY2, elucidating the complex interplay of multiple ARFs in AUX/IAA-mediated fiber cell growth. This work enhances our understanding of single-cell development and has potential implications for advancing plant growth strategies and agricultural enhancements.
PMID: 38527791
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P1100-1102 doi: 10.1093/plphys/kiae162
Auxin treatments protect male reproductive development against cold stress.
Assistant Features Editor, Plant Physiology, American Society of Plant Biologists.; Department of Developmental Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg 22609, Germany.
PMID: 38501611
Plant Physiol , IF:8.34 , 2024 Jun , V195 (3) : P2274-2288 doi: 10.1093/plphys/kiae143
JASMONATE ZIM-domain protein 3 regulates photomorphogenesis and thermomorphogenesis through inhibiting PIF4 in Arabidopsis.
Key Laboratory of Photobiology, Chinese Academy of Sciences, Institute of Botany, Beijing 100093, China.; University of Chinese Academy of Sciences, Beijing 100049, China.
Light and temperature are 2 major environmental factors that affect the growth and development of plants during their life cycle. Plants have evolved complex mechanisms to adapt to varying external environments. Here, we show that JASMONATE ZIM-domain protein 3 (JAZ3), a jasmonic acid signaling component, acts as a factor to integrate light and temperature in regulating seedling morphogenesis. JAZ3 overexpression transgenic lines display short hypocotyls under red, far-red, and blue light and warm temperature (28 degrees C) conditions compared to the wild type in Arabidopsis (Arabidopsis thaliana). We show that JAZ3 interacts with the transcription factor PHYTOCHROME-INTERACTING FACTOR4 (PIF4). Interestingly, JAZ3 spontaneously undergoes liquid-liquid phase separation (LLPS) in vitro and in vivo and promotes LLPS formation of PIF4. Moreover, transcriptomic analyses indicate that JAZ3 regulates the expression of genes involved in many biological processes, such as response to auxin, auxin-activated signaling pathway, regulation of growth, and response to red light. Finally, JAZ3 inhibits the transcriptional activation activity and binding ability of PIF4. Collectively, our study reveals a function and molecular mechanism of JAZ3 in regulating plant growth in response to environmental factors such as light and temperature.
PMID: 38487893
Plant Physiol , IF:8.34 , 2024 Jun , V195 (3) : P1969-1980 doi: 10.1093/plphys/kiae134
Ethylene regulates auxin-mediated root gravitropic machinery and controls root angle in cereal crops.
Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.; Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK.; International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, Hyderabad, India.
Root angle is a critical factor in optimizing the acquisition of essential resources from different soil depths. The regulation of root angle relies on the auxin-mediated root gravitropism machinery. While the influence of ethylene on auxin levels is known, its specific role in governing root gravitropism and angle remains uncertain, particularly when Arabidopsis (Arabidopsis thaliana) core ethylene signaling mutants show no gravitropic defects. Our research, focusing on rice (Oryza sativa L.) and maize (Zea mays), clearly reveals the involvement of ethylene in root angle regulation in cereal crops through the modulation of auxin biosynthesis and the root gravitropism machinery. We elucidated the molecular components by which ethylene exerts its regulatory effect on auxin biosynthesis to control root gravitropism machinery. The ethylene-insensitive mutants ethylene insensitive2 (osein2) and ethylene insensitive like1 (oseil1), exhibited substantially shallower crown root angle compared to the wild type. Gravitropism assays revealed reduced root gravitropic response in these mutants. Hormone profiling analysis confirmed decreased auxin levels in the root tips of the osein2 mutant, and exogenous auxin (NAA) application rescued root gravitropism in both ethylene-insensitive mutants. Additionally, the auxin biosynthetic mutant mao hu zi10 (mhz10)/tryptophan aminotransferase2 (ostar2) showed impaired gravitropic response and shallow crown root angle phenotypes. Similarly, maize ethylene-insensitive mutants (zmein2) exhibited defective gravitropism and root angle phenotypes. In conclusion, our study highlights that ethylene controls the auxin-dependent root gravitropism machinery to regulate root angle in rice and maize, revealing a functional divergence in ethylene signaling between Arabidopsis and cereal crops. These findings contribute to a better understanding of root angle regulation and have implications for improving resource acquisition in agricultural systems.
PMID: 38446735
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P1114-1116 doi: 10.1093/plphys/kiae132
Two auxins are better than one: BiAux joins forces with auxin to enhance lateral root formation.
Assistant Features Editor, Plant Physiology, American Society of Plant Biologists.; Department of Biology, Stanford University, Stanford, CA 94305, USA.
PMID: 38445801
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P1660-1680 doi: 10.1093/plphys/kiae130
CALMODULIN-LIKE16 and PIN-LIKES7a cooperatively regulate rice seedling primary root elongation under chilling.
MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Low-temperature sensitivity at the germination stage is a challenge for direct seeding of rice in Asian countries. How Ca2+ and auxin (IAA) signaling regulate primary root growth under chilling remains unexplored. Here, we showed that OsCML16 interacted specifically with OsPILS7a to improve primary root elongation of early rice seedlings under chilling. OsCML16, a subgroup 6c member of the OsCML family, interacted with multiple cytosolic loop regions of OsPILS7a in a Ca2+-dependent manner. OsPILS7a localized to the endoplasmic reticulum membranes and functioned as an auxin efflux carrier in a yeast growth assay. Transgenics showed that presence of OsCML16 enhanced primary root elongation under chilling, whereas the ospils7a knockout mutant lines showed the opposite phenotype. Moreover, under chilling conditions, OsCML16 and OsPILS7a-mediated Ca2+ and IAA signaling and regulated the transcription of IAA signaling-associated genes (OsIAA11, OsIAA23, and OsARF16) and cell division marker genes (OsRAN1, OsRAN2, and OsLTG1) in primary roots. These results show that OsCML16 and OsPILS7a cooperatively regulate primary root elongation of early rice seedlings under chilling. These findings enhance our understanding of the crosstalk between Ca2+ and IAA signaling and reveal insights into the mechanisms underlying cold-stress response during rice germination.
PMID: 38445796
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P1312-1332 doi: 10.1093/plphys/kiae123
Tetrad stage transient cold stress skews auxin-mediated energy metabolism balance in Chinese cabbage pollen.
Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.; Hainan Institute of Zhejiang University, Sanya 572024, China.; Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.; College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China.
Changing ambient temperature often impairs plant development and sexual reproduction, particularly pollen ontogenesis. However, mechanisms underlying cold stress-induced male sterility are not well understood. Here, we exposed Chinese cabbage (Brassica campestris) to different cold conditions during flowering and demonstrated that the tetrad stage was the most sensitive. After completion of pollen development at optimal conditions, transient cold stress at the tetrad stage still impacted auxin levels, starch and lipid accumulation, and pollen germination, ultimately resulting in partial male sterility. Transcriptome and metabolome analyses and histochemical staining indicated that the reduced pollen germination rate was due to the imbalance of energy metabolism during pollen maturation. The investigation of beta-glucuronidase (GUS)-overexpressing transgenic plants driven by the promoter of DR5 (DR5::GUS report system) combined with cell tissue staining and metabolome analysis further validated that cold stress during the tetrad stage reduced auxin levels in mature pollen grains. Low-concentration auxin treatment on floral buds at the tetrad stage before cold exposure improved the cold tolerance of mature pollen grains. Artificially changing the content of endogenous auxin during pollen maturation by spraying chemical reagents and loss-of-function investigation of the auxin biosynthesis gene YUCCA6 by artificial microRNA technology showed that starch overaccumulation severely reduced the pollen germination rate. In summary, we revealed that transient cold stress at the tetrad stage of pollen development in Chinese cabbage causes auxin-mediated starch-related energy metabolism imbalance that contributes to the decline in pollen germination rate and ultimately seed set.
PMID: 38438131
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P1694-1711 doi: 10.1093/plphys/kiae090
Synthetically derived BiAux modulates auxin co-receptor activity to stimulate lateral root formation.
Centro de Biotecnologia y Genomica de Plantas (UPM-INIA/CSIC), Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcon, Madrid, Spain.; Departamento de Biotecnologia-Biologia Vegetal, Escuela Tecnica Superior de Ingenieria Agronomica, Alimentaria y de Biosistemas, Universidad Politecnica de Madrid (UPM), 28040 Madrid, Spain.; Universidad Francisco de Vitoria, Facultad de Ciencias Experimentales, Edificio E., 28223 Pozuelo de Alarcon, Madrid, Spain.; Departamento de Quimica en Ciencias Farmaceuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramon y Cajal s/n, 28040 Madrid, Spain.; Centro de Metabolomica y Bioanalisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanizacion Monteprincipe, 28660 Boadilla del Monte, Madrid, Spain.
The root system plays an essential role in plant growth and adaptation to the surrounding environment. The root clock periodically specifies lateral root prebranch sites (PBS), where a group of pericycle founder cells (FC) is primed to become lateral root founder cells and eventually give rise to lateral root primordia or lateral roots (LRs). This clock-driven organ formation process is tightly controlled by modulation of auxin content and signaling. Auxin perception entails the physical interaction of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) or AUXIN SIGNALING F-BOX (AFBs) proteins with AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressors to form a co-receptor system. Despite the apparent simplicity, the understanding of how specific auxin co-receptors are assembled remains unclear. We identified the compound bis-methyl auxin conjugated with N-glucoside, or BiAux, in Arabidopsis (Arabidopsis thaliana) that specifically induces the formation of PBS and the emergence of LR, with a slight effect on root elongation. Docking analyses indicated that BiAux binds to F-box proteins, and we showed that BiAux function depends on TIR1 and AFB2 F-box proteins and AUXIN RESPONSE FACTOR 7 activity, which is involved in FC specification and LR formation. Finally, using a yeast (Saccharomyces cerevisiae) heterologous expression system, we showed that BiAux favors the assemblage of specific co-receptors subunits involved in LR formation and enhances AUXIN/INDOLE-3-ACETIC ACID 28 protein degradation. These results indicate that BiAux acts as an allosteric modulator of specific auxin co-receptors. Therefore, BiAux exerts a fine-tune regulation of auxin signaling aimed to the specific formation of LR among the many development processes regulated by auxin.
PMID: 38378170
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P1229-1255 doi: 10.1093/plphys/kiae085
Defying gravity: WEEP promotes negative gravitropism in peach trees by establishing asymmetric auxin gradients.
Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.; Department of Biology, Duke University, Durham, NC 27708, USA.; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The peach (Prunus persica) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Little is known about the function of WEEP despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.
PMID: 38366651
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P924-939 doi: 10.1093/plphys/kiae088
Far-red light-enhanced apical dominance stimulates flower and fruit abortion in sweet pepper.
Horticulture and Product Physiology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.; Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.; Laboratory of Cell and Developmental Biology, Cluster Plant Developmental Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Far-red radiation affects many plant processes, including reproductive organ abortion. Our research aimed to determine the role of apical dominance in far-red light-induced flower and fruit abortion in sweet pepper (Capsicum annuum L.). We conducted several climate room experiments where plants were grown under white- or red-rich LED light, with or without additional far-red light. Additional far-red light enhanced apical dominance: it increased auxin levels in the apices of dominant shoots, and caused a greater difference in internode length and apical auxin levels between dominant and subordinate shoots. Additional far-red light stimulated fruit abortion in intact plants but not in decapitated plants, suggesting a crucial role of shoot apices in this effect. However, reducing basipetal auxin transport in the stems with N-1-naphthylphthalamic acid did not influence far-red light-stimulated fruit abortion, although auxin levels in the stem were largely reduced. Applying the synthetic auxin 1-naphthaleneacetic acid on decapitated apices did not influence fruit abortion. However, applying the auxin biosynthesis inhibitor yucasin to shoot apices reduced fruit abortion regardless of the light conditions, accompanied by slight shoot growth retardation. These findings suggest that the basipetal auxin stream does not mediate far-red light-stimulated fruit abortion. Far-red light-stimulated fruit abortion was associated with reduced sucrose accumulation and lower invertase activities in flowers. We suggest that under additional far-red light conditions, increased auxin levels in shoot apices promote fruit abortion probably through enhanced competition for assimilates between apices and flowers, which limits assimilate import into flowers.
PMID: 38366641
Plant Physiol , IF:8.34 , 2024 May , V195 (2) : P1053-1068 doi: 10.1093/plphys/kiae025
Transcription factor WRKY75 maintains auxin homeostasis to promote tomato defense against Pseudomonas syringae.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong 271018, China.; School of Landscape Architecture, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China.; Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
The hemibiotrophic bacterial pathogen Pseudomonas syringae infects a range of plant species and causes enormous economic losses. Auxin and WRKY transcription factors play crucial roles in plant responses to P. syringae, but their functional relationship in plant immunity remains unclear. Here, we characterized tomato (Solanum lycopersicum) SlWRKY75, which promotes defenses against P. syringae pv. tomato (Pst) DC3000 by regulating plant auxin homeostasis. Overexpressing SlWRKY75 resulted in low free indole-3-acetic acid (IAA) levels, leading to attenuated auxin signaling, decreased expansin transcript levels, upregulated expression of PATHOGENESIS-RELATED GENES (PRs) and NONEXPRESSOR OF PATHOGENESIS-RELATED GENE 1 (NPR1), and enhanced tomato defenses against Pst DC3000. RNA interference-mediated repression of SlWRKY75 increased tomato susceptibility to Pst DC3000. Yeast one-hybrid, electrophoretic mobility shift assays, and luciferase activity assays suggested that SlWRKY75 directly activates the expression of GRETCHEN HAGEN 3.3 (SlGH3.3), which encodes an IAA-amido synthetase. SlGH3.3 enhanced tomato defense against Pst DC3000 by converting free IAA to the aspartic acid (Asp)-conjugated form IAA-Asp. In addition, SlWRKY75 interacted with a tomato valine-glutamine (VQ) motif-containing protein 16 (SlVQ16) in vivo and in vitro. SlVQ16 enhanced SlWRKY75-mediated transcriptional activation of SlGH3.3 and promoted tomato defense responses to Pst DC3000. Our findings illuminate a mechanism in which the SlVQ16-SlWRKY75 complex participates in tomato pathogen defense by positively regulating SlGH3.3-mediated auxin homeostasis.
PMID: 38245840
Sci Total Environ , IF:7.963 , 2024 Jun , V946 : P174198 doi: 10.1016/j.scitotenv.2024.174198
Plant metabolic responses to soil herbicide residues differ under herbivory in two woodland strawberry genotypes.
Biodiversity Unit, University of Turku, 20014 Turku, Finland. Electronic address: Benjamin.fuchs@utu.fi.; Department of Biology, University of Turku, 20014 Turku, Finland.; Biodiversity Unit, University of Turku, 20014 Turku, Finland.; Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojova 263, 16502 Prague, Czech Republic.; Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland.; Natural Chemistry Research Group, Department of Chemistry, FI-20014, University of Turku, Finland.; Biodiversity Unit, University of Turku, 20014 Turku, Finland; Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, As, Norway.
The use of glyphosate-based herbicides (GBHs) to control weeds has increased exponentially in recent decades, and their residues and degradation products have been found in soils across the globe. GBH residues in soil have been shown to affect plant physiology and specialised metabolite biosynthesis, which, in turn, may impact plant resistance to biotic stressors. In a greenhouse study, we investigated the interactive effects between soil GBH residues and herbivory on the performance, phytohormone concentrations, phenolic compound concentrations and volatile organic compound (VOC) emissions of two woodland strawberry (Fragaria vesca) genotypes, which were classified as herbivore resistant and herbivore susceptible. Plants were subjected to herbivory by strawberry leaf beetle (Galerucella tenella) larvae, and to GBH residues by growing in soil collected from a field site with GBH treatments twice a year over the past eight years. Soil GBH residues reduced the belowground biomass of the susceptible genotype and the aboveground biomass of both woodland strawberry genotypes. Herbivory increased the belowground biomass of the resistant genotype and the root-shoot ratio of both genotypes. At the metabolite level, herbivory induced the emission of several VOCs. Jasmonic acid, abscisic acid and auxin concentrations were induced by herbivory, in contrast to salicylic acid, which was only induced by herbivory in combination with soil GBH residues in the resistant genotype. The concentrations of phenolic compounds were higher in the resistant genotype compared to the susceptible genotype and were induced by soil GBH residues in the resistant genotype. Our results indicate that soil GBH residues can differentially affect plant performance, phytohormone concentrations and phenolic compound concentrations under herbivore attack, in a genotype-dependent manner. Soil GBH altered plant responses to herbivory, which may impact plant resistance traits and species interactions. With ongoing agrochemical pollution, we need to consider plant cultivars with better resistance to polluted soils while maintaining plant resilience under challenging environmental conditions.
PMID: 38914330
Sci Total Environ , IF:7.963 , 2024 Sep , V942 : P173775 doi: 10.1016/j.scitotenv.2024.173775
High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China.
Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.; Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria.; Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China. Electronic address: jxjiang@ujs.edu.cn.
The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO(3)(-) accumulation in S. salsa roots, while salinity stress influenced soil pH through H(+) discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.
PMID: 38844238
Sci Total Environ , IF:7.963 , 2024 Jun , V929 : P172693 doi: 10.1016/j.scitotenv.2024.172693
Mechanism of flavonols on detoxification, migration and transformation of indium in rhizosphere system.
School of Life Sciences, Qilu Normal University, Jinan 250200, China.; School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. Electronic address: 14016@sdjzu.edu.cn.; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China.; School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China. Electronic address: zbinzhang@yeah.net.
Soil contamination by toxic heavy metal induces serious environmental hazards. In recent years, the use of indium (In) in semiconductor products has increased considerably and the release of In is inevitable, which will pose great risk to the ecosystem. The interaction between metal and plants which are the fundamental components of all ecosystems are an indispensable aspect of indium assessment and remediation. The role of flavonols, which is essential to plant resistance to In stress, remains largely unknown. FLS1 related lines of A. thaliana (Col, fls1-3 and OE) were exposed to In stress in soil and flavonols as root exudates were analyzed in exogenous application test. The accumulation and release of flavonols could be induced by In stress. However, flavonols exhibited different function in vivo and in vitro of plant. The basic function of flavonols was to affect root morphology via regulating auxin, but being intervened by In stress. The synthesis and accumulation of flavonols in vivo could activate the antioxidant system and the metal detoxification system to alleviate the toxic effects of In on plant. In addition, plants could make phone calls to rhizosphere microbes for help when exposed to In. Flavonols in vitro might act as the information transmission. Combination of endogenous and exogenous flavonols could affect the migration and transformation of In in soil-plant system via metal complexation and transportation pathway.
PMID: 38663607
Curr Opin Plant Biol , IF:7.834 , 2024 Jun , V81 : P102566 doi: 10.1016/j.pbi.2024.102566
Insights into dynamic coenocytic endosperm development: Unraveling molecular, cellular, and growth complexity.
Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA.; Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA. Electronic address: tomo.k@uky.edu.
The endosperm, a product of double fertilization, is one of the keys to the evolution and success of angiosperms in conquering the land. While there are differences in endosperm development among flowering plants, the most common form is coenocytic growth, where the endosperm initially undergoes nuclear division without cytokinesis and eventually becomes cellularized. This complex process requires interplay among networks of transcription factors such as MADS-box, auxin response factors (ARFs), and phytohormones. The role of cytoskeletal elements in shaping the coenocytic endosperm and influencing seed growth also becomes evident. This review offers a recent understanding of the molecular and cellular dynamics in coenocytic endosperm development and their contributions to the final seed size.
PMID: 38830335
Curr Opin Plant Biol , IF:7.834 , 2024 Jun , V81 : P102565 doi: 10.1016/j.pbi.2024.102565
Illuminating the role of the calyptra in sporophyte development.
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA. Electronic address: jbudke@utk.edu.
The study of moss calyptra form and function began almost 250 years ago, but calyptra research has remained a niche endeavor focusing on only a small number of species. Recent advances have focused on calyptra cuticular waxes, which function in dehydration protection of the immature sporophyte apex. The physical presence of the calyptra also plays a role in sporophyte development, potentially via its influence on auxin transport. Progress developing genomic resources for mosses beyond the model Physcomitrium patens, specifically for species with larger calyptrae and taller sporophytes, in combination with advances in CRISPR-Cas9 genome editing will enable the influence of the calyptra on gene expression and the production of RNAs and proteins that coordinate sporophyte development to be explored.
PMID: 38824880
Free Radic Biol Med , IF:7.376 , 2024 Jun doi: 10.1016/j.freeradbiomed.2024.06.013
Pulsed high power microwave seeds priming modulates germination, growth, redox homeostasis, and hormonal shifts in barley for improved seedling growth: Unleashing the molecular dynamics.
Plasma Bioscience Research Center (PBRC), Kwangwoon University, Seoul, South Korea; Department of Electrical and Biological Physics, Kwangwoon University, Seoul, South Korea.; Department of Electrical and Biological Physics, Kwangwoon University, Seoul, South Korea; Department of Plasma Bio Display, Kwangwoon University, Seoul, South Korea.; Plasma Bioscience Research Center (PBRC), Kwangwoon University, Seoul, South Korea; Department of Electrical and Biological Physics, Kwangwoon University, Seoul, South Korea; Department of Plasma Bio Display, Kwangwoon University, Seoul, South Korea. Electronic address: ehchoi@kw.ac.kr.
Increasing the seed germination potential and seedling growth rates play a pivotal role in increasing overall crop productivity. Seed germination and early vegetative (seedling) growth are critical developmental stages in plants. High-power microwave (HPM) technology has facilitated both the emergence of novel applications and improvements to existing in agriculture. The implications of pulsed HPM on agriculture remain unexplored. In this study, we have investigated the effects of pulsed HPM exposure on barley germination and seedling growth, elucidating the plausible underlying mechanisms. Barley seeds underwent direct HPM irradiation, with 60 pulses by 2.04 mJ/pulse, across three distinct irradiation settings: dry, submerged in deionized (DI) water, and submerged in DI water one day before exposure. Seed germination significantly increased in all HPM-treated groups, where the HPM-dry group exhibited a notable increase, with a 2.48-fold rise at day 2 and a 1.9-fold increment at day 3. Similarly, all HPM-treated groups displayed significant enhancements in water uptake, and seedling growth (weight and length), as well as elevated levels of chlorophyll, carotenoids, and total soluble protein content. The obtained results indicate that when comparing three irradiation setting, HPM-dry showed the most promising effects. condition HPM seed treatment increases the level of reactive species within the barley seedlings, thereby modulating plant biochemistry, physiology, and different cellular signaling cascades via induced enzymatic activities. Notably, the markers associated with plant growth are upregulated and growth inhibitory markers are downregulated post-HPM exposure. Under optimal HPM-dry treatment, auxin (IAA) levels increased threefold, while ABA levels decreased by up to 65%. These molecular findings illuminate the intricate regulatory mechanisms governing phenotypic changes in barley seedlings subjected to HPM treatment. The results of this study might play a key role to understand molecular mechanisms after pulsed-HPM irradiation of seeds, contributing significantly to address the global need of sustainable crop yield.
PMID: 38901500
Plant Cell Environ , IF:7.228 , 2024 Jun doi: 10.1111/pce.14991
PagKNAT2/6b promotes shoot branching by attenuating auxin-strigolactone signalling in poplar.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou, Zhejiang, China.; The Engineering Research, Institute of Agriculture and Forestry, Ludong University, Yantai, Shandong, China.; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.; Taishan Academy of Forestry Sciences, Taian, Shandong, China.
Shoot branching from axillary bud (AB) directly determines plant architecture. However, the mechanism through which AB remains dormant or emerges to form branches as plants grow remains largely unknown. Here, the auxin-strigolactone (IAA-SL) pathway was first shown to regulate shoot branching in poplar, and we found that PagKNAT2/6b could modulate this pathway. PagKNAT2/6b was expressed mainly in the shoot apical meristem and AB and was induced by shoot apex damage. PagKNAT2/6b overexpressing poplar plants (PagKNAT2/6b OE) exhibited multiple branches that mimicked the branching phenotype of nontransgenic plants after decapitation treatment, while compared with nontransgenic controls, PagKNAT2/6b antisense transgenic poplar and Pagknat2/6b mutant lines exhibited a significantly decreased number of branches after shoot apex damage treatment. In addition, we found that PagKNAT2/6b directly inhibits the expression of the key IAA synthesis gene PagYUC6a, which is specifically expressed in the shoot apex. Moreover, overexpression of PagYUC6a in the PagKNAT2/6b OE background reduced the number of branches after shoot apex damage treatment. Overall, we conclude that PagKNAT2/6b responds to shoot apical injury and regulates shoot branching through the IAA-SL pathway. These findings may provide a theoretical basis and candidate genes for genetic engineering to create new forest tree species with different crown types.
PMID: 38847345
Plant Cell Environ , IF:7.228 , 2024 Jun doi: 10.1111/pce.14989
The endophytic fungus Serendipita indica affects auxin distribution in Arabidopsis thaliana roots through alteration of auxin transport and conjugation to promote plant growth.
Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentacion (INIA/CSIC), Campus de Montegancedo, Madrid, Spain.; Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany.; RIKEN Center for Sustainable Resource Science, Yokohama, Japan.; Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.; Instituto de Ciencias Biologicas, Campus Talca, Universidad de Talca, Talca, Chile.; Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, Talca, Chile.; Institute of Botany, Technische Universitat Dresden, Dresden, Germany.; Department for Molecular Biology, Ruder Boskovic Institute, Zagreb, Croatia.; Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.; INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Universite Paris-Saclay, Versailles, France.; Departamento de Biotecnologia-Biologia Vegetal, Escuela Tecnica Superior de Ingenieria Agronomica, Alimentaria y de Biosistemas, Universidad Politecnica de Madrid (UPM), Madrid, Spain.
Plants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of interorganismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis of Arabidopsis thaliana with the beneficial root colonizing endophyte Serendipita indica represents a well-studied system. Colonization of Arabidopsis roots with S. indica promotes plant growth and stress tolerance of the host plant. However, until now, the molecular mechanism by which S. indica reprograms plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis between A. thaliana and S. indica. Our experiments revealed the sustained stimulation of auxin signalling in fungus infected Arabidopsis roots and disclosed the essential role of tightly controlled auxin conjugation in the plant-fungus interaction. It particularly highlighted the importance of two GRETCHEN HAGEN 3 (GH3) genes, GH3.5 and GH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of the PIN2 auxin transporter gene in roots of Arabidopsis seedlings infected with S. indica and demonstrate that this transcriptional adjustment affects auxin signalling in roots, which results in increased plant growth.
PMID: 38847336
Plant Cell Environ , IF:7.228 , 2024 Jun , V47 (6) : P2058-2073 doi: 10.1111/pce.14853
Phytochrome-interacting factors play shared and distinct roles in regulating shade avoidance responses in Populus trees.
School of Life Sciences, Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China.; Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China.
Plants adjust their growth and development in response to changing light caused by canopy shade. The molecular mechanisms underlying shade avoidance responses have been widely studied in Arabidopsis and annual crop species, yet the shade avoidance signalling in woody perennial trees remains poorly understood. Here, we first showed that PtophyB1/2 photoreceptors serve conserved roles in attenuating the shade avoidance syndrome (SAS) in poplars. Next, we conducted a systematic identification and characterization of eight PtoPIF genes in Populus tomentosa. Knocking out different PtoPIFs led to attenuated shade responses to varying extents, whereas overexpression of PtoPIFs, particularly PtoPIF3.1 and PtoPIF3.2, led to constitutive SAS phenotypes under normal light and enhanced SAS responses under simulated shade. Notably, our results revealed that distinct from Arabidopsis PIF4 and PIF5, which are major regulators of SAS, the Populus homologues PtoPIF4.1 and PtoPIF4.2 seem to play a minor role in controlling shade responses. Moreover, we showed that PtoPIF3.1/3.2 could directly activate the expression of the auxin biosynthetic gene PtoYUC8 in response to shade, suggesting a conserved PIF-YUC-auxin pathway in modulating SAS in tree. Overall, our study provides insights into shared and divergent functions of PtoPIF members in regulating various aspects of the SAS in Populus.
PMID: 38404129
Chemosphere , IF:7.086 , 2024 Jun , V362 : P142604 doi: 10.1016/j.chemosphere.2024.142604
Salicylic acid-mediated alleviation of salt stress: Insights from physiological and transcriptomic analysis in Asarum sieboldii Miq.
School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China. Electronic address: liuzhong@sjtu.edu.cn.
As global agriculture faces the pressing threat of salt stress, innovative solutions are imperative for sustainable agriculture. The remarkable potential of salicylic acid (SA) in enhancing plant resilience against environmental stressors has recently gained attention. However, the specific molecular mechanisms by which SA mitigates salt stress in Asarum sieboldii Miq., a valuable medicinal plant, remain poorly understood. Here, we evaluated the physiological and transcriptomic regulatory responses of A. sieboldii under salt stress (100 mM NaCl), both in the presence (1 mM SA) and absence of exogenous SA. The results highlighted that SA significantly alleviates salt stress, primarily through enhancing antioxidant activities as evidenced by increased superoxide dismutase, and peroxidase activities. Additionally, we observed an increment in chlorophyll (a and b), proline, total soluble sugar, and plant fresh weight, along with a decrease in malondialdehyde contents. Transcriptome analysis suggested consistency in the regulation of many differentially expressed genes and transcription factors (TFs); however, genes targets (GSTs, TIR1, and NPR1), and TFs (MYB, WRKY, TCP, and bHLH) possessed expressional uniqueness, and majority had significantly up-regulated trends in SA-coupled salt stress treatments. Further, bioinformatics and KEGG enrichment analysis indicated several SA-induced significantly enriched biological pathways. Specifically, plant hormone signal transduction was identified as being populated with key genes distinctive to auxin, cytokinin, ethylene, and salicylic acid signaling, suggesting their important role in salt stress alleviation. Inclusively, this report presents a comprehensive analysis encompassing gene targets, TFs, and biological pathways, and these insights may offer a valuable contribution to our knowledge of SA-mediated regulation and its crucial role in enhancing plant defense against diverse abiotic stressors.
PMID: 38876329
Chemosphere , IF:7.086 , 2024 Jun , V357 : P141910 doi: 10.1016/j.chemosphere.2024.141910
Biomass ash as soil fertilizers: Supercharging biomass accumulation by shifting auxin distribution.
Yunnan Tobacco Company Qujing Company, Qujing, 655002, Yunnan, China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.; Yunnan Tobacco Company Yuxi Company, Yuxi, 652500, Yunnan, China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: ylzhang@njau.edu.cn.
Growing quantities of biomass ashes (phyto-ashs) are currently produced worldwide due to the increasing biomass consumption in energy applications. Utilization of phyto-ash in agriculture is environmentally friendly solution. However, mechanisms involving the coordination of carbon metabolism and distribution in plants and soil amendment are not well known. In the present study, tobacco plants were chemically-fertilized with or without 2 per thousand phyto-ash addition. The control had sole chemical fertilizer; for two phyto-ash treatments, the one (T1) received comparable levels of nitrogen, phophorus, and potassium from phyto-ash and fertilizers as the control and another (T2) had 2 per thousand of phyto-ash and the same rates of fertilizers as the control. Compared with the control, phyto-ash addition improved the soil pH from 5.94 to about 6.35; T2 treatment enhanced soil available potassium by 30% but no difference of other elements was recorded among three treatments. Importantly, bacterial (but not fungal) communities were significantly enriched by phyto-ash addition, with the rank of richness as: T2 > T1 > control. Consistent with amelioration of soil properties, phyto-ash promoted plant growth through enlarged leaf area and photosynthesis and induced outgrowth of lateral roots (LRs). Interestingly, increased auxin content was recorded in 2(nd) and 3(rd) leaves and roots under phyto-ash application, also with the rank level as T2 > T1 > control, paralleling with higher transcripts of auxin synthetic genes in the topmost leaf and stronger [(3)H]IAA activity under phyto-ash addition. Furthermore, exogenous application of analog exogenous auxin (NAA) restored leaf area, photosynthesis and LR outgrowth to the similar level as T2 treatment; conversely, application of auxin transport inhibitor (NPA) under T2 treatment retarded leaf and root development. We demonstrated that phyto-ash addition improved soil properties and thus facilitated carbon balance within plants and biomass accumulation in which shifting auxin distribution plays an important role.
PMID: 38582170
J Integr Plant Biol , IF:7.061 , 2024 Jun doi: 10.1111/jipb.13726
BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice.
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China.; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
Tiller angle is a key agricultural trait that establishes plant architecture, which in turn strongly affects grain yield by influencing planting density in rice. The shoot gravity response plays a crucial role in the regulation of tiller angle in rice, but the underlying molecular mechanism is largely unknown. Here, we report the identification of the BIG TILLER ANGLE2 (BTA2), which regulates tiller angle by controlling the shoot gravity response in rice. Loss-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base, leading to impaired gravitropism and therefore a big tiller angle. BTA2 interacted with AUXIN RESPONSE FACTOR7 (ARF7) to modulate rice tiller angle through the gravity signaling pathway. The BTA2 protein was highly conserved during evolution. Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication. Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions. Our findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity response. Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.
PMID: 38940609
J Integr Plant Biol , IF:7.061 , 2024 Jun doi: 10.1111/jipb.13720
MYB2 and MYB108 regulate lateral root development by interacting with LBD29 in Arabidopsis thaliana.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China.; Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
AUXIN RESPONSE FACTOR 7 (ARF7)-mediated auxin signaling plays a key role in lateral root (LR) development by regulating downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor genes, including LBD16, LBD18, and LBD29. LBD proteins are believed to regulate the transcription of downstream genes as homodimers or heterodimers. However, whether LBD29 forms dimers with other proteins to regulate LR development remains unknown. Here, we determined that the Arabidopsis thaliana (L.) Heynh. MYB transcription factors MYB2 and MYB108 interact with LBD29 and regulate auxin-induced LR development. Both MYB2 and MYB108 were induced by auxin in an ARF7-dependent manner. Disruption of MYB2 by fusion with an SRDX domain severely affected auxin-induced LR formation and the ability of LBD29 to induce LR development. By contrast, overexpression of MYB2 or MYB108 resulted in greater LR numbers, except in the lbd29 mutant background. These findings underscore the interdependence and importance of MYB2, MYB108, and LBD29 in regulating LR development. In addition, MYB2-LBD29 and MYB108-LBD29 complexes promoted the expression of CUTICLE DESTRUCTING FACTOR 1 (CDEF1), a member of the GDSL (Gly-Asp-Ser-Leu) lipase/esterase family involved in LR development. In summary, this study identified MYB2-LBD29 and MYB108-LBD29 regulatory modules that act downstream of ARF7 and intricately control auxin-mediated LR development.
PMID: 38923126
J Integr Plant Biol , IF:7.061 , 2024 Jun , V66 (6) : P1206-1226 doi: 10.1111/jipb.13646
The transcriptional control of LcIDL1-LcHSL2 complex by LcARF5 integrates auxin and ethylene signaling for litchi fruitlet abscission.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.; Dongguan Botanical Garden, Dongguan, 523128, China.; Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo, 0316, Norway.; College of Agriculture, Guangxi University, Nanning, 530004, China.
At the physiological level, the interplay between auxin and ethylene has long been recognized as crucial for the regulation of organ abscission in plants. However, the underlying molecular mechanisms remain unknown. Here, we identified transcription factors involved in indoleacetic acid (IAA) and ethylene (ET) signaling that directly regulate the expression of INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and its receptor HAESA (HAE), which are key components initiating abscission. Specifically, litchi IDA-like 1 (LcIDL1) interacts with the receptor HAESA-like 2 (LcHSL2). Through in vitro and in vivo experiments, we determined that the auxin response factor LcARF5 directly binds and activates both LcIDL1 and LcHSL2. Furthermore, we found that the ETHYLENE INSENSITIVE 3-like transcription factor LcEIL3 directly binds and activates LcIDL1. The expression of IDA and HSL2 homologs was enhanced in LcARF5 and LcEIL3 transgenic Arabidopsis plants, but reduced in ein3 eil1 mutants. Consistently, the expressions of LcIDL1 and LcHSL2 were significantly decreased in LcARF5- and LcEIL3-silenced fruitlet abscission zones (FAZ), which correlated with a lower rate of fruitlet abscission. Depletion of auxin led to an increase in 1-aminocyclopropane-1-carboxylic acid (the precursor of ethylene) levels in the litchi FAZ, followed by abscission activation. Throughout this process, LcARF5 and LcEIL3 were induced in the FAZ. Collectively, our findings suggest that the molecular interactions between litchi AUXIN RESPONSE FACTOR 5 (LcARF5)-LcIDL1/LcHSL2 and LcEIL3-LcIDL1 signaling modules play a role in regulating fruitlet abscission in litchi and provide a long-sought mechanistic explanation for how the interplay between auxin and ethylene is translated into the molecular events that initiate abscission.
PMID: 38517216
J Exp Bot , IF:6.992 , 2024 Jun doi: 10.1093/jxb/erae284
Raffinose catabolism enhances maize waterlogging tolerance by stimulating adventitious root growth and development.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.; The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China.; Department of Horticulture, Seed Biology, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA.
Raffinose mitigates plant heat-, drought- and cold- stresses; however, whether raffinose contributes to plant waterlogging tolerance is unknown. The maize zmrafs-1 mutant seedlings lacking raffinose, generate fewer and shorter adventitious root (AR) and are more sensitive to waterlogging stress, while overexpression of ZmRAFS increases raffinose content, stimulates AR formation, and enhances the waterlogging tolerance of maize seedlings. Transcriptome analysis of NS (Null segregant) seedlings compared with that of zmrafs-1, particularly when waterlogged, revealed that the expression of genes related to galactose metabolism and the auxin biosynthetic pathway were upregulated by raffinose. Additionally, Indole-3-acetic acid (IAA) amounts significantly decreased or increased in zmrafs-1 or ZmRAFS-overexpressing seedlings, respectively. Inhibition of the hydrolysis of raffinose by DGJ (1-deoxygalactonojirimycin) decreased the waterlogging tolerance of maize seedlings, decreased the expression of genes encoding proteins related to auxin transport-related genes as well as the IAA level in the seedlings, suggesting that the hydrolysis of raffinose is necessary for maize waterlogging tolerance. These data demonstrate that raffinose catabolism stimulates adventitious root formation via auxin signaling pathway to enhance maize waterlogging tolerance.
PMID: 38938017
J Exp Bot , IF:6.992 , 2024 Jun doi: 10.1093/jxb/erae282
Arinole, a novel auxin-stimulating benzoxazole, affects root growth and promotes adventitious root formation.
Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium.; Laboratory of Integrated Molecular Plant Physiological Research (IMPRES), Department of Biology, Faculty of Sciences, University of Antwerp, Antwerp, Belgium.; Laboratory of Organic Synthesis, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Ghent, Belgium.; NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Ghent, Belgium.; Laboratory for Applied In Vitro Plant Biotechnology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Belgium.; Natural Products Chemistry Lab, Department of Biochemistry, Okayama University of Science, Okayama, Japan.
The triple response phenotype is characteristic for seedlings treated with the phytohormone ethylene or its direct precursor 1-aminocyclopropane-carboxylic acid and is often employed to find novel chemical tools to probe ethylene responses. We identified a benzoxazole-urea derivative (B2) partially mimicking ethylene effects in a triple response bioassay. A thorough phenotypic analysis demonstrated that B2 and its closest analogue arinole (ARI) induced phenotypic responses reminiscent of seedlings with elevated levels of auxin, including impaired hook development and inhibition of seedling growth. Specifically, ARI reduced longitudinal cell elongation in roots, while promoting cell division. In contrast to other natural or synthetic auxins, ARI mostly acts as an inducer of adventitious root development, with only limited effects on lateral root development. Quantification of free auxins and auxin biosynthetic precursors as well as auxin-related gene expression demonstrated that ARI boosts global auxin levels. In addition, analyses of auxin reporter lines and mutants, besides pharmacological assays with auxin-related inhibitors, confirmed that ARI effects are facilitated by TRYPTOPHAN AMINOTRANSFERASE1 (TAA1)-mediated auxin synthesis. ARI treatment resulted in AR formation in an array of species, including Arabidopsis, pea, tomato, poplar, and lavender, a desirable trait in both agriculture and horticulture.
PMID: 38920303
J Exp Bot , IF:6.992 , 2024 Jun doi: 10.1093/jxb/erae277
Mediator complex: an important regulator of root system architecture.
International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.; Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
Mediator, a multiprotein complex, is an important component of the transcription machinery. In plants, the latest reports from our group and some other studies have established that Mediator functions as a signal processor that conveys transcriptional signals from transcription factors to RNA polymerase II. It has been found to be involved in different developmental and stress-adaptation conditions ranging from embryo, root, and shoot development to flowering and senescence and also in response to different biotic and abiotic stresses. In the last one decade, significant progress has been made in understanding the role of Mediator subunits in root development. They have been shown to transcriptionally regulate development of almost all the components of root system architecture - primary root, lateral root and root hair. Their role has also been appreciated in nutrient acquisition through root. In this review, we have discussed all the known functions of Mediator subunits during root development. We have also highlighted the role of Mediator as a nodal point for processing different hormone signaling that regulate root morphogenesis and growth.
PMID: 38881317
J Exp Bot , IF:6.992 , 2024 Jun doi: 10.1093/jxb/erae260
Exploring the puzzle of Reactive Oxygen Species (ROS) acting on root hair cells.
Fundacion Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP C1405BWE, Argentina.; Centro de Biotecnologia Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.; ANID - Millennium Science Initiative Program - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
Reactive oxygen species (ROS) are essential signaling molecules that enable cells to respond rapidly to a range of stimuli. The capacity of plants to recognize various stressors, incorporate a variety of environmental inputs, and initiate stress-response networks depends on ROS. Plants develop resilience and defensive systems as a result of these processes. Root hairs (RHs) are central components of the root biology since they increase the surface area of the root, anchor it in the soil, increase its ability to absorb water and nutrients, and foster interactions between microorganisms. In this review, we specifically focused on RHs cells and we highlighted the identification of ROS receptors, important new regulatory hubs that connect ROS production, transport, and signaling in the context of two hormonal pathways (auxin and ethylene) and under low temperature environmental input related to nutrients. As ROS plays a crucial role in regulating cell elongation rates, RHs are rapidly gaining traction as a very valuable single plant cell model for investigating ROS homeostasis and signaling. These promising findings might soon aid in the development of plants and roots that are more resilient to environmental stressors.
PMID: 38833316
J Exp Bot , IF:6.992 , 2024 Jun doi: 10.1093/jxb/erae245
A gain-of-function mutation in BnaIAA13 disrupts vascular tissue and lateral root development in Brassica napus.
National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.; College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.; Yazhouwan National Laboratory, Sanya, Hainan, 572025, China.
Rapeseed (Brassica napus) is an important oilseed crop worldwide. Plant vascular tissues are responsible for material transport and provide mechanical support. The lateral roots (LRs) absorb sufficient water and nutrients. The genetic basis of vascular tissues and LRs development in rapeseed remains unknown. This study characterized an EMS-mutagenized rapeseed mutant, T16, which showed dwarf stature, reduced LRs, and leaf wilting. Scanning electron microscopy observations showed that the internode-cell shortened. Observations of the tissue sections revealed defects in the development of vascular bundles in the stems and petioles. Genetic analysis revealed that the phenotypes of T16 were controlled by a single semi-dominant nuclear gene. Map-based cloning and genetic complementarity confirmed that BnaA03.IAA13 is the functional gene, a G-to-A mutation in second exon changed the glycine at the 79th position to glutamic acid, disrupting the conserved degron motif VGWPP. Transcriptome analysis in roots and stems showed that auxin and cytokinin signaling pathways were disordered in T16. Evolutionary analysis showed that AUXIN/INDOLE-3-ACETIC ACID was conserved during plant evolution. The heterozygote of T16 significantly reduced the plant height while maintaining other agronomic traits. Our findings provide novel insights into the regulatory mechanisms of vascular tissues and LRs development, and provide a new germplasm resource for rapeseed breeding.
PMID: 38824403
J Exp Bot , IF:6.992 , 2024 Jun , V75 (12) : P3685-3699 doi: 10.1093/jxb/erae196
RHO OF PLANTS signalling and the activating ROP GUANINE NUCLEOTIDE EXCHANGE FACTORS: specificity in cellular signal transduction in plants.
Plant Systems Biology, School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 8, 85354 Freising, Germany.
Every cell constantly receives signals from its neighbours or the environment. In plants, most signals are perceived by RECEPTOR-LIKE KINASEs (RLKs) and then transmitted into the cell. The molecular switches RHO OF PLANTS (ROP) are critical proteins for polar signal transduction and regulate multiple cell polarity processes downstream of RLKs. Many ROP-regulating proteins and scaffold proteins of the ROP complex are known. However, the spatiotemporal ROP signalling complex composition is not yet understood. Moreover, how specificity is achieved in different ROP signalling pathways within one cell still needs to be determined. This review gives an overview of recent advances in ROP signalling and how specificity by downstream scaffold proteins can be achieved. The composition of the ROP signalling complexes is discussed, focusing on the possibility of the simultaneous presence of ROP activators and inactivators within the same complex to balance ROP activity. Furthermore, this review highlights the function of plant-specific ROP GUANINE NUCLEOTIDE EXCHANGE FACTORS polarizing ROP signalling and defining the specificity of the initiated ROP signalling pathway.
PMID: 38683617
J Exp Bot , IF:6.992 , 2024 Jun , V75 (11) : P3368-3387 doi: 10.1093/jxb/erae119
A tomato B-box protein regulates plant development and fruit quality through the interaction with PIF4, HY5, and RIN transcription factors.
Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Rua do Matao 277, 05508-090, Sao Paulo, Brasil.; IFEVA, Facultad de Agronomia, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Cientificas y Tecnicas, Avenida San Martin 4453, Buenos Aires C1417DSE, Argentina.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, Ghent, Belgium.; Center for Plant Systems Biology, VIB, Technologiepark-Zwijnaarde 71, Ghent, Belgium.; Departamento de Biologia, Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Avenida Bandeirantes 3900, 14040-901, Ribeirao Preto, Brasil.
During the last decade, knowledge about BBX proteins has greatly increased. Genome-wide studies identified the BBX gene family in several ornamental, industry, and food crops; however, reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during the life span of plants. Through inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)-auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later in development, it controls the balance between cell division and expansion to guarantee correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), up-regulates flavonoid biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology because they affect not only multiple processes during plant development but they also regulate other genes at the transcriptional and post-translational levels.
PMID: 38492237
J Exp Bot , IF:6.992 , 2024 Jun , V75 (11) : P3351-3367 doi: 10.1093/jxb/erae102
Development of pollinated and unpollinated ovules in Ginkgo biloba: unravelling the role of pollen in ovule tissue maturation.
Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Arcavacata of Rende (Cosenza), Italy.; Botanical Garden, University of Padova, 25123 Padova, Italy.; Department of Biology, University of Padova, 35121 Padova, Italy.; Department of Biosciences, University of Milano, 20133 Milano, Italy.; Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (Di.S.A.A.), University of Milano, 20133 Milano, Italy.
In gymnosperms such as Ginkgo biloba, the arrival of pollen plays a key role in ovule development, before fertilization occurs. Accordingly, G. biloba female plants geographically isolated from male plants abort all their ovules after the pollination drop emission, which is the event that allows the ovule to capture pollen grains. To decipher the mechanism induced by pollination required to avoid ovule senescence and then abortion, we compared the transcriptomes of pollinated and unpollinated ovules at three time points after the end of the emission of pollination drop. Transcriptomic and in situ expression analyses revealed that several key genes involved in programmed cell death such as senescence and apoptosis, DNA replication, and cell cycle regulation were differentially expressed in unpollinated ovules compared to pollinated ovules. We provide evidence that the pollen captured by the pollination drop affects auxin local accumulation and might cause deregulation of key genes required for the ovule's programmed cell death, activating both the cell cycle regulation and DNA replication genes.
PMID: 38459807
Int J Biol Macromol , IF:6.953 , 2024 Jun , V271 (Pt 1) : P132544 doi: 10.1016/j.ijbiomac.2024.132544
BnaC06.WIP2-BnaA09.STM transcriptional regulatory module promotes leaf lobe formation in Brassica napus.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.; Hybrid Rapeseed Research Center of Shaanxi Province, Yangling 712100, Shaanxi, China.; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China. Electronic address: cmx786@nwafu.edu.cn.
The lobed leaves of rapeseed (Brassica napus L.) offer significant advantages in dense planting, leading to increased yield. Although AtWIP2, a C2H2 zinc finger transcription factor, acts as a regulator of leaf development in Arabidopsis thaliana, the function and regulatory mechanisms of BnaWIP2 in B. napus remain unclear. Here, constitutive expression of the BnaC06.WIP2 paralog, predominantly expressed in leaf serrations, produced lobed leaves in both A. thaliana and B. napus. We demonstrated that BnaC06.WIP2 directly repressed the expression of BnaA01.TCP4, BnaA03.TCP4, and BnaC03.TCP4 and indirectly inhibited the expression of BnaA05.BOP1 and BnaC02.AS2 to promote leaf lobe formation. On the other hand, we discovered that BnaC06.WIP2 modulated the levels of endogenous gibberellin, cytokinin, and auxin, and controlled the auxin distribution in B. napus leaves, thus accelerating leaf lobe formation. Meanwhile, we revealed that BnaA09.STM physically interacted with BnaC06.WIP2, and ectopic expression of BnaA09.STM generated smaller and lobed leaves in B. napus. Furthermore, we found that BnaC06.WIP2 and BnaA09.STM synergistically promoted leaf lobe formation through forming transcriptional regulatory module. Collectively, our findings not only facilitate in-depth understanding of the regulatory mechanisms underlying lobed leaf formation, but also are helpful for guiding high-density breeding practices through improving leaf morphology in B. napus.
PMID: 38782318
Development , IF:6.868 , 2024 Jun , V151 (11) doi: 10.1242/dev.202810
Heterogeneous identity, stiffness and growth characterise the shoot apex of Arabidopsis stem cell mutants.
Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, 69364 Lyon Cedex 07, France.; Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bengaluru, India.; PLATIM-LyMIC, Universite de Lyon, ENS de Lyon, Inserm, CNRS, SFR Biosciences US8 UAR3444, UCB Lyon 1, 69364 Lyon Cedex 07, France.; Physikalisches Institut, Rheinische Friedrich-Wilhelms-Universitat, 53115 Bonn, Germany.; Department of Mechanical Engineering, Indian Institute of Science, 560012 Bengaluru, India.
Stem cell homeostasis in the shoot apical meristem involves a core regulatory feedback loop between the signalling peptide CLAVATA3 (CLV3), produced in stem cells, and the transcription factor WUSCHEL, expressed in the underlying organising centre. clv3 mutant meristems display massive overgrowth, which is thought to be caused by stem cell overproliferation, although it is unknown how uncontrolled stem cell divisions lead to this altered morphology. Here, we reveal local buckling defects in mutant meristems, and use analytical models to show how mechanical properties and growth rates may contribute to the phenotype. Indeed, clv3 mutant meristems are mechanically more heterogeneous than the wild type, and also display regional growth heterogeneities. Furthermore, stereotypical wild-type meristem organisation, in which cells simultaneously express distinct fate markers, is lost in mutants. Finally, cells in mutant meristems are auxin responsive, suggesting that they are functionally distinguishable from wild-type stem cells. Thus, all benchmarks show that clv3 mutant meristem cells are different from wild-type stem cells, suggesting that overgrowth is caused by the disruption of a more complex regulatory framework that maintains distinct genetic and functional domains in the meristem.
PMID: 38752444
Hortic Res , IF:6.793 , 2024 Jun , V11 (6) : Puhae114 doi: 10.1093/hr/uhae114
Comparative transcriptome and functional analyses provide insights into the key factors regulating shoot regeneration in highbush blueberry.
Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
Establishing an efficient plant regeneration system is a crucial prerequisite for genetic engineering technology in plants. However, the regeneration rate exhibits considerable variability among genotypes, and the key factors underlying shoot regeneration capacity remain largely elusive. Blueberry leaf explants cultured on a medium rich in cytokinins exhibit direct shoot organogenesis without prominent callus formation, which holds promise for expediting genetic transformation while minimizing somatic mutations during culture. The objective of this study is to unravel the molecular and genetic determinants that govern cultivar-specific shoot regeneration potential in highbush blueberry (Vaccinium corymbosum L.). We conducted comparative transcriptome analysis using two highbush blueberry genotypes: 'Blue Muffin' ('BM') displaying a high regeneration rate (>80%) and 'O'Neal' ('ON') exhibiting a low regeneration rate (<10%). The findings revealed differential expression of numerous auxin-related genes; notably, 'BM' exhibited higher expression of auxin signaling genes compared to 'ON'. Among blueberry orthologs of transcription factors involved in meristem formation in Arabidopsis, expression of VcENHANCER OF SHOOT REGENERATION (VcESR), VcWUSCHEL (VcWUS), and VcCUP-SHAPED COTYLEDON 2.1 were significantly higher in 'BM' relative to 'ON'. Exogenous application of auxin promoted regeneration, as well as VcESR and VcWUS expression, whereas inhibition of auxin biosynthesis yielded the opposite effects. Overexpression of VcESR in 'BM' promoted shoot regeneration under phytohormone-free conditions by activating the expression of cytokinin- and auxin-related genes. These findings provide new insights into the molecular mechanisms underlying blueberry regeneration and have practical implications for enhancing plant regeneration and transformation techniques.
PMID: 38919558
mSystems , IF:6.496 , 2024 Jun : Pe0016524 doi: 10.1128/msystems.00165-24
Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica.
Department of Biotechnology and Environmental Protection, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain.; Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, Spain.
The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria. IMPORTANCE: Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.
PMID: 38837409
Plant J , IF:6.417 , 2024 Jul , V119 (1) : P176-196 doi: 10.1111/tpj.16752
Ocimum kilimandscharicum 4CL11 negatively regulates adventitious root development via accumulation of flavonoid glycosides.
Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.; Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India.
4-Coumarate-CoA Ligase (4CL) is an important enzyme in the phenylpropanoid biosynthesis pathway. Multiple 4CLs are identified in Ocimum species; however, their in planta functions remain enigmatic. In this study, we independently overexpressed three Ok4CL isoforms from Ocimum kilimandscharicum (Ok4CL7, -11, and -15) in Nicotiana benthamiana. Interestingly, Ok4CL11 overexpression (OE) caused a rootless or reduced root growth phenotype, whereas overexpression of Ok4CL15 produced normal adventitious root (AR) growth. Ok4CL11 overexpression in N. benthamiana resulted in upregulation of genes involved in flavonoid biosynthesis and associated glycosyltransferases accompanied by accumulation of specific flavonoid-glycosides (kaempferol-3-rhamnoside, kaempferol-3,7-O-bis-alpha-l-rhamnoside [K3,7R], and quercetin-3-O-rutinoside) that possibly reduced auxin levels in plants, and such effects were not seen for Ok4CL7 and -15. Docking analysis suggested that auxin transporters (PINs/LAXs) have higher binding affinity to these specific flavonoid-glycosides, and thus could disrupt auxin transport/signaling, which cumulatively resulted in a rootless phenotype. Reduced auxin levels, increased K3,7R in the middle and basal stem sections, and grafting experiments (intra and inter-species) indicated a disruption of auxin transport by K3,7R and its negative effect on AR development. Supplementation of flavonoids and the specific glycosides accumulated by Ok4CL11-OE to the wild-type N. benthamiana explants delayed the AR emergence and also inhibited AR growth. While overexpression of all three Ok4CLs increased lignin accumulation, flavonoids, and their specific glycosides were accumulated only in Ok4CL11-OE lines. In summary, our study reveals unique indirect function of Ok4CL11 to increase specific flavonoids and their glycosides, which are negative regulators of root growth, likely involved in inhibition of auxin transport and signaling.
PMID: 38575203
Plant J , IF:6.417 , 2024 Jun , V118 (6) : P2233-2248 doi: 10.1111/tpj.16741
A microRNA528-ZmLac3 module regulates low phosphate tolerance in maize.
School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.; Shandong Zhongnong Tiantai Seed Co., Ltd, Linyi, 273300, China.; Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany.
MicroRNAs are known to play a crucial role in plant development and physiology and become a target for investigating the regulatory mechanism underlying plant low phosphate tolerance. ZmmiR528 has been shown to display significantly different expression levels between wild-type and low Pi-tolerant maize mutants. However, its functional role in maize low Pi tolerance remains unknown. In the present study, we studied the role and underlying molecular mechanism of miR528 in maize with low Pi tolerance. Overexpression of ZmmiR528 in maize resulted in impaired root growth, reduced Pi uptake capacity and compromised resistance to Pi deficiency. By contrast, transgenic maize plants suppressing ZmmiR528 expression showed enhanced low Pi tolerance. Furthermore, ZmLac3 and ZmLac5 which encode laccase were identified and verified as targets of ZmmiR528. ZmLac3 transgenic plants were subsequently generated and were also found to play key roles in regulating maize root growth, Pi uptake and low Pi tolerance. Furthermore, auxin transport was found to be potentially involved in ZmLac3-mediated root growth. Moreover, we conducted genetic complementary analysis through the hybridization of ZmmiR528 and ZmLac3 transgenic plants and found a favorable combination with breeding potential, namely anti-miR528:ZmLac3OE hybrid maize, which exhibited significantly increased low Pi tolerance and markedly alleviated yield loss caused by low Pi stress. Our study has thus identified a ZmmiR528-ZmLac3 module regulating auxin transport and hence root growth, thereby determining Pi uptake and ultimately low Pi tolerance, providing an effective approach for low Pi tolerance improvement through manipulating the expression of miRNA and its target in maize.
PMID: 38569011
Plant J , IF:6.417 , 2024 Jul , V119 (1) : P218-236 doi: 10.1111/tpj.16754
Knockout of endoplasmic reticulum-localized molecular chaperone HSP90.7 impairs seedling development and cellular auxin homeostasis in Arabidopsis.
Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.; Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada.
The Arabidopsis endoplasmic reticulum-localized heat shock protein HSP90.7 modulates tissue differentiation and stress responses; however, complete knockout lines have not been previously reported. In this study, we identified and analyzed a mutant allele, hsp90.7-1, which was unable to accumulate the HSP90.7 full-length protein and showed seedling lethality. Microscopic analyses revealed its essential role in male and female fertility, trichomes and root hair development, proper chloroplast function, and apical meristem maintenance and differentiation. Comparative transcriptome and proteome analyses also revealed the role of the protein in a multitude of cellular processes. Particularly, the auxin-responsive pathway was specifically downregulated in the hsp90.7-1 mutant seedlings. We measured a much-reduced auxin content in both root and shoot tissues. Through comprehensive histological and molecular analyses, we confirmed PIN1 and PIN5 accumulations were dependent on the HSP90 function, and the TAA-YUCCA primary auxin biosynthesis pathway was also downregulated in the mutant seedlings. This study therefore not only fulfilled a gap in understanding the essential role of HSP90 paralogs in eukaryotes but also provided a mechanistic insight on the ER-localized chaperone in regulating plant growth and development via modulating cellular auxin homeostasis.
PMID: 38565312
Plant J , IF:6.417 , 2024 Jun , V118 (6) : P1991-2002 doi: 10.1111/tpj.16723
IbNF-YA1 is a key factor in the storage root development of sweet potato.
Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China.
As a major worldwide root crop, the mechanism underlying storage root yield formation has always been a hot topic in sweet potato [Ipomoea batatas (L.) Lam.]. Previously, we conducted the transcriptome database of differentially expressed genes between the cultivated sweet potato cultivar "Xushu18," its diploid wild relative Ipomoea triloba without storage root, and their interspecific somatic hybrid XT1 with medium-sized storage root. We selected one of these candidate genes, IbNF-YA1, for subsequent analysis. IbNF-YA1 encodes a nuclear transcription factor Y subunit alpha (NF-YA) gene, which is significantly induced by the natural auxin indole-3-acetic acid (IAA). The storage root yield of the IbNF-YA1 overexpression (OE) plant decreased by 29.15-40.22% compared with the wild type, while that of the RNAi plant increased by 10.16-21.58%. Additionally, IAA content increased significantly in OE plants. Conversely, the content of IAA decreased significantly in RNAi plants. Furthermore, real-time quantitative reverse transcription-PCR (qRT-PCR) analysis demonstrated that the expressions of the key genes IbYUCCA2, IbYUCCA4, and IbYUCCA8 in the IAA biosynthetic pathway were significantly changed in transgenic plants. The results indicated that IbNF-YA1 could directly target IbYUCCA4 and activate IbYUCCA4 transcription. The IAA content of IbYUCCA4 OE plants increased by 71.77-98.31%. Correspondingly, the storage root yield of the IbYUCCA4 OE plant decreased by 77.91-80.52%. These findings indicate that downregulating the IbNF-YA1 gene could improve the storage root yield in sweet potato.
PMID: 38549549
Plant J , IF:6.417 , 2024 Jun , V118 (6) : P1732-1746 doi: 10.1111/tpj.16683
Hydrotropism mechanisms and their interplay with gravitropism.
Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978, Israel.; Cell and Developmental Biology Department, School of Biological Sciences, University of California San Diego, La Jolla, California, 92093-0116, USA.; Faculty of Agriculture, Food and Environment, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
Plants partly optimize their water recruitment from the growth medium by directing root growth toward a moisture source, a phenomenon termed hydrotropism. The default mechanism of downward growth, termed gravitropism, often functions to counteract hydrotropism when the water-potential gradient deviates from the gravity vector. This review addresses the identity of the root sites in which hydrotropism-regulating factors function to attenuate gravitropism and the interplay between these various factors. In this context, the function of hormones, including auxin, abscisic acid, and cytokinins, as well as secondary messengers, calcium ions, and reactive oxygen species in the conflict between these two opposing tropisms is discussed. We have assembled the available data on the effects of various chemicals and genetic backgrounds on both gravitropism and hydrotropism, to provide an up-to-date perspective on the interactions that dictate the orientation of root tip growth. We specify the relevant open questions for future research. Broadening our understanding of root mechanisms of water recruitment holds great potential for providing advanced approaches and technologies that can improve crop plant performance under less-than-optimal conditions, in light of predicted frequent and prolonged drought periods due to global climate change.
PMID: 38394056
Mol Ecol , IF:6.185 , 2024 Jun : Pe17437 doi: 10.1111/mec.17437
Ecological transcriptomics reveals stress response pathways of a ground-herb species in a waterlogging gradient of Amazonian riparian forests.
Laboratory of Evolutionary Ecology and Genomics of Neotropical Plants, Department of Plant Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Sao Paulo, Brazil.; Institute of Biodiversity and Forests, Universidade Federal do Oeste do Para, Santarem, Para, Brazil.; Vale Institute of Technology Sustainable Development, Belem, Para, Brazil.; Laboratory of Crop Physiology-Department of Plant Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Sao Paulo, Brazil.; Sao Paulo State University (UNESP), Institute of Biosciences, Rio Claro, Sao Paulo, Brazil.; Laboratory of Computational, Evolutionary, and Systems Biology, Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, Piracicaba, Sao Paulo, Brazil.; Ecology, Monitoring and Sustainable Use of Wetlands (MAUA Research Group), National Institute for Amazon Research (INPA), Manaus, Amazonas, Brazil.; Botany Department, Institute of Biological Sciences; Universidade de Brasilia, Brasilia, Distrito Federal, Brazil.
Environmental stress is a fundamental facet of life and a significant driver of natural selection in the wild. Gene expression diversity may facilitate adaptation to environmental changes, without necessary genetic change, but its role in adaptive divergence remains largely understudied in Neotropical systems. In Amazonian riparian forests, species distribution is predominantly influenced by species' waterlogging tolerance. The flooding gradient delineates distinct wetland forest types, shaping habitats and species characteristics. Here we investigated the molecular basis of environmental stress response in a tropical ground-herb species (Ischnosiphon puberulus) to environmental variation in Amazonian riparian forests. We compared environmental variables and gene expression profiles from individuals collected in two forest types: Igapo and Terra firme in the Amazonian riparian forests. Predictable seasonal flooding poses a significant challenge in Igapo compared to Terra firme environments, with the former presenting higher water column height and longer flooding duration. Our findings suggest that contrasting environmental conditions related to flooding regimes are important drivers of population genetic differentiation and differential gene expression in I. puberulus. Enriched gene ontology terms highlight associations with environmental stresses, such as defence response, water transport, phosphorylation, root development, response to auxin, salicylic acid and oxidative stress. By uncovering key environmental stress response pathways conserved across populations, I. puberulus offers novel genetic insights into the molecular basis of plant reactions to environmental constraints found in flooded areas of this highly biodiverse neotropical ecosystem.
PMID: 38887167
Int J Mol Sci , IF:5.923 , 2024 Jun , V25 (12) doi: 10.3390/ijms25126791
Knockdown of microRNA390 Enhances Maize Brace Root Growth.
National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China.; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.; Department of Biotechnology, Sharda University, Greater Noida 201306, India.; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA.; The Shennong Laboratory, Zhengzhou 450002, China.
Brace root architecture is a critical determinant of maize's stalk anchorage and nutrition uptake, influencing root lodging resistance, stress tolerance, and plant growth. To identify the key microRNAs (miRNAs) in control of maize brace root growth, we performed small RNA sequencing using brace root samples at emergence and growth stages. We focused on the genetic modulation of brace root development in maize through manipulation of miR390 and its downstream regulated auxin response factors (ARFs). In the present study, miR167, miR166, miR172, and miR390 were identified to be involved in maize brace root growth in inbred line B73. Utilizing short tandem target mimic (STTM) technology, we further developed maize lines with reduced miR390 expression and analyzed their root architecture compared to wild-type controls. Our findings show that STTM390 maize lines exhibit enhanced brace root length and increased whorl numbers. Gene expression analyses revealed that the suppression of miR390 leads to upregulation of its downstream regulated ARF genes, specifically ZmARF11 and ZmARF26, which may significantly alter root architecture. Additionally, loss-of-function mutants for ZmARF11 and ZmARF26 were characterized to further confirm the role of these genes in brace root growth. These results demonstrate that miR390, ZmARF11, and ZmARF26 play crucial roles in regulating maize brace root growth; the involved complicated molecular mechanisms need to be further explored. This study provides a genetic basis for breeding maize varieties with improved lodging resistance and adaptability to diverse agricultural environments.
PMID: 38928499
Int J Mol Sci , IF:5.923 , 2024 Jun , V25 (11) doi: 10.3390/ijms25116150
The Mechanism of Exogenous Salicylic Acid and 6-Benzylaminopurine Regulating the Elongation of Maize Mesocotyl.
College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China.; Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China.
The elongation of the mesocotyl plays an important role in the emergence of maize deep-sowing seeds. This study was designed to explore the function of exogenous salicylic acid (SA) and 6-benzylaminopurine (6-BA) in the growth of the maize mesocotyl and to examine its regulatory network. The results showed that the addition of 0.25 mmol/L exogenous SA promoted the elongation of maize mesocotyls under both 3 cm and 15 cm deep-sowing conditions. Conversely, the addition of 10 mg/L exogenous 6-BA inhibited the elongation of maize mesocotyls. Interestingly, the combined treatment of exogenous SA-6-BA also inhibited the elongation of maize mesocotyls. The longitudinal elongation of mesocotyl cells was the main reason affecting the elongation of maize mesocotyls. Transcriptome analysis showed that exogenous SA and 6-BA may interact in the hormone signaling regulatory network of mesocotyl elongation. The differential expression of genes related to auxin (IAA), jasmonic acid (JA), brassinosteroid (BR), cytokinin (CTK) and SA signaling pathways may be related to the regulation of exogenous SA and 6-BA on the growth of mesocotyls. In addition, five candidate genes that may regulate the length of mesocotyls were screened by Weighted Gene Co-Expression Network Analysis (WGCNA). These genes may be involved in the growth of maize mesocotyls through auxin-activated signaling pathways, transmembrane transport, methylation and redox processes. The results enhance our understanding of the plant hormone regulation of mesocotyl growth, which will help to further explore and identify the key genes affecting mesocotyl growth in plant hormone signaling regulatory networks.
PMID: 38892338
Int J Mol Sci , IF:5.923 , 2024 Jun , V25 (11) doi: 10.3390/ijms25116149
Endogenous Hormone Levels and Transcriptomic Analysis Reveal the Mechanisms of Bulbil Initiation in Pinellia ternata.
College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.
Pinellia ternata is a medicinal plant that has important pharmacological value, and the bulbils serve as the primary reproductive organ; however, the mechanisms underlying bulbil initiation remain unclear. Here, we characterized bulbil development via histological, transcriptomic, and targeted metabolomic analyses to unearth the intricate relationship between hormones, genes, and bulbil development. The results show that the bulbils initiate growth from the leaf axillary meristem (AM). In this stage, jasmonic acid (JA), abscisic acid (ABA), isopentenyl adenosine (IPA), and salicylic acid (SA) were highly enriched, while indole-3-acetic acid (IAA), zeatin, methyl jasmonate (MeJA), and 5-dexoxystrigol (5-DS) were notably decreased. Through OPLS-DA analysis, SA has emerged as the most crucial factor in initiating and positively regulating bulbil formation. Furthermore, a strong association between IPA and SA was observed during bulbil initiation. The transcriptional changes in IPT (Isopentenyltransferase), CRE1 (Cytokinin Response 1), A-ARR (Type-A Arabidopsis Response Regulator), B-ARR (Type-B Arabidopsis Response Regulator), AUX1 (Auxin Resistant 1), ARF (Auxin Response Factor), AUX/IAA (Auxin/Indole-3-acetic acid), GH3 (Gretchen Hagen 3), SAUR (Small Auxin Up RNA), GA2ox (Gibberellin 2-oxidase), GA20ox (Gibberellin 20-oxidase), AOS (Allene oxide synthase), AOC (Allene oxide cyclase), OPR (Oxophytodienoate Reductase), JMT (JA carboxy l Methyltransferase), COI1 (Coronatine Insensitive 1), JAZ (Jasmonate ZIM-domain), MYC2 (Myelocytomatosis 2), D27 (DWARF27), SMAX (Suppressor of MAX2), PAL (Phenylalanine Ammonia-Lyase), ICS (Isochorismate Synthase), NPR1 (Non-expressor of Pathogenesis-related Genes1), TGA (TGACG Sequence-specific Binding), PR-1 (Pathogenesis-related), MCSU (Molybdenium Cofactor Sulfurase), PP2C (Protein Phosphatase 2C), and SnRK (Sucrose Non-fermenting-related Protein Kinase 2) were highly correlated with hormone concentrations, indicating that bulbil initiation is coordinately controlled by multiple phytohormones. Notably, eight TFs (transcription factors) that regulate AM initiation have been identified as pivotal regulators of bulbil formation. Among these, WUS (WUSCHEL), CLV (CLAVATA), ATH1 (Arabidopsis Thaliana Homeobox Gene 1), and RAX (Regulator of Axillary meristems) have been observed to exhibit elevated expression levels. Conversely, LEAFY demonstrated contrasting expression patterns. The intricate expression profiles of these TFs are closely associated with the upregulated expression of KNOX(KNOTTED-like homeobox), suggesting a intricate regulatory network underlying the complex process of bulbil initiation. This study offers a profound understanding of the bulbil initiation process and could potentially aid in refining molecular breeding techniques specific to P. ternata.
PMID: 38892337
Int J Mol Sci , IF:5.923 , 2024 Jun , V25 (11) doi: 10.3390/ijms25116127
Gene Regulatory Network Controlling Flower Development in Spinach (Spinacia oleracea L.).
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China.
Spinach (Spinacia oleracea L.) is a dioecious, diploid, wind-pollinated crop cultivated worldwide. Sex determination plays an important role in spinach breeding. Hence, this study aimed to understand the differences in sexual differentiation and floral organ development of dioecious flowers, as well as the differences in the regulatory mechanisms of floral organ development of dioecious and monoecious flowers. We compared transcriptional-level differences between different genders and identified differentially expressed genes (DEGs) related to spinach floral development, as well as sex-biased genes to investigate the flower development mechanisms in spinach. In this study, 9189 DEGs were identified among the different genders. DEG analysis showed the participation of four main transcription factor families, MIKC_MADS, MYB, NAC, and bHLH, in spinach flower development. In our key findings, abscisic acid (ABA) and gibberellic acid (GA) signal transduction pathways play major roles in male flower development, while auxin regulates both male and female flower development. By constructing a gene regulatory network (GRN) for floral organ development, core transcription factors (TFs) controlling organ initiation and growth were discovered. This analysis of the development of female, male, and monoecious flowers in spinach provides new insights into the molecular mechanisms of floral organ development and sexual differentiation in dioecious and monoecious plants in spinach.
PMID: 38892313
Int J Mol Sci , IF:5.923 , 2024 May , V25 (11) doi: 10.3390/ijms25116091
Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain.
Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan.; Department of Agronomy, Brawijaya University, Malang 65145, Indonesia.
The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis. Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis, positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.
PMID: 38892282
Front Plant Sci , IF:5.753 , 2024 , V15 : P1419764 doi: 10.3389/fpls.2024.1419764
Harnessing plant growth-promoting rhizobacteria, Bacillus subtilis and B. aryabhattai to combat salt stress in rice: a study on the regulation of antioxidant defense, ion homeostasis, and photosynthetic parameters.
Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh.; Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.; Department of Agriculture, Noakhali Science and Technology University, Noakhali, Bangladesh.; Department of Agronomy, Kansas State University, Manhattan, KS, United States.
INTRODUCTION: The ongoing global expansion of salt-affected land is a significant factor, limiting the growth and yield of crops, particularly rice (Oryza sativa L). This experiment explores the mitigation of salt-induced damage in rice (cv BRRI dhan100) following the application of plant growth-promoting rhizobacteria (PGPR). METHODS: Rice seedlings, at five- and six-weeks post-transplanting, were subjected to salt stress treatments using 50 and 100 mM NaCl at seven-day intervals. Bacterial cultures consisting of endophytic PGPR (Bacillus subtilis and B. aryabhattai) and an epiphytic PGPR (B. aryabhattai) were administered at three critical stages: transplantation of 42-day-old seedlings, vegetative stage at five weeks post-transplantation, and panicle initiation stage at seven weeks post-transplantation. RESULTS: Salt stress induced osmotic stress, ionic imbalances, and oxidative damage in rice plants, with consequent negative effects on growth, decrease in photosynthetic efficiency, and changes in hormonal regulation, along with increased methylglyoxal (MG) toxicity. PGPR treatment alleviated salinity effects by improving plant antioxidant defenses, restoring ionic equilibrium, enhancing water balance, increasing nutrient uptake, improving photosynthetic attributes, bolstering hormone synthesis, and enhancing MG detoxification. DISCUSSION: These findings highlight the potential of PGPR to bolster physiological and biochemical functionality in rice by serving as an effective buffer against salt stress-induced damage. B. subtilis showed the greatest benefits, while both the endophytic and epiphytic B. aryabhattai had commendable effects in mitigating salt stress-induced damage in rice plants.
PMID: 38938633
Front Plant Sci , IF:5.753 , 2024 , V15 : P1394337 doi: 10.3389/fpls.2024.1394337
Comprehensive analyses of the ARF gene family in cannabis reveals their potential roles in regulating cannabidiol biosynthesis and male flower development.
Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomic, Changsha Medical University, Changsha, China.; Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, China.; Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
BACKGROUND: Cannabidiol (CBD), as an important therapeutic property of the cannabis plants, is mainly produced in the flower organs. Auxin response factors (ARFs) are play a crucial role in flower development and secondary metabolite production. However, the specific roles of ARF gene family in cannabis remain unknown. METHODS: In this study, various bioinformatics analysis of CsARF genes were conducted using online website and bioinformatics, quantitative real time PCR technology was used to investigate the expression patterns of the CsARF gene family in different tissues of different cannabis varieties, and subcellular localization analysis was performed in tobacco leaf. RESULTS: In this study, 22 CsARF genes were identified and found to be unevenly distributed across 9 chromosomes of the cannabis genome. Phylogenetic analysis revealed that the ARF proteins were divided into 4 subgroups. Duplication analysis identified one pair of segmental/whole-genome duplicated CsARF, and three pairs of tandemly duplicated CsARF. Collinearity analysis revealed that two CsARF genes, CsARF4 and CsARF19, were orthologous in both rice and soybean. Furthermore, subcellular localization analysis showed that CsARF2 was localized in the nucleus. Tissue-specific expression analysis revealed that six genes were highly expressed in cannabis male flowers, and among these genes, 3 genes were further found to be highly expressed at different developmental stages of male flowers. Meanwhile, correlation analysis between the expression level of CsARF genes and CBD content in two cultivars 'H8' and 'Y7' showed that the expression level of CsARF13 was negatively correlated with CBD content, while the expression levels of six genes were positively correlated with CBD content. In addition, most of CsARF genes were responsive to IAA treatment. CONCLUSION: Our study laid a foundation for the further studies of CsARFs function in cannabis, and provides candidate genes for breeding varieties with high CBD yield in cannabis production.
PMID: 38903430
Front Plant Sci , IF:5.753 , 2024 , V15 : P1391173 doi: 10.3389/fpls.2024.1391173
Multiple transcription factors involved in the response of Chinese cabbage against Plasmodiophora brassicae.
College of Horticulture, Shenyang Agricultural University, Shenyang, China.; State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; Institute of Vegetable Research, Liaoning Academy of Agricultural Sciences, Shenyang, China.; College of Plant Protection, Shenyang Agricultural University, Shenyang, China.
Clubroot disease, which is caused by the obligate biotrophic protist Plasmodiophora brassicae, leads to the formation of galls, commonly known as pathogen-induced tumors, on the roots of infected plants. The identification of crucial regulators of host tumor formation is essential to unravel the mechanisms underlying the proliferation and differentiation of P. brassicae within plant cells. To gain insight into this process, transcriptomic analysis was conducted to identify key genes associated with both primary and secondary infection of P. brassicae in Chinese cabbage. Our results demonstrate that the k-means clustering of subclass 1, which exhibited specific trends, was closely linked to the infection process of P. brassicae. Of the 1610 differentially expressed genes (DEGs) annotated in subclass 1, 782 were identified as transcription factors belonging to 49 transcription factor families, including bHLH, B3, NAC, MYB_related, WRKY, bZIP, C2H2, and ERF. In the primary infection, several genes, including the predicted Brassica rapa probable pectate lyase, RPM1-interacting protein 4-like, L-type lectin-domain-containing receptor kinase, G-type lectin S-receptor-like serine, B. rapa photosystem II 22 kDa protein, and MLP-like protein, showed significant upregulation. In the secondary infection stage, 45 of 50 overlapping DEGs were upregulated. These upregulated DEGs included the predicted B. rapa endoglucanase, long-chain acyl-CoA synthetase, WRKY transcription factor, NAC domain-containing protein, cell division control protein, auxin-induced protein, and protein variation in compound-triggered root growth response-like and xyloglucan glycosyltransferases. In both the primary and secondary infection stages, the DEGs were predicted to be Brassica rapa putative disease resistance proteins, L-type lectin domain-containing receptor kinases, ferredoxin-NADP reductases, 1-aminocyclopropane-1-carboxylate synthases, histone deacetylases, UDP-glycosyltransferases, putative glycerol-3-phosphate transporters, and chlorophyll a-binding proteins, which are closely associated with plant defense responses, biosynthetic processes, carbohydrate transport, and photosynthesis. This study revealed the pivotal role of transcription factors in the initiation of infection and establishment of intracellular parasitic relationships during the primary infection stage, as well as the proliferation and differentiation of the pathogen within the host cell during the secondary infection stage.
PMID: 38903421
Front Plant Sci , IF:5.753 , 2024 , V15 : P1398818 doi: 10.3389/fpls.2024.1398818
Enigmatic role of auxin response factors in plant growth and stress tolerance.
Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China.; Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China.
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
PMID: 38903418
Theor Appl Genet , IF:5.699 , 2024 Jun , V137 (7) : P157 doi: 10.1007/s00122-024-04655-4
Transcriptomic and physiological analysis provide new insight into seed shattering mechanism in Pennisetum alopecuroides 'Liqiu'.
Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.; College of Grassland Science and Technology, Sichuan Agriculture University, Chengdu, 610000, People's Republic of China.; Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China. fanxifengcau@163.com.; Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China. yysen2008@sina.com.
Through the histological, physiological, and transcriptome-level identification of the abscission zone of Pennisetum alopecuroides 'Liqiu', we explored the structure and the genes related to seed shattering, ultimately revealing the regulatory network of seed shattering in P. alopecuroides. Pennisetum alopecuroides is one of the most representative ornamental grass species of Pennisetum genus. It has unique inflorescence, elegant appearance, and strong stress tolerance. However, the shattering of seeds not only reduces the ornamental effect, but also hinders the seed production. In order to understand the potential mechanisms of seed shattering in P. alopecuroides, we conducted morphological, histological, physiological, and transcriptomic analyses on P. alopecuroides cv. 'Liqiu'. According to histological findings, the seed shattering of 'Liqiu' was determined by the abscission zone at the base of the pedicel. Correlation analysis showed that seed shattering was significantly correlated with cellulase, lignin, auxin, gibberellin, cytokinin and jasmonic acid. Through a combination of histological and physiological analyses, we observed the accumulation of cellulase and lignin during 'Liqiu' seed abscission. We used PacBio full-length transcriptome sequencing (SMRT) combined with next-generation sequencing (NGS) transcriptome technology to improve the transcriptome data of 'Liqiu'. Transcriptomics further identified many differential genes involved in cellulase, lignin and plant hormone-related pathways. This study will provide new insights into the research on the shattering mechanism of P. alopecuroides.
PMID: 38861001
Theor Appl Genet , IF:5.699 , 2024 Jun , V137 (6) : P145 doi: 10.1007/s00122-024-04657-2
Major quantitative trait locus qLA3.1 is related to tomato leaf angle by regulating cell length at the petiole base.
College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.; College of Horticulture, Jilin Agricultural University, Xincheng Street 2888, Changchun, 130118, China.; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China. 2017500022@syau.edu.cn.; Key Laboratory of Protected Horticulture of Education Ministry, Shenyang, 110866, Liaoning, China. 2017500022@syau.edu.cn.; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China. jiangj_syau@syau.edu.cn.; Key Laboratory of Protected Horticulture of Education Ministry, Shenyang, 110866, Liaoning, China. jiangj_syau@syau.edu.cn.
qLA3.1, controlling leaf angle in tomato, was fine-mapped to an interval of 4.45 kb on chromosome A03, and one gene encoding auxin response factor was identified as a candidate gene. Leaf angle is a crucial trait in plant architecture that plays an important role in achieving optimal plant structure. However, there are limited reports on gene localization, cloning, and the function of plant architecture in horticultural crops, particularly regarding leaf angle. In this study, we selected 'Z3' with erect leaves and 'Heinz1706' with horizontal leaves as the phenotype and cytological observation. We combined bulked segregant analysis and fine genetic mapping to identify a candidate gene, known as, i.e., qLA3.1, which was related to tomato leaf angle. Through multiple analyses, we found that Solyc03g113410 was the most probably candidate for qLA3.1, which encoded the auxin response factor SlARF11 in tomato and was homologous to OsARF11 related to leaf angle in rice. We discovered that silencing SlARF11 resulted in upright leaves, while plants with over-expressed SlARF11 exhibited horizontal leaves. We also found that cultivars with erect leaves had a mutation from base G to base A. Moreover, quantitative analysis of plants treated with hormones indicated that SlARF11 might participate in cell elongation and the activation of genes related to auxin and brassinosteroid pathways. Transcriptome analysis further validated that SlARF11 may regulate leaf angle through hormone signaling pathways. These data support the idea that the auxin response factor SlARF11 may have an important function in tomato leaf petiole angles.
PMID: 38822827
iScience , IF:5.458 , 2024 Jun , V27 (6) : P109936 doi: 10.1016/j.isci.2024.109936
The first intron of ARF7 is required for expression in root tips.
School of Biosciences, University of Nottingham, Loughborough, UK.; Department of Biosciences, Durham University, Durham, UK.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France.; International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
Auxin regulates plant growth and development through the transcription factors of the AUXIN RESPONSE FACTOR (ARF) gene family. ARF7 is one of five activators that bind DNA and elicit downstream transcriptional responses. In roots, ARF7 regulates growth, gravitropism and redundantly with ARF19, lateral root organogenesis. In this study we analyzed ARF7 cis-regulation, using different non-coding sequences of the ARF7 locus to drive GFP. We show that constructs containing the first intron led to increased signal in the root tip. Although bioinformatics analyses predicted several transcription factor binding sites in the first intron, we were unable to significantly alter expression of GFP in the root by mutating these. We instead observed the intronic sequences needed to be present within the transcribed sequences to drive expression in the root meristem. These data support a mechanism by which intron-mediated enhancement regulates the tissue specific expression of ARF7 in the root meristem.
PMID: 38832021
Microbiol Res , IF:5.415 , 2024 Jul , V284 : P127726 doi: 10.1016/j.micres.2024.127726
Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.
CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China. Electronic address: sandhya@xtbg.ac.cn.; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China.; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China. Electronic address: yangxd@xtbg.ac.cn.
Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.
PMID: 38643524
Biochem Soc Trans , IF:5.407 , 2024 Jun , V52 (3) : P1191-1197 doi: 10.1042/BST20230836
Lessons from natural molecular glue degraders.
Department of Pharmacology, University of Washington, Seattle, WA, U.S.A.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, U.S.A.
Molecular glue (MG) degraders include plant hormones and therapeutic drugs and have become a hot topic in drug discovery. Unlike bivalent proteolysis targeting chimeras (PROTACs), monovalent MGs can trigger the degradation of non-ligandable proteins by enhancing their interaction with E3 ubiquitin ligases. Here, I analyze the characteristics of natural MG degraders, contrast them with synthetic ones, and provide a rationale for optimizing MGs. In natural MG-based degradation systems, a stable complex is only formed when all three partners (MG, E3 ligase, and substrate) are present, while the affinities between any two components are either weak or undetectable. After the substrate is degraded, the MG will dissociate from its receptor (E3 ligase) due to their low micromolar affinity. In contrast, synthetic MGs, such as immunomodulatory drugs (IMiDs) and CR8, are potent inhibitors of their receptors by blocking the CRBN-native substrate interaction or by occupying the active site of CDK12. Inspired by nature, the affinities of IMiDs to CRBN can be reduced to make those compounds degraders without the E3-inhibitory activity, therefore, minimizing the interference with the physiological substrates of CRBN. Similarly, the CR8-CDK interaction can be weakened to uncouple the degrader function from the kinase inhibition. To mimic natural examples and reduce side effects, future development of MG degraders that lack the inhibitory activity should be considered.
PMID: 38864421
Food Chem X , IF:5.182 , 2024 Jun , V22 : P101306 doi: 10.1016/j.fochx.2024.101306
Exogenous silicon applied at appropriate concentrations is effective at improving tomato nutritional and flavor qualities.
College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China.; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China.
Silicon can mitigate biotic and abiotic stresses in various plants; however, its effects on tomato quality under normal growth conditions are remain unclear. We used a randomized design with four Si treatments, CON (0 mmol/L), T1 (0.6 mmol/L), T2 (1.2 mmol/L), and T3 (1.8 mmol/L) on tomato fruit components Chlorogenic acid and rutin, among polyphenolic components, were increased by 56.99% and 20.31%, respectively, with T2 treatment compared to CON concentrations. T2 increased the sugar-acid ratio by 19.21%, compared to that with the CON treatment, and increased fruit Ca and Mg contents, compared to those with other treatments, improving the characteristic aroma. Furthermore, silicon application reduced the abscisic acid content by 112%, promoting ripening. Endogenous gibberellin, auxin, and salicylic acid, which retard fruit ripening and softening, were increased by 34.96%, 14.56%, and 35.21%, respectively. These findings have far-reaching implications for exogenous Si applications to enrich tomato nutritional and flavor qualities.
PMID: 38550882
Plant Methods , IF:4.993 , 2024 Jun , V20 (1) : P84 doi: 10.1186/s13007-024-01182-7
Mapping the membrane orientation of auxin homeostasis regulators PIN5 and PIN8 in Arabidopsis thaliana root cells reveals their divergent topology.
Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic.; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic. tomasz.nodzynski@ceitec.muni.cz.
PIN proteins establish the auxin concentration gradient, which coordinates plant growth. PIN1-4 and 7 localized at the plasma membrane (PM) and facilitate polar auxin transport while the endoplasmic reticulum (ER) localized PIN5 and PIN8 maintain the intracellular auxin homeostasis. Although an antagonistic activity of PIN5 and PIN8 proteins in regulating the intracellular auxin homeostasis and other developmental events have been reported, the membrane topology of these proteins, which might be a basis for their antagonistic function, is poorly understood. In this study we optimized digitonin based PM-permeabilizing protocols coupled with immunocytochemistry labeling to map the membrane topology of PIN5 and PIN8 in Arabidopsis thaliana root cells. Our results indicate that, except for the similarities in the orientation of the N-terminus, PIN5 and PIN8 have an opposite orientation of the central hydrophilic loop and the C-terminus, as well as an unequal number of transmembrane domains (TMDs). PIN8 has ten TMDs with groups of five alpha-helices separated by the central hydrophilic loop (HL) residing in the ER lumen, and its N- and C-terminals are positioned in the cytoplasm. However, the topology of PIN5 comprises nine TMDs. Its N-terminal end and the central HL face the cytoplasm while its C-terminus resides in the ER lumen. Overall, this study shows that PIN5 and PIN8 proteins have a divergent membrane topology while introducing a toolkit of methods for studying membrane topology of integral proteins including those localized at the ER membrane.
PMID: 38825682
Plant Cell Physiol , IF:4.927 , 2024 Jun doi: 10.1093/pcp/pcae071
Radicle growth regulation of root parasitic plants by auxin-related compounds.
Laboratory of Plant Chemical Regulation, School of Agriculture, Meiji University. 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, Japan.; RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan.; Department of Bioscience, Okayama University of Science, 1-1 Ridaimachi, Kita-ku, Okayama, Okayama, Japan.
Root parasitic plants in the Orobancheceae, such as Striga and Orobanche, cause significant damage to crop production. The germination step of these root parasitic plants is induced by host-root-derived strigolactones (SLs). After germination, the radicles elongate toward the host and invade the host root. We have previously discovered that a simple amino acid, tryptophan (Trp), as well as its metabolite, the plant hormone indole-3-acetic acid (IAA), can inhibit radicle elongation of Orobanche minor. These results suggest that auxin plays a crucial role in the radicle elongation step in root parasitic plants. In this report, we used various auxin chemical probes to dissect the auxin function in the radicle growth of O. minor and Striga hermonthica. We found that synthetic auxins inhibited radicle elongation. In addition, auxin receptor antagonist, auxinole, rescued the inhibition of radicle growth by exogenous IAA. Moreover, a polar transport inhibitor of auxin, N-1-naphthylphthalamic acid (NPA), affected radicle bending. We also proved that exogenously applied Trp is converted into IAA in O. minor seeds, and auxinole partly rescued this radicle elongation. Our data demonstrate a pivotal role of auxin in radicle growth. Thus, manipulation of auxin function in root parasitic plants should offer a useful approach to combat these parasites.
PMID: 38943636
Plant Cell Physiol , IF:4.927 , 2024 Jun doi: 10.1093/pcp/pcae067
Characterization of the Arabidopsis mutant oligocellula6-D reveals the importance of leaf initiation in determining final leaf size.
Department of Life Science, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan.; Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.; Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.; Research Center for Life Science, College of Science, Rikkyo University.
The leaf is a determinate organ with a final size under genetic control. Numerous factors that regulate final leaf size have been identified in Arabidopsis thaliana; although most of these factors play their roles during the growth of leaf primordia, much less is known about leaf initiation and its effects on final leaf size. In this study, we characterized oligocellula6-D (oli6-D), a semidominant mutant of Arabidopsis thaliana with smaller leaves than the wild type due to its reduced leaf cell numbers. A time-course analysis showed that oli6-D had approximately 50% fewer leaf cells, even immediately after leaf initiation; this difference was maintained throughout leaf development. Next-generation sequencing showed that oli6-D had chromosomal duplication involving 2-kbp and 3-Mbp regions of chromosomes 2 and 4, respectively. Several duplicated genes examined had approximately twofold higher expression levels, and at least one gene acquired a new intron/exon structure due to a chromosome fusion event. oli6-D showed reduced auxin responses in leaf primordia, primary roots, and embryos as well as reduced apical dominance and partial auxin-resistant root growth. CRISPR/Cas9-mediated genome editing enabled the removal of a 3-Mbp duplicated segment, the largest targeted deletion in plants thus far. As a result, oli6-D restored the wild-type leaf phenotypes, demonstrating that oli6-D is a gain-of-function mutant. Our results suggest a new regulatory point of leaf size determination that functions at a very early stage of leaf development and is negatively regulated by one or more genes located in the duplicated chromosomal segments.
PMID: 38878059
Pest Manag Sci , IF:4.845 , 2024 Jul , V80 (7) : P3675-3683 doi: 10.1002/ps.8071
A novel mutation in IAA16 is associated with dicamba resistance in Chenopodium album.
School of Agriculture and Environment, Massey University, Palmerston North, New Zealand.; AgResearch Grasslands Research Center, Palmerston North, New Zealand.; Department of Agronomy and Seed Industry, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.; Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China.; Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
BACKGROUND: Resistance to dicamba in Chenopodium album was first documented over a decade ago, however, the molecular basis of dicamba resistance in this species has not been elucidated. In this research, the resistance mechanism in a dicamba-resistant C. album phenotype was investigated using a transcriptomics (RNA-sequence) approach. RESULTS: The dose-response assay showed that the resistant (R) phenotype was nearly 25-fold more resistant to dicamba than a susceptible (S) phenotype of C. album. Also, dicamba treatment significantly induced transcription of the known auxin-responsive genes, Gretchen Hagen 3 (GH3), small auxin-up RNAs (SAURs), and 1-aminocyclopropane-1-carboxylate synthase (ACS) genes in the susceptible phenotype. Comparing the transcripts of auxin TIR/AFB receptors and auxin/indole-3-acetic acid (AUX/IAA) proteins identified from C. album transcriptomic analysis revealed that the R phenotype contained a novel mutation at the first codon of the GWPPV degron motif of IAA16, resulting in an amino acid substitution of glycine (G) with aspartic acid (D). Sequencing the IAA16 gene in other R and S individuals further confirmed that all the R individuals contained the mutation. CONCLUSION: In this research, we describe the dicamba resistance mechanism in the only case of dicamba-resistant C. album reported to date. Prior work has shown that the dicamba resistance allele confers significant growth defects to the R phenotype investigated here, suggesting that dicamba-resistant C. album carrying this novel mutation in the IAA16 gene may not persist at high frequencies upon removal of dicamba application. (c) 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
PMID: 38459963
Plant Sci , IF:4.729 , 2024 Jun : P112160 doi: 10.1016/j.plantsci.2024.112160
Integrating Histology and Phytohormone/Metabolite Profiling to Understanding Rooting in Yellow Camellia Cuttings.
Department of Biochemistry and Genetics, Clemson University, Clemson, SC 29634.; D.W. Daniel High School, Central, SC 29630.; Department of Biochemistry and Genetics, Clemson University, Clemson, SC 29634. Electronic address: hliang@clemson.edu.
Vegetative propagation through cutting is a widely used clonal approach for maintaining desired genotypes. However, some woody species have difficulty forming adventitious roots (ARs) with this approach, including yellow camellia (YC) C. nitidissima. Yellow camellias, prized for their ornamental value and potential health benefits in tea, remain difficult to propagate clonally due to this rooting recalcitrance. As part of the efforts to understand YC cuttings' recalcitrance, we conducted a detailed investigation into AR formation in yellow camellia cuttings via histology and endogenous phytohormone dynamics during this process. We also compared YC endogenous phytohormone and metabolite phytohormone profiles with those of easy-to-root poplar and willow cuttings. Our results indicate that the induction of ARs in YC cuttings is achievable through auxin treatment, and YC ARs are initiated from cambial derivatives and develop a vascular system connected with that of the stem. During AR induction, endogenous hormones showed a dynamic profile, with IAA continuing to increase starting 9 days after auxin induction. JA, JA-Ile, and OPDA showed a similar trend as IAA but decreased by the 45(th) day. Cytokinin first decreased to its lowest level by the 18(th) day and then increased. SA largely exhibited an increasing trend with a drop on the 36(th) day, while ABA first increased to its peak level by the 18(th) day and then decreased. Compared to poplar, YC cuttings had a low level of IAA, IAA-Asp, and OPDA, and a high level of cytokinin and SA. Metabolite profiling highlighted significant down-accumulation of compounds associated with AR formation in yellow camellias, such as citric and ascorbic acid, fructose, sucrose, flavonoids, and phenolic acid derivatives. Our study reveals the unfavorable endogenous hormone and metabolite profiles underlying the rooting recalcitrance of YC cuttings, providing valuable knowledge for addressing this challenge in clonal propagation.
PMID: 38908800
Plant Sci , IF:4.729 , 2024 Jul , V344 : P112103 doi: 10.1016/j.plantsci.2024.112103
PbARF19-mediated auxin signaling regulates lignification in pear fruit stone cells.
Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.; Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: taost@njau.edu.cn.
The stone cells in pear fruits cause rough flesh and low juice, seriously affecting the taste. Lignin has been demonstrated as the main component of stone cells. Auxin, one of the most important plant hormone, regulates most physiological processes in plants including lignification. However, the concentration effect and regulators of auxin on pear fruits stone cell formation remains unclear. Here, endogenous indole-3-acetic acid (IAA) and stone cells were found to be co-localized in lignified cells by immunofluorescence localization analysis. The exogenous treatment of different concentrations of IAA demonstrated that the application of 200 microM IAA significantly reduced stone cell content, while concentrations greater than 500 microM significantly increased stone cell content. Besides, 31 auxin response factors (ARFs) were identified in pear genome. Putative ARFs were predicted as critical regulators involved in the lignification of pear flesh cells by phylogenetic relationship and expression analysis. Furthermore, the negative regulation of PbARF19 on stone cell formation in pear fruit was demonstrated by overexpression in pear fruitlets and Arabidopsis. These results illustrated that the PbARF19-mediated auxin signal plays a critical role in the lignification of pear stone cell by regulating lignin biosynthetic genes. This study provides theoretical and practical guidance for improving fruit quality in pear production.
PMID: 38657909
Plant Sci , IF:4.729 , 2024 Jun , V343 : P112064 doi: 10.1016/j.plantsci.2024.112064
Abolishing ARF8A activity promotes disease resistance in tomato.
Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel; School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv 69978, Israel.; Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel.; Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.; School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv 69978, Israel.; Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel. Electronic address: mayabar@volcani.agri.gov.il.
Auxin response factors (ARFs) are a family of transcription factors that regulate auxin-dependent developmental processes. Class A ARFs function as activators of auxin-responsive gene expression in the presence of auxin, while acting as transcriptional repressors in its absence. Despite extensive research on the functions of ARF transcription factors in plant growth and development, the extent, and mechanisms of their involvement in plant resistance, remain unknown. We have previously reported that mutations in the tomato AUXIN RESPONSE FACTOR8 (ARF8) genes SlARF8A and SlARF8B result in the decoupling of fruit development from pollination and fertilization, leading to partial or full parthenocarpy and increased yield under extreme temperatures. Here, we report that fine-tuning of SlARF8 activity results in increased resistance to fungal and bacterial pathogens. This resistance is mostly preserved under fluctuating temperatures. Thus, fine-tuning SlARF8 activity may be a potent strategy for increasing overall growth and yield.
PMID: 38492890
Plant Sci , IF:4.729 , 2024 Jun , V343 : P112057 doi: 10.1016/j.plantsci.2024.112057
Partially knocking out NtPDK1a/1b/1c/1d simultaneously in Nicotiana tabacum using CRISPR/CAS9 technology results in auxin-related developmental defects.
College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China.; College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China; Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China; Institute of Genetics and Developmental Biology, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: jzliu@zjnu.cn.
The eukaryotic AGC protein kinase subfamily (protein kinase A/ protein kinase G/ protein kinase C-family) is involved in regulating numerous biological processes across kingdoms, including growth and development, and apoptosis. PDK1(3-phosphoinositide-dependent protein kinase 1) is a conserved serine/threonine kinase in eukaryotes, which is both a member of AGC kinase and a major regulator of many other downstream AGC protein kinase family members. Although extensively investigated in model plant Arabidopsis, detailed reports for tobacco PDK1s have been limited. To better understand the functions of PDK1s in tobacco, CRISPR/CAS9 transgenic lines were generated in tetraploid N. tabacum, cv. Samsun (NN) with 5-7 of the 8 copies of 4 homologous PDK1 genes in tobacco genome (NtPDK1a/1b/1c/1d homologs) simultaneously knocked out. Numerous developmental defects were observed in these NtPDK1a/1b/1c/1d CRISPR/CAS9 lines, including cotyledon fusion leaf shrinkage, uneven distribution of leaf veins, convex veins, root growth retardation, and reduced fertility, all of which reminiscence of impaired polar auxin transport. The severity of these defects was correlated with the number of knocked out alleles of NtPDK1a/1b/1c/1d. Consistent with the observation in Arabidopsis, it was found that the polar auxin transport, and not auxin biosynthesis, was significantly compromised in these knockout lines compared with the wild type tobacco plants. The fact that no homozygous plant with all 8 NtPDK1a/1b/1c/1d alleles being knocked out suggested that knocking out 8 alleles of NtPDK1a/1b/1c/1d could be lethal. In conclusion, our results indicated that NtPDK1s are versatile AGC kinases that participate in regulation of tobacco growth and development via modulating polar auxin transport. Our results also indicated that CRISPR/CAS9 technology is a powerful tool in resolving gene redundancy in polyploidy plants.
PMID: 38460553
Plant Cell Rep , IF:4.57 , 2024 Jun , V43 (7) : P169 doi: 10.1007/s00299-024-03250-7
Comparative transcriptomic analysis of the nodulation-competent zone and inference of transcription regulatory network in silicon applied Glycine max [L.]-Merr. Roots.
Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea.; Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.; Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, USA.; Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea.; Watson Crick Centre for Molecular Medicine, Islamia University of Science and Technology, Awantipora, Pulwama, J&K, India.; Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511, Egypt.; Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea. yschung@jejunu.ac.kr.; Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. kyh1229@knu.ac.kr.; Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea. kyh1229@knu.ac.kr.
The study unveils Si's regulatory influence by regulating DEGs, TFs, and TRs. Further bHLH subfamily and auxin transporter pathway elucidates the mechanisms enhancing root development and nodulation. Soybean is a globally important crop serving as a primary source of vegetable protein for millions of individuals. The roots of these plants harbour essential nitrogen fixing structures called nodules. This study investigates the multifaceted impact of silicon (Si) application on soybean, with a focus on root development, and nodulation employing comprehensive transcriptomic analyses and gene regulatory network. RNA sequence analysis was utilised to examine the change in gene expression and identify the noteworthy differentially expressed genes (DEGs) linked to the enhancement of soybean root nodulation and root development. A set of 316 genes involved in diverse biological and molecular pathways are identified, with emphasis on transcription factors (TFs) and transcriptional regulators (TRs). The study uncovers TF and TR genes, categorized into 68 distinct families, highlighting the intricate regulatory landscape influenced by Si in soybeans. Upregulated most important bHLH subfamily and the involvement of the auxin transporter pathway underscore the molecular mechanisms contributing to enhanced root development and nodulation. The study bridges insights from other research, reinforcing Si's impact on stress-response pathways and phenylpropanoid biosynthesis crucial for nodulation. The study reveals significant alterations in gene expression patterns associated with cellular component functions, root development, and nodulation in response to Si.
PMID: 38864921
Plant Cell Rep , IF:4.57 , 2024 Jun , V43 (7) : P165 doi: 10.1007/s00299-024-03260-5
Genome-wide identification of the SAUR gene family and screening for SmSAURs involved in root development in Salvia miltiorrhiza.
College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.; Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China.; Shaanxi Tasly Plants Pharmaceutical Co., Ltd., Shangluo, 726000, Shaanxi, China.; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China. zhangsc@yzu.edu.cn.
SmSAUR4, SmSAUR18, SmSAUR28, SmSAUR37, and SmSAUR38 were probably involved in the auxin-mediated root development in Salvia miltiorrhiza. Salvia miltiorrhiza is a widely utilized medicinal plant in China. Its roots and rhizomes are the main medicinal portions and are closely related to the quality of this herb. Previous studies have revealed that auxin plays pivotal roles in S. miltiorrhiza root development. Whether small auxin-up RNA genes (SAURs), which are crucial early auxin response genes, are involved in auxin-mediated root development in S. miltiorrhiza is worthy of investigation. In this study, 55 SmSAUR genes in S. miltiorrhiza were identified, and their physical and chemical properties, gene structure, cis-acting elements, and evolutionary relationships were analyzed. The expression levels of SmSAUR genes in different organs of S. miltiorrhiza were detected using RNA-seq combined with qRT‒PCR. The root development of S. miltiorrhiza seedlings was altered by the application of indole-3-acetic acid (IAA), and Pearson correlation coefficient analysis was conducted to screen SmSAURs that potentially participate in this physiological process. The diameter of primary lateral roots was positively correlated with SmSAUR4. The secondary lateral root number was positively correlated with SmSAUR18 and negatively correlated with SmSAUR4. The root length showed a positive correlation with SmSAUR28 and SmSAUR37 and a negative correlation with SmSAUR38. The fresh root biomass exhibited a positive correlation with SmSAUR38 and a negative correlation with SmSAUR28. The aforementioned SmSAURs were likely involved in auxin-mediated root development in S. miltiorrhiza. Our study provides a comprehensive overview of SmSAURs and provides the groundwork for elucidating the molecular mechanism underlying root morphogenesis in this species.
PMID: 38861173
DNA Res , IF:4.458 , 2024 Jun , V31 (3) doi: 10.1093/dnares/dsae017
High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China.; Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China.
Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.
PMID: 38809753
Sci Rep , IF:4.379 , 2024 Jun , V14 (1) : P14801 doi: 10.1038/s41598-024-65855-y
Interacting effects of phytohormones and fruit pruning on the morpho-physiological and biochemical attributes of bell pepper.
Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.; Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran. mhaghighi@cc.iut.ac.ir.; Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, Menesi Str. 44, 1118, Budapest, Hungary. mirmazloum.seyediman@uni-mate.hu.
Several factors, such as pruning and phytohormones, have demonstrated an influence on both the quantity and quality in the bell pepper. A factorial experiment using a completely randomized design was conducted on the Lumos yellow bell in a greenhouse. Treatments were the fruit pruning (0, 10, and 30%) and foliar application of phytohormones auxin (AUX) and gibberellic acid (GA(3)) at concentrations of 10 microM AUX, 10 microM GA(3), 10 microM AUX + 10 microM GA(3)+, and 20 microM AUX + 10 microM GA(3) along with controls. The plants were sprayed with phytohormones in four growth stages (1: flowering stage when 50% of the flowers were on the plant, 2: fruiting stage when 50% of the fruits were the size of peas, 3: fruit growth stage when 50% of the fruits had reached 50% of their growth, and 4: ripening stage when 50% of the fruits were at color break). The results of the present investigation showed that pruning rate of 30% yielded the highest flesh thickness and vitamin C content, decreased seed count and hastened fruit ripening. The use of GA(3) along with AUX has been observed to augment diverse fruit quality characteristics. According to the results, the application of 10% pruning in combination with 20 microM AUX and 10 microM GA(3) demonstrated the most significant levels of carotenoids, chlorophyll, and fruit length. The experimental group subjected to the combined treatment of 30% pruning and 10 microM AUX + 10 microM GA(3) showed the most noteworthy levels of vitamin C, fruit weight, and fruit thickness. The groups that received the 10 microM GA(3) and 20 microM AUX + 10 microM GA(3) treatments exhibited the most favorable fruit flavor. According to the research results, the implementation of hormonal treatments 10 microM AUX and 10 microM AUX + 10 microM GA(3) in combination with a 30% pruning strategy resulted in the most advantageous yield of bell peppers.
PMID: 38926600
Sci Rep , IF:4.379 , 2024 Jun , V14 (1) : P13484 doi: 10.1038/s41598-024-58949-0
Differential gene expression in irradiated potato tubers contributed to sprout inhibition and quality retention during a commercial scale storage.
Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.; Natural Storage Solutions Private Limited, Gandhinagar, 382 729, India.; Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India. sgautam@barc.gov.in.; Homi Bhabha National Institute, Mumbai, 400 094, India. sgautam@barc.gov.in.
Current study is the first ever storage cum market trial of radiation processed (28 tons) of potato conducted in India at a commercial scale. The objective was to affirm the efficacy of very low dose of gamma radiation processing of potato for extended storage with retained quality and to understand the plausible mechanism at the gene modulation level for suppression of potato sprouting. Genes pertaining to abscisic acid (ABA) biosynthesis were upregulated whereas its catabolism was downregulated in irradiated potatoes. Additionally, genes related to auxin buildup were downregulated in irradiated potatoes. The change in the endogenous phytohormone contents in irradiated potato with respect to the control were found to be correlated well with the differential expression level of certain related genes. Irradiated potatoes showed retention of processing attributes including cooking and chip-making qualities, which could be attributed to the elevated expression of invertase inhibitor in these tubers. Further, quality retention in radiation treated potatoes may also be related to inhibition in the physiological changes due to sprout inhibition. Ecological and economical analysis of national and global data showed that successful adoption of radiation processing may gradually replace sprout suppressants like isopropyl N-(3-chlorophenyl) carbamate (CIPC), known to leave residue in the commodity, stabilize the wholesale annual market price, and provide a boost to the industries involved in product manufacturing.
PMID: 38866836
Plant Physiol Biochem , IF:4.27 , 2024 Jun , V213 : P108827 doi: 10.1016/j.plaphy.2024.108827
Genomic analysis of PIN-FORMED genes reveals the roles of SmPIN3 in root architecture development in Salvia miltiorrhiza.
College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.; Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China. Electronic address: zhangsc@yzu.edu.cn.
Salvia miltiorrhiza is a widely utilized medicinal herb in China. Its roots serve as crucial raw materials for multiple drugs. The root morphology is essential for the quality of this herb, but little is known about the molecular mechanism underlying the root development in S. miltiorrhiza. Previous study reveals that the polar auxin transport is critical for lateral root development in S. miltiorrhiza. Whether the auxin efflux carriers PIN-FORMEDs (PINs) are involved in this process is worthy investigation. In this study, we identified nine SmPIN genes in S. miltiorrhiza, and their chromosome localization, physico-chemical properties, and phylogenetic relationship were analyzed. SmPINs were unevenly distributed across four chromosomes, and a variety of hormone responsive elements were detected in their promoter regions. The SmPIN proteins were divided into three branches according to the phylogenetic relationship. SmPINs with close evolutionary distance showed similar conserved motif features. The nine SmPINs showed distinct tissue-specific expression patterns and most of them were auxin-inducible genes. We generated SmPIN3 overexpression S. miltiorrhiza seedlings to investigate the function of SmPIN3 in the root development in this species. The results demonstrated that SmPIN3 regulated the root morphogenesis of S. miltiorrhiza by simultaneously affecting the lateral root development and the root anatomical structure. The root morphology, patterns of root xylem and phloem as well as the expressions of genes in the auxin signaling pathway all altered in the SmPIN3 overexpression lines. Our findings provide new insights for elucidating the regulatory roles of SmPINs in the auxin-mediated root development in S. miltiorrhiza.
PMID: 38875779
Plant Physiol Biochem , IF:4.27 , 2024 Jun , V213 : P108813 doi: 10.1016/j.plaphy.2024.108813
Plastid dynamism integrates development and environment.
Department of Environmental Biology, Sapienza University of Rome, Italy. Electronic address: mariamaddalena.altamura@uniroma1.it.; Department of Environmental Biology, Sapienza University of Rome, Italy.
In land plants plastid type differentiation occurs concomitantly with cellular differentiation and the transition from one type to another is under developmental and environmental control. Plastid dynamism is based on a bilateral communication between plastids and nucleus through anterograde and retrograde signaling. Signaling occurs through the interaction with specific phytohormones (abscisic acid, strigolactones, jasmonates, gibberellins, brassinosteroids, ethylene, salicylic acid, cytokinin and auxin). The review is focused on the modulation of plastid capabilities at both transcriptional and post-translational levels at the crossroad between development and stress, with a particular attention to the chloroplast, because the most studied plastid type. The role of plastid-encoded and nuclear-encoded proteins for plastid development and stress responses, and the changes of plastid fate through the activity of stromules and plastoglobules, are discussed. Examples of plastid dynamism in response to soil stress agents (salinity, lead, cadmium, arsenic, and chromium) are described. Albinism and root greening are described based on the modulation activities of auxin and cytokinin. The physiological and functional responses of the sensory epidermal and vascular plastids to abiotic and biotic stresses along with their specific roles in stress sensing are described together with their potential modulation of retrograde signaling pathways. Future research perspectives include an in-depth study of sensory plastids to explore their potential for establishing a transgenerational memory to stress. Suggestions about anterograde and retrograde pathways acting at interspecific level and on the lipids of plastoglobules as a novel class of plastid morphogenic agents are provided.
PMID: 38861821
Plant Physiol Biochem , IF:4.27 , 2024 Jul , V212 : P108761 doi: 10.1016/j.plaphy.2024.108761
Abscisic acid induces PpeKIL1 to terminate fruit growth and promote fruit abortion in peach (Prunus persica).
Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: huichou1987@126.com.; Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: wangxiao@aaas.org.cn.; Egyptian Deserts Genbank, Desert Research Center, Cairo, Egypt. Electronic address: mohamed.amar@wbgcas.cn.; Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: shengyu@aaas.org.cn.; Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: spei2491@gmail.com.; School of Life Science, Anhui Agricultural University, No. 130, Changjiangxi Road, Hefei, 230036, China. Electronic address: 978221324@qq.com.; School of Life Science, Anhui Agricultural University, No. 130, Changjiangxi Road, Hefei, 230036, China. Electronic address: wangyunyun@stu.ahau.edu.cn.; Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: xieqingmei@aaas.org.cn.; Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: 543613921@qq.com.; Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: panhaifa@aaas.org.cn.; Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China. Electronic address: jinyunzhang600@163.com.
Abnormal pollination from chance events or hybridization between species leads to unusual embryo development, resulting in fruit abortion. To elucidate the mechanism underlying fruit abortion, we conducted a comprehensive analysis of the transcriptome and hormone profiles in aborting fruits (AF) derived from an interspecific cross between the peach cultivar 'Huangjinmi 3' and the Prunus mume cultivar 'Jiangmei', as well as in normal-seeded fruits (NF) resulting from an intraspecific cross of 'Huangjinmi 3' with the 'Manyuanhong' peach cultivars. Growth of AF was inhibited during the exponential growth phase, with up-regulation of oxidative stress related genes and down-regulation of DNA replication and cell cycle genes. Accumulation of the tissue growth-related hormones auxin and cytokinin was reduced in AF, while levels of the growth inhibiting hormone abscisic acid (ABA) were higher compared to NF. The increased ABA concentration aligned with down-regulation of the ABA catabolism gene CYP707A2, which encodes abscisic acid 8'-hydroxylase. Correlation analysis showed ABA could explain the maximum proportion of differently expressed genes between NF and AF. We also showed that expression of KIRA1-LIKE1 (PpeKIL1), a peach ortholog of the Arabidopsis KIRA1 gene, was up-regulated in AF. PpeKIL1 promotes senescence or delays normal growth in tobacco and Arabidopsis, and its promoter activity increases with exogenous ABA treatment. Our study demonstrates a candidate mechanism where ABA induces expression of PpeKIL1, which further blocks normal fruit growth and triggers fruit abscission.
PMID: 38805756
Plant Physiol Biochem , IF:4.27 , 2024 Jul , V212 : P108731 doi: 10.1016/j.plaphy.2024.108731
Seed endophytic bacterium Lysinibacillus sp. (ZM1) from maize (Zea mays L.) shapes its root architecture through modulation of auxin biosynthesis and nitrogen metabolism.
Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 276957612, USA. Electronic address: gpal@ncsu.edu.; National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.; Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.; Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA.; Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India. Electronic address: skverma.bot@bhu.ac.in.
Seed endophytic bacteria have been shown to promote the growth and development of numerous plants. However, the underlying mechanism still needs to be better understood. The present study aims to investigate the role of a seed endophytic bacterium Lysinibacillus sp. (ZM1) in promoting plant growth and shaping the root architecture of maize seedlings. The study explores how bacteria-mediated auxin biosynthesis and nitrogen metabolism affect plant growth promotion and shape the root architecture of maize seedlings. The results demonstrate that ZM1 inoculation significantly enhances root length, root biomass, and the number of seminal roots in maize seedlings. Additionally, the treated seedlings exhibit increased shoot biomass and higher levels of photosynthetic pigments. Confocal laser scanning microscopy (CLSM) analysis revealed extensive colonization of ZM1 on root hairs, as well as in the cortical and stellar regions of the root. Furthermore, LC-MS analysis demonstrated elevated auxin content in the roots of the ZM1 treated maize seedlings compared to the uninoculated control. Inoculation with ZM1 significantly increased the levels of endogenous ammonium content, GS, and GOGAT enzyme activities in the roots of treated maize seedlings compared to the control, indicating enhanced nitrogen metabolism. Furthermore, inoculation of bacteria under nitrogen-deficient conditions enhanced plant growth, as evidenced by increased root shoot length, fresh and dry weights, average number of seminal roots, and content of photosynthetic pigments. Transcript analysis indicated upregulation of auxin biosynthetic genes, along with genes involved in nitrogen metabolism at different time points in roots of ZM1-treated maize seedlings. Collectively, our findings highlight the positive impact of Lysinibacillus sp. ZM1 inoculation on maize seeds by improving root architecture through modulation of auxin biosynthesis and affecting various nitrogen metabolism related parameters. These findings provide valuable insights into the potential utilization of seed endophytic bacteria as biofertilizers to enhance plant growth and yield in nutrient deficient soils.
PMID: 38761545
Plant Physiol Biochem , IF:4.27 , 2024 Jun , V211 : P108676 doi: 10.1016/j.plaphy.2024.108676
Identification and functional characterization of ABC transporters for selenium accumulation and tolerance in soybean.
National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China.; Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China. Electronic address: leiming@gxyyzwy.com.; National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China. Electronic address: lily7819@whpu.edu.cn.
ATP-binding cassette (ABC) transporters were crucial for various physiological processes like nutrition, development, and environmental interactions. Selenium (Se) is an essential micronutrient for humans, and its role in plants depends on applied dosage. ABC transporters are considered to participate in Se translocation in plants, but detailed studies in soybean are still lacking. We identified 196 ABC genes in soybean transcriptome under Se exposure using next-generation sequencing and single-molecule real-time sequencing technology. These proteins fell into eight subfamilies: 8 GmABCA, 51 GmABCB, 39 GmABCC, 5 GmABCD, 1 GmABCE, 10 GmABCF, 74 GmABCG, and 8 GmABCI, with amino acid length 121-3022 aa, molecular weight 13.50-341.04 kDa, and isoelectric point 4.06-9.82. We predicted a total of 15 motifs, some of which were specific to certain subfamilies (especially GmABCB, GmABCC, and GmABCG). We also found predicted alternative splicing in GmABCs: 60 events in selenium nanoparticles (SeNPs)-treated, 37 in sodium selenite (Na(2)SeO(3))-treated samples. The GmABC genes showed differential expression in leaves and roots under different application of Se species and Se levels, most of which are belonged to GmABCB, GmABCC, and GmABCG subfamilies with functions in auxin transport, barrier formation, and detoxification. Protein-protein interaction and weighted gene co-expression network analysis suggested functional gene networks with hub ABC genes, contributing to our understanding of their biological functions. Our results illuminate the contributions of GmABC genes to Se accumulation and tolerance in soybean and provide insight for a better understanding of their roles in soybean as well as in other plants.
PMID: 38714125
BMC Plant Biol , IF:4.215 , 2024 Jun , V24 (1) : P613 doi: 10.1186/s12870-024-05301-3
GmHXK2 promotes the salt tolerance of soybean seedlings by mediating AsA synthesis, and auxin synthesis and distribution.
School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, PR China.; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, PR China. cherish_lab@163.com.
BACKGROUND: Salt is an important factor that affects crop productivity. Plant hexokinases (HXKs) are key enzymes in the glycolytic pathway and sugar signaling transduction pathways of plants. In previous studies, we identified and confirmed the roles of GmHXK2 in salt tolerance. RESULTS: In this study, we analyzed the tissue-specific expression of GmHXK2 at different growth stages throughout the plant's life cycle. The results showed that GmHXK2 was expressed significantly in all tissues at vegetative stages, including germination and seedling. However, no expression was detected in the pods, and there was little expression in flowers during the later mature period. Arabidopsis plants overexpressing the GmHXK2 (OE) had more lateral roots. The OE seedlings also produced higher levels of auxin and ascorbic acid (AsA). Additionally, the expression levels of genes PMM, YUC4/YUC6/YUC8, and PIN/LAX1,LAX3, which are involved respectively in the synthesis of AsA and auxin, as well as polar auxin transport, were upregulated in OE plants. This upregulation occurred specifically under exogenous glucose treatment. AtHKT1, AtSOS1, and AtNHX1 were up-regulated in OE plants under salt stress, suggesting that GmHXK2 may modulate salt tolerance by maintaining ion balance within the cells and alleviating damage caused by salt stress. Additionally, we further confirmed the interaction between GmHXK2 and the protein GmPMM through yeast two-hybridization and bimolecular fluorescence complementation assays, respectively. CONCLUSION: The expression of GmHXK2 gene in plants is organ-specific and developmental stage specific. GmHXK2 not only regulates the synthesis of AsA and the synthesis and distribution of auxin, but also promotes root elongation and induces lateral root formation, potentially enhancing soil water absorption. This study reveals the crosstalk between sugar signaling and hormone signaling in plants, where GmHXK2 acts as a glucose sensor through its interaction with GmPMM, and sheds light on the molecular mechanism by which GmHXK2 gene is involved in salt tolerance in plants.
PMID: 38937682
BMC Plant Biol , IF:4.215 , 2024 Jun , V24 (1) : P581 doi: 10.1186/s12870-024-05277-0
Physiological and transcriptome analysis of changes in endogenous hormone and sugar content during the formation of tender asparagus stems.
College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.; Agricultural Equipment Research Institute, Chengdu Academy of Agricultural and Forest Sciences, Chengdu, 611130, China.; College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China. zhengyx13520@sicau.edu.cn.
Asparagus is a nutritionally dense stem vegetable whose growth and development are correlated with its quality and yield. To investigate the dynamic changes and underlying mechanisms during the elongation and growth process of asparagus stems, we documented the growth pattern of asparagus and selected stem segments from four consecutive elongation stages using physiological and transcriptome analyses. Notably, the growth rate of asparagus accelerated at a length of 25 cm. A significant decrease in the concentration of sucrose, fructose, glucose, and additional sugars was observed in the elongation region of tender stems. Conversely, the levels of auxin and gibberellins(GAs) were elevated along with increased activity of enzymes involved in sucrose degradation. A significant positive correlation existed between auxin, GAs, and enzymes involved in sucrose degradation. The ABA content gradually increased with stem elongation. The tissue section showed that cell elongation is an inherent manifestation of stem elongation. The differential genes screened by transcriptome analysis were enriched in pathways such as starch and sucrose metabolism, phytohormone synthesis metabolism, and signal transduction. The expression levels of genes such as ARF, GA20ox, NCED, PIF4, and otherswere upregulated during stem elongation, while DAO, GA2ox, and other genes were downregulated. The gene expression level was consistent with changes in hormone content and influenced the cell length elongation. Additionally, the expression results of RT-qPCR were consistent with RNA-seq. The observed variations in gene expression levels, endogenous hormones and sugar changes during the elongation and growth of asparagus tender stems offer valuable insights for future investigations into the molecular mechanisms of asparagus stem growth and development and provide a theoretical foundation for cultivation and production practices.
PMID: 38898382
BMC Plant Biol , IF:4.215 , 2024 Jun , V24 (1) : P551 doi: 10.1186/s12870-024-05263-6
Transcriptomics analyses reveal the key genes involved in stamen petaloid formation in Alcea rosea L.
College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China.; College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China. jiayin_cn@163.com.
Alcea rosea L. is a traditional flower with a long cultivation history. It is extensively cultivated in China and is widely planted in green belt parks or used as cut flowers and potted ornamental because of its rich colors and flower shapes. Double-petal A. rosea flowers have a higher aesthetic value compared to single-petal flowers, a phenomenon determined by stamen petaloid. However, the underlying molecular mechanism of this phenomenon is still very unclear. In this study, an RNA-based comparative transcriptomic analysis was performed between the normal petal and stamen petaloid petal of A. rosea. A total of 3,212 differential expressed genes (DEGs), including 2,620 up-regulated DEGs and 592 down-regulated DEGs, were identified from 206,188 unigenes. Numerous DEGs associated with stamen petaloid were identified through GO and KEGG enrichment analysis. Notably, there were 63 DEGs involved in the plant hormone synthesis and signal transduction, including auxin, cytokinin, gibberellin, abscisic acid, ethylene, brassinosteroid, jasmonic acid, and salicylic acid signaling pathway and 56 key transcription factors (TFs), such as MADS-box, bHLH, GRAS, and HSF. The identification of these DEGs provides an important clue for studying the regulation pathway and mechanism of stamen petaloid formation in A. rosea and provides valuable information for molecular plant breeding.
PMID: 38877392
BMC Plant Biol , IF:4.215 , 2024 Jun , V24 (1) : P511 doi: 10.1186/s12870-024-05210-5
Why can Mikania micrantha cover trees quickly during invasion?
Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.; School of Life Sciences, Huizhou University, Huizhou, 516007, China.; Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.; Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China. pengchl@scib.ac.cn.
The invasion of Mikania micrantha by climbing and covering trees has rapidly caused the death of many shrubs and trees, seriously endangering forest biodiversity. In this study, M. micrantha seedlings were planted together with local tree species (Cryptocarya concinna) to simulate the process of M. micrantha climbing under the forest. We found that the upper part of the M. micrantha stem lost its support after climbing to the top of the tree, grew in a turning and creeping manner, and then grew branches rapidly to cover the tree canopy. Then, we simulated the branching process through turning treatment. We found that a large number of branches had been formed near the turning part of the M. micrantha stem (TP). Compared with the upper part of the main stem (UP), the contents of plant hormones (auxin, cytokinin, gibberellin), soluble sugars (sucrose, glucose, fructose) and trehalose-6-phosphate (T6P) were significantly accumulated at TP. Further combining the transcriptome data of different parts of the main stem under erect or turning treatment, a hypothetical regulation model to illustrate how M. micrantha can quickly cover trees was proposed based on the regulation of sugars and hormones on plant branching; that is, the lack of support after ascending the top of the tree led to turning growth of the main stem, and the enhancement of sugars and T6P levels in the TP may first drive the release of nearby dormant buds. Plant hormone accumulation may regulate the entrance of buds into sustained growth and maintain the elongation of branches together with sugars to successfully covering trees.
PMID: 38844870
BMC Plant Biol , IF:4.215 , 2024 May , V24 (1) : P482 doi: 10.1186/s12870-024-05204-3
Appropriate mowing can promote the growth of Anabasis aphylla through the auxin metabolism pathway.
Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China.; Key Laboratory of Special Fruit and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.; Southern Xinjiang Research Institute, Shihezi University, Tumushuk, 843806, Xinjiang, China. 17699436688@163.com.; Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China. panzhenyuandawood@163.com.
Anabasis aphylla (A. aphylla), a species of the Amaranthaceae family, is widely distributed in northwestern China and has high pharmacological value and ecological functions. However, the growth characteristics are poorly understood, impeding its industrial development for biopesticide development. Here, we explored the regenerative capacity of A. aphylla. To this end, different lengths of the secondary branches of perennial branches were mowed at the end of March before sprouting. The four treatments were no mowing (M0) and mowing 1/3, 2/3, and the entire length of the secondary branches of perennial branches (M1-M3, respectively). Next, to evaluate the compensatory growth after mowing, new assimilate branches' related traits were recorded every 30 days, and the final biomass was recorded. The mowed plants showed a greater growth rate of assimilation branches than un-mowed plants. Additionally, with the increasing mowing degree, the growth rate and the final biomass of assimilation branches showed a decreasing trend, with the greatest growth rate and final biomass in response to M1. To evaluate the mechanism of the compensatory growth after mowing, a combination of dynamic (0, 1, 5, and 8 days after mowing) plant hormone-targeted metabolomics and transcriptomics was performed for the M0 and M1 treatment. Overall, 26 plant hormone metabolites were detected, 6 of which significantly increased after mowing compared with control: Indole-3-acetyl-L-valine methyl ester, Indole-3-carboxylic acid, Indole-3-carboxaldehyde, Gibberellin A24, Gibberellin A4, and cis (+)-12-oxo-phytodienoic acid. Additionally, 2,402 differentially expressed genes were detected between the mowed plants and controls. By combining clustering analysis based on expression trends after mowing and gene ontology analysis of each cluster, 18 genes related to auxin metabolism were identified, 6 of which were significantly related to auxin synthesis. Our findings suggest that appropriate mowing can promote A. aphylla growth, regulated by the auxin metabolic pathway, and lays the foundation for the development of the industrial value of A. aphylla.
PMID: 38822275
BMC Plant Biol , IF:4.215 , 2024 Jun , V24 (1) : P485 doi: 10.1186/s12870-024-05174-6
Molecular mechanism of brassinosteroids involved in root gravity response based on transcriptome analysis.
College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, 710119, PR China.; Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, Shaanxi Province, 716000, PR China.; College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, 710119, PR China. hong@snnu.edu.cn.
BACKGROUND: Brassinosteroids (BRs) are a class of phytohormones that regulate a wide range of developmental processes in plants. BR-associated mutants display impaired growth and response to developmental and environmental stimuli. RESULTS: Here, we found that a BR-deficient mutant det2-1 displayed abnormal root gravitropic growth in Arabidopsis, which was not present in other BR mutants. To further elucidate the role of DET2 in gravity, we performed transcriptome sequencing and analysis of det2-1 and bri1-116, bri1 null mutant allele. Expression levels of auxin, gibberellin, cytokinin, and other related genes in the two mutants of det2-1 and bri1-116 were basically the same. However, we only found that a large number of JAZ (JASMONATE ZIM-domain) genes and jasmonate synthesis-related genes were upregulated in det2-1 mutant, suggesting increased levels of endogenous JA. CONCLUSIONS: Our results also suggested that DET2 not only plays a role in BR synthesis but may also be involved in JA regulation. Our study provides a new insight into the molecular mechanism of BRs on the root gravitropism.
PMID: 38822229
BMC Plant Biol , IF:4.215 , 2024 May , V24 (1) : P473 doi: 10.1186/s12870-024-05195-1
Integrated analyses of ionomics, phytohormone profiles, transcriptomics, and metabolomics reveal a pivotal role of carbon-nano sol in promoting the growth of tobacco plants.
Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.; Beijing Life Science Academy (BLSA), Beijing, 102209, China.; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.; Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China. chen_qiansi@163.com.; Beijing Life Science Academy (BLSA), Beijing, 102209, China. chen_qiansi@163.com.
BACKGROUND: Carbon nano sol (CNS) can markedly affect the plant growth and development. However, few systematic analyses have been conducted on the underlying regulatory mechanisms in plants, including tobacco (Nicotiana tabacum L.). RESULTS: Integrated analyses of phenome, ionome, transcriptome, and metabolome were performed in this study to elucidate the physiological and molecular mechanisms underlying the CNS-promoting growth of tobacco plants. We found that 0.3% CNS, facilitating the shoot and root growth of tobacco plants, significantly increased shoot potassium concentrations. Antioxidant, metabolite, and phytohormone profiles showed that 0.3% CNS obviously reduced reactive oxygen species production and increased antioxidant enzyme activity and auxin accumulation. Comparative transcriptomics revealed that the GO and KEGG terms involving responses to oxidative stress, DNA binding, and photosynthesis were highly enriched in response to exogenous CNS application. Differential expression profiling showed that NtNPF7.3/NtNRT1.5, potentially involved in potassium/auxin transport, was significantly upregulated under the 0.3% CNS treatment. High-resolution metabolic fingerprints showed that 141 and 163 metabolites, some of which were proposed as growth regulators, were differentially accumulated in the roots and shoots under the 0.3% CNS treatment, respectively. CONCLUSIONS: Taken together, this study revealed the physiological and molecular mechanism underlying CNS-mediated growth promotion in tobacco plants, and these findings provide potential support for improving plant growth through the use of CNS.
PMID: 38811869
Planta , IF:4.116 , 2024 Jun , V260 (1) : P30 doi: 10.1007/s00425-024-04463-6
Ectopic expression of OsWOX9A alters leaf anatomy and plant architecture in rice.
Hainan Institute, Yazhou Bay Science and Technology City, Zhejiang University, Sanya, 572025, China.; National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China.; Hainan Institute, Yazhou Bay Science and Technology City, Zhejiang University, Sanya, 572025, China. 0015611@zju.edu.cn.; Hainan Seed Industry Laboratory, Yazhou Bay Science and Technology City, Sanya, 572025, China. 0015611@zju.edu.cn.
Ectopic expression of OsWOX9A induces narrow adaxially rolled rice leaves with larger bulliform cells and fewer large veins, probably through regulating the expression of auxin-related and expansin genes. The WUSCHEL-related homeobox (WOX) family plays a pivotal role in plant development by regulating genes involved in various aspects of growth and differentiation. OsWOX9A (DWT1) has been linked to tiller growth, uniform plant growth, and flower meristem activity. However, its impact on leaf growth and development in rice has not been studied. In this study, we investigated the biological role of OsWOX9A in rice growth and development using transgenic plants. Overexpression of OsWOX9A conferred narrow adaxially rolled rice leaves and altered plant architecture. These plants exhibited larger bulliform cells and fewer larger veins compared to wild-type plants. OsWOX9A overexpression also reduced plant height, tiller number, and seed-setting rate. Comparative transcriptome analysis revealed several differentially expressed auxin-related and expansin genes in OsWOX9A overexpressing plants, consistent with their roles in leaf and plant development. These results indicate that the ectopic expression of OsWOX9A may have multiple effects on the development and growth of rice, providing a more comprehensive picture of how the WOX9 subfamily contributes to leaf development and plant architecture.
PMID: 38879830
Planta , IF:4.116 , 2024 Jun , V260 (1) : P24 doi: 10.1007/s00425-024-04459-2
Structure and dynamics of microbial communities associated with the resurrection plant Boea hygrometrica in response to drought stress.
State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China. sunrunze@ibcas.ac.cn.; China National Botanical Garden, 100093, Beijing, China. sunrunze@ibcas.ac.cn.; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.; University of Chinese Academy of Sciences, 100049, Beijing, China.; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China. deng@ibcas.ac.cn.; China National Botanical Garden, 100093, Beijing, China. deng@ibcas.ac.cn.
The resurrection plant Boea hygrometrica selectively recruits and assembles drought-specific microbial communities across the plant-soil compartments, which may benefit plant growth and fitness under extreme drought conditions. Plant-associated microbes are essential for facilitating plant growth and fitness under drought stress. The resurrection plant Boea hygrometrica in natural habitats with seasonal rainfall can survive rapid desiccation, yet their interaction with microbiomes under drought conditions remains unexplored. This study examined the bacterial and fungal microbiome structure and drought response across plant-soil compartments of B. hygrometrica by high-throughput amplicon sequencing of 16S rRNA gene and internal transcribed spacer. Our results demonstrated that the diversity, composition, and functional profile of the microbial community varied considerably across the plant-soil compartments and were strongly affected by drought stress. Bacterial and fungal diversity was significantly reduced from soil to endosphere and belowground to aboveground compartments. The compartment-specific enrichment of the dominant bacteria phylum Cyanobacteriota and genus Methylorubrum in leaf endosphere, genera Pseudonocardia in rhizosphere soil and Actinoplanes in root endosphere, and fungal phylum Ascomycota in the aboveground compartments and genera Knufia in root endosphere and Cladosporium in leaf endosphere composed part of the core microbiota with corresponding enrichment of beneficial functions for plant growth and fitness. Moreover, the recruitment of dominant microbial genera Sphingosinicella and Plectosphaerella, Ceratobasidiaceae mycorrhizal fungi, and numerous plant growth-promoting bacteria involving nutrient supply and auxin regulation was observed in desiccated B. hygrometrica plants. Our results suggest that the stable assembled drought-specific microbial community of B. hygrometrica may contribute to plant survival under extreme environments and provide valuable microbial resources for the microbe-mediated drought tolerance enhancement in crops.
PMID: 38858226
Genes (Basel) , IF:4.096 , 2024 Jun , V15 (6) doi: 10.3390/genes15060760
A Small Auxin-Up RNA Gene, IbSAUR36, Regulates Adventitious Root Development in Transgenic Sweet Potato.
Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Key Laboratory of Phylogeny and Comparative Genomics of the Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China.
Small auxin-upregulated RNAs (SAURs), as the largest family of early auxin-responsive genes, play important roles in plant growth and development processes, such as auxin signaling and transport, hypocotyl development, and tolerance to environmental stresses. However, the functions of few SAUR genes are known in the root development of sweet potatoes. In this study, an IbSAUR36 gene was cloned and functionally analyzed. The IbSAUR36 protein was localized to the nucleus and plasma membrane. The transcriptional level of this gene was significantly higher in the pencil root and leaf.This gene was strongly induced by indole-3-acetic acid (IAA), but it was downregulated under methyl-jasmonate(MeJA) treatment. The promoter of IbSAUR36 contained the core cis-elements for phytohormone responsiveness. Promoter beta-glucuronidase (GUS) analysis in Arabidopsis showed that IbSAUR36 is highly expressed in the young tissues of plants, such as young leaves, roots, and buds. IbSAUR36-overexpressing sweet potato roots were obtained by an efficient Agrobacterium rhizogenes-mediated root transgenic system. We demonstrated that overexpression of IbSAUR36 promoted the accumulation of IAA, upregulated the genes encoding IAA synthesis and its signaling pathways, and downregulated the genes encoding lignin synthesis and JA signaling pathways. Taken together, these results show that IbSAUR36 plays an important role in adventitious root (AR) development by regulating IAA signaling, lignin synthesis, and JA signaling pathways in transgenic sweet potatoes.
PMID: 38927696
Plant Mol Biol , IF:4.076 , 2024 Jun , V114 (4) : P75 doi: 10.1007/s11103-024-01470-9
Maize auxin response factor ZmARF1 confers multiple abiotic stresses resistances in transgenic Arabidopsis.
Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan, China.; Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China.; Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China. luyanli@sicau.edu.cn.; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China. luyanli@sicau.edu.cn.; Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China. wfk124@sicau.edu.cn.; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China. wfk124@sicau.edu.cn.
Prolonged exposure to abiotic stresses causes oxidative stress, which affects plant development and survival. In this research, the overexpression of ZmARF1 improved tolerance to low Pi, drought and salinity stresses. The transgenic plants manifested tolerance to low Pi by their superior root phenotypic traits: root length, root tips, root surface area, and root volume, compared to wide-type (WT) plants. Moreover, the transgenic plants exhibited higher root and leaf Pi content and upregulated the high affinity Pi transporters PHT1;2 and phosphorus starvation inducing (PSI) genes PHO2 and PHR1 under low Pi conditions. Transgenic Arabidopsis displayed tolerance to drought and salt stress by maintaining higher chlorophyll content and chlorophyll fluorescence, lower water loss rates, and ion leakage, which contributed to the survival of overexpression lines compared to the WT. Transcriptome profiling identified a peroxidase gene, POX, whose transcript was upregulated by these abiotic stresses. Furthermore, we confirmed that ZmARF1 bound to the auxin response element (AuxRE) in the promoter of POX and enhanced its transcription to mediate tolerance to oxidative stress imposed by low Pi, drought and salt stress in the transgenic seedlings. These results demonstrate that ZmARF1 has significant potential for improving the tolerance of crops to multiple abiotic stresses.
PMID: 38878261
Biophys J , IF:4.033 , 2024 Jun doi: 10.1016/j.bpj.2024.06.017
Auxin-mediated stress relaxation in pericycle and endoderm remodelling drive lateral root initiation.
Technical University of Munich, Germany; TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA).; Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.; Technical University of Munich, Germany; TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA). Electronic address: alexis.maizel@cos.uni-heidelberg.de.; Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany. Electronic address: alexis.maizel@cos.uni-heidelberg.de.
Plant development relies on the precise coordination of cell growth, which is influenced by the mechanical constraints imposed by rigid cell walls. The hormone auxin plays a crucial role in regulating this growth by altering the mechanical properties of cell walls. During the post-embryonic formation of lateral roots, pericycle cells deep within the main root are triggered by auxin to resume growth and divide to form a new root. This growth involves a complex interplay between auxin, growth, and the resolution of mechanical conflicts with the overlying endodermis. However, the exact mechanisms by which this coordination is achieved are still unknown. Here, we propose a model that integrates tissue mechanics and auxin transport, revealing a connection between the auxin-induced relaxation of mechanical stress in the pericycle and auxin signalling in the endodermis. We show that the endodermis initially limits the growth of pericycle cells, resulting in a modest initial expansion. However, the associated stress relaxation is sufficient to redirect auxin to the overlying endodermis, which then actively accommodates the growth, allowing for the subsequent development of the lateral root. Our model uncovers that increased pericycle turgor and decreased endodermal resistance licence expansion of the pericycle and how the topology of the endodermis influences the formation of the new root. These findings highlight the interconnected relationship between mechanics and auxin flow during lateral root initiation, emphasizing the vital role of the endodermis in shaping root development through mechanotransduction and auxin signalling.
PMID: 38902924
Phytopathology , IF:4.025 , 2024 Jun , V114 (6) : P1196-1205 doi: 10.1094/PHYTO-11-23-0445-R
Indole Alkaloid Production by the Halo Blight Bacterium Treated with the Phytoalexin Genistein.
Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705.
When Pseudomonas savastanoi pv. phaseolicola, the bacterium that causes halo blight, induces hypersensitive immunity in common bean leaves, salicylic acid and phytoalexins accumulate at the site of infection. Both salicylic acid and the phytoalexin resveratrol exert antibiotic activities and toxicities in vitro, adversely disrupting the P. savastanoi pv. phaseolicola proteome and metabolism and stalling replication and motility. These efficacious properties likely contribute to the cessation of bacterial spread in beans. Genistein is an isoflavonoid phytoalexin that also accumulates during bean immunity, so we tested its antibiotic potential in vitro. Quantitative proteomics revealed that genistein did not induce proteomic changes in P. savastanoi pv. phaseolicola in the same way that salicylic acid or resveratrol did. Rather, a dioxygenase that could function to metabolize genistein was among the most highly induced enzymes. Indeed, high-throughput metabolomics provided direct evidence for genistein catabolism. Metabolomics also revealed that genistein induced the bacterium to produce indole compounds, several of which had structural similarity to auxin. Additional mass spectrometry analyses proved that the bacterium produced an isomer of the auxin indole-3-acetic acid but not indole-3-acetic acid proper. These results reveal that P. savastanoi pv. phaseolicola can tolerate bean genistein and that the bacterium likely responds to bean-produced genistein during infection, using it as a signal to increase pathogenicity, possibly by altering host cell physiology or metabolism through the production of potential auxin mimics.
PMID: 38281161
BMC Genomics , IF:3.969 , 2024 Jun , V25 (1) : P567 doi: 10.1186/s12864-024-10467-z
Genome-wide characterization, functional analysis, and expression profiling of the Aux/IAA gene family in spinach.
Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.; Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran. soorni@iut.ac.ir.
BACKGROUND: The auxin/indole-3-acetic acid (Aux/IAA) gene family is a crucial element of the auxin signaling pathway, significantly influencing plant growth and development. Hence, we conducted a comprehensive investigation of Aux/IAAs gene family using the Sp75 and Monoe-Viroflay genomes in spinach. RESULTS: A total of 24 definitive Aux/IAA genes were identified, exhibiting diverse attributes in terms of amino acid length, molecular weight, and isoelectric points. This diversity underscores potential specific roles within the family, such as growth regulation and stress response. Structural analysis revealed significant variations in gene length and molecular weight. These variations indicate distinct roles within the Aux/IAA gene family. Chromosomal distribution analysis exhibited a dispersed pattern, with chromosomes 4 and 1 hosting the highest and lowest numbers of Aux/IAA genes, respectively. Phylogenetic analysis grouped the identified genes into distinct clades, revealing potential evolutionary relationships. Notably, the phylogenetic tree highlighted specific gene clusters suggesting shared genetic ancestry and potential functional synergies within spinach. Expression analysis under NAA treatment unveiled gene-specific and time-dependent responses, with certain genes exhibiting distinct temporal expression patterns. Specifically, SpoIAA5 displayed a substantial increase at 2 h post-NAA treatment, while SpoIAA7 and SpoIAA9 demonstrated continuous rises, peaking at the 4-hour time point. CONCLUSIONS: These observations indicate a complex interplay of gene-specific and temporal regulation in response to auxin. Moreover, the comparison with other plant species emphasized both shared characteristics and unique features in Aux/IAA gene numbers, providing insights into the evolutionary dynamics of this gene family. This comprehensive characterization of Aux/IAA genes in spinach not only establishes the foundation for understanding their specific functions in spinach development but also provides a valuable resource for experimental validation and further exploration of their roles in the intricate network of auxin signaling pathways.
PMID: 38840073
Plants (Basel) , IF:3.935 , 2024 Jun , V13 (12) doi: 10.3390/plants13121677
Bacterial Spermosphere Inoculants Alter N. benthamiana-Plant Physiology and Host Bacterial Microbiome.
Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA.; Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany.; Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA.
In this study, we investigated the interplay between the spermosphere inoculum, host plant physiology, and endophytic compartment (EC) microbial community. Using 16S ribosomal RNA gene sequencing of root, stem, and leaf endophytic compartment communities, we established a baseline microbiome for Nicotiana sp. Phenotypic differences were observed due to the addition of some bacterial inoculants, correlated with endogenous auxin loads using transgenic plants expressing the auxin reporter pB-GFP::P87. When applied as spermosphere inoculants, select bacteria were found to create reproducible variation within the root EC microbiome and, more systematically, the host plant physiology. Our findings support the assertion that the spermosphere of plants is a zone that can influence the EC microbiome when applied in a greenhouse setting.
PMID: 38931109
Plants (Basel) , IF:3.935 , 2024 Jun , V13 (12) doi: 10.3390/plants13121620
Transcriptome Analysis of Early Lateral Root Formation in Tomato.
State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Lateral roots (LRs) receive signals from the inter-root environment and absorb water and nutrients from the soil. Auxin regulates LR formation, but the mechanism in tomato remains largely unknown. In this study, 'Ailsa Craig' tomato LRs appeared on the third day and were unevenly distributed in primary roots. According to the location of LR occurrence, roots were divided into three equal parts: the shootward part of the root (RB), the middle part of the root (RM), and the tip part of the root (RT). Transverse sections of roots from days 1 to 6 revealed that the number of RB cells and the root diameter were significantly increased compared with RM and RT. Using roots from days 1 to 3, we carried out transcriptome sequencing analysis. Identified genes were classified into 16 co-expression clusters based on K-means, and genes in four associated clusters were highly expressed in RB. These four clusters (3, 5, 8, and 16) were enriched in cellulose metabolism, microtubule, and peptide metabolism pathways, all closely related to LR development. The four clusters contain numerous transcription factors linked to LR development including transcription factors of LATERAL ORGAN BOUNDRIES (LOB) and MADS-box families. Additionally, auxin-related genes GATA23, ARF7, LBD16, EXP, IAA4, IAA7, PIN1, PIN2, YUC3, and YUC4 were highly expressed in RB tissue. Free IAA content in 3 d RB was notably higher, reaching 3.3-5.5 ng/g, relative to RB in 1 d and 2 d. The LR number was promoted by 0.1 muM of exogenous IAA and inhibited by exogenous NPA. We analyzed the root cell state and auxin signaling module during LR formation. At a certain stage of pericycle cell development, LR initiation is regulated by auxin signaling modules IAA14-ARF7/ARF19-LBD16-CDKA1 and IAA14-ARF7/ARF19-MUS/MUL-XTR6/EXP. Furthermore, as a key regulatory factor, auxin regulates the process of LR initiation and LR primordia (LRP) through different auxin signaling pathway modules.
PMID: 38931052
Plant Reprod , IF:3.767 , 2024 Jun doi: 10.1007/s00497-024-00503-z
Identification of male sterility-related genes in Saccharum officinarum and Saccharum spontaneum.
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.; Hawaii Agriculture Research Center, Waipahu, HI, 96797, USA.; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. rayming@illinois.edu.; Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. rayming@illinois.edu.
Candidate male sterility genes were identified in sugarcane, which interacts with kinase-related proteins, transcription factors, and plant hormone signaling pathways to regulate stamen and anther development. Saccharum officinarum is a cultivated sugarcane species that its predominant feature is high sucrose content in stems. Flowering is necessary for breeding new cultivars but will terminate plant growth and reduce sugar yield. The wild sugarcane species Saccharum spontaneum has robust and viable pollen, whereas most S. officinarum accessions are male sterile, which is a desirable trait of a maternal parent in sugarcane breeding. To study male sterility and related regulatory pathways in sugarcane, we carried out RNAseq using flowers in different developmental stages between male-sterile S. officinarum accession 'LA Purple' and fertile S. spontaneum accession 'SES208'. Gene expression profiles were used to detect how genes are differentially expressed between male sterile and fertile flowers and to identify candidate genes for male sterility. Weighted gene correlation networks analysis (WGCNA) was conducted to investigate the regulatory networks. Transcriptomic analyses showed that 988 genes and 2888 alleles were differentially expressed in S. officinarum compared to S. spontaneum. Ten differentially expressed genes and thirty alleles were identified as candidate genes and alleles for male sterility in sugarcane. The gene Sspon.03G0007630 and two alleles of the gene Sspon.08G0002270, Sspon.08G0002270-2B and Sspon.08G0014700-1A, were involved in the early stamen or carpel development stages, while the remaining genes were classified into the post-meiosis stage. Gibberellin, auxin, and jasmonic acid signaling pathways are involved in the stamen development in sugarcane. The results expanded our knowledge of male sterility-related genes in sugarcane and generated genomic resources to facilitate the selection of ideal maternal parents to improve breeding efficiency.
PMID: 38844561
Plant Reprod , IF:3.767 , 2024 Jun doi: 10.1007/s00497-024-00504-y
An epiQTL underlying asexual seed formation in Arabidopsis.
Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Muhlenberg 1, 14476, Potsdam, Germany.; Business Academy Aarhus, 8260, Viby J, Denmark.; Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Muhlenberg 1, 14476, Potsdam, Germany. figueiredo@mpimp-golm.mpg.de.
The DNA methylation status at an epigenetic quantitative trait locus in the Arabidopsis chromosome 2 is linked to the formation of apomictic-like endosperms. Seed development in most angiosperms is coupled to fertilization of the maternal gametes by two sperm cells. However, apomictic species can reproduce asexually via seeds. This trait is of great agricultural interest, as it would fix complex genotypes and allow for pollen-independent seed production. However, engineering full apomixis requires three independent processes: apomeiosis, parthenogenesis and autonomous endosperm development. While the first two have been successfully engineered in some crops, the formation of autonomous endosperms remains a challenge. Although it is known that this trait is under epigenetic control, such as of DNA methylation, the underlying mechanisms remain mostly undiscovered. Here, using epigenetic recombinant inbred lines, we identified an epigenetic quantitative trait locus in the Arabidopsis chromosome 2, which correlates with permissiveness for the formation of asexual seeds: hypomethylation at this genomic region allows the formation of larger autonomous endosperms. Importantly, the methylation at this locus only correlates with asexual seed size, and not to the size of sexual seeds or that of other organs. With this, we aim to show that screening for epialleles is a promising strategy to uncover loci underlying relevant traits and could pave the way to identifying genes necessary for the engineering of apomixis.
PMID: 38836892
Gene , IF:3.688 , 2024 Oct , V926 : P148623 doi: 10.1016/j.gene.2024.148623
Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus.
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China.; National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: liuyongzhong@mail.hzau.edu.cn.
Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.
PMID: 38821328
Gene , IF:3.688 , 2024 Aug , V921 : P148532 doi: 10.1016/j.gene.2024.148532
Identification of cotton PIP5K genes and role of GhPIP5K9a in primary root development.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.; Anyang Academy of Agricultural Sciences, Anyang 455000, China.; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China. Electronic address: fsl427@126.com.; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China. Electronic address: 13837240176@163.com.
Phosphatidylinositol 4 phosphate 5-kinase (PIP5K) is crucial for the phosphatidylinositol (PI) signaling pathway. It plays a significant role in plant growth and development, as well as stress response. However, its effects on cotton are unknown. This study identified PIP5K genes from four cotton species and conducted bioinformatic analyses, with a particular emphasis on the functions of GhPIP5K9a in primary roots. The results showed that cotton PIP5Ks were classified into four subgroups. Analysis of gene structure and motif composition showed obvious conservation within each subgroup. Synteny analysis suggested that the PIP5K gene family experienced significant expansion due to both whole-genome duplication (WGD) and segmental duplication. Transcriptomic data analysis revealed that the majority of GhPIP5K genes had the either low or undetectable levels of expression. Moreover, GhPIP5K9a is highly expressed in the root and was located in plasmalemma. Suppression of GhPIP5K9a transcripts resulted in longer primary roots, longer primary root cells and increased auxin polar transport-related genes expression, and decreased abscisic acid (ABA) content, indicating that GhPIP5K9a negatively regulates cotton primary root growth. This study lays the foundation for further exploration of the role of the PIP5K genes in cotton.
PMID: 38705423
Gene , IF:3.688 , 2024 Jul , V915 : P148423 doi: 10.1016/j.gene.2024.148423
The vesicle trafficking gene, OsRab7, is critical for pollen development and male fertility in cytoplasmic male-sterility rice.
Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Sciences, Nanchang University, Nanchang 330031, China.; Department of Chemistry, University of Kentucky, Lexington, United States.; Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China. Electronic address: liuwei@gdaas.cn.; Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Sciences, Nanchang University, Nanchang 330031, China. Electronic address: xiaojuepeng@ncu.edu.cn.
Rice cytoplasmic male sterility (CMS) provides an exceptional model for studying genetic interaction within plant nuclei given its inheritable trait of non-functional male gametophyte. Gaining a comprehensive understanding of the genes and pathways associated with the CMS mechanism is imperative for improving the vigor of hybrid rice agronomically, such as its productivity. Here, we observed a significant decrease in the expression of a gene named OsRab7 in the anther of the CMS line (SJA) compared to the maintainer line (SJB). OsRab7 is responsible for vesicle trafficking and loss function of OsRab7 significantly reduced pollen fertility and setting rate relative to the wild type. Meanwhile, over-expression of OsRab7 enhanced pollen fertility in the SJA line while a decrease in its expression in the SJB line led to the reduced pollen fertility. Premature tapetum and abnormal development of microspores were observed in the rab7 mutant. The expression of critical genes involved in tapetum development (OsMYB103, OsPTC1, OsEAT1 and OsAP25) and pollen development (OsMSP1, OsDTM1 and OsC4) decreased significantly in the anther of rab7 mutant. Reduced activities of the pDR5::GUS marker in the young panicle and anther of the rab7 mutant were also observed. Furthermore, the mRNA levels of genes involved in auxin biosynthesis (YUCCAs), auxin transport (PINs), auxin response factors (ARFs), and members of the IAA family (IAAs) were all downregulated in the rab7 mutant, indicating its impact on auxin signaling and distribution. In summary, these findings underscore the importance of OsRab7 in rice pollen development and its potential link to cytoplasmic male sterility.
PMID: 38575100
Gene , IF:3.688 , 2024 Jun , V910 : P148336 doi: 10.1016/j.gene.2024.148336
Genome-wide identification and expression analysis of the Dof gene family reveals their involvement in hormone response and abiotic stresses in sunflower (Helianthus annuus L.).
Department of Life Sciences, Changzhi University, Changzhi 046011, China.; School of Life Science, Shanxi Normal University, Taiyuan 030031, China.; Department of Life Sciences, Changzhi University, Changzhi 046011, China. Electronic address: tznius@126.com.; Department of Life Sciences, Changzhi University, Changzhi 046011, China. Electronic address: akeliu@126.com.
DNA binding with one finger (Dof), plant-specific zinc finger transcription factors, can participate in various physiological and biochemical processes during the life of plants. As one of the most important oil crops in the world, sunflower (Helianthus annuus L.) has significant economic and ornamental value. However, a systematic analysis of H. annuus Dof (HaDof) members and their functions has not been extensively conducted. In this study, we identified 50 HaDof genes that are unevenly distributed on 17 chromosomes of sunflower. We present a comprehensive overview of the HaDof genes, including their chromosome locations, phylogenetic analysis, and expression profile characterization. Phylogenetic analysis classified the 366 Dof members identified from 11 species into four groups (further subdivided into nine subfamilies). Segmental duplications are predominantly contributed to the expansion of sunflower Dof genes, and all segmental duplicate gene pairs are under purifying selection due to strong evolutionary constraints. Furthermore, we observed differential expression patterns for HaDof genes in normal tissues as well as under hormone treatment or abiotic stress conditions by analyzing RNA-seq data from previous studies and RT-qPCR data in our current study. The expression of HaDof04 and HaDof43 were not detected in any samples, which implied that they may be gradually undergoing pseudogenization process. Some HaDof genes, such as HaDof25 and HaDof30, showed responsiveness to exogenous plant hormones, such as kinetin, brassinosteroid, auxin or strigolactone, while others like HaDof15 and HaDof35 may participate in abiotic stress resistance of sunflower seedling. Our study represents the initial step towards understanding the phylogeny and expression characterization of sunflower Dof family genes, which may provide valuable reference information for functional studies on hormone response, abiotic stress resistance, and molecular breeding in sunflower and other species.
PMID: 38447680
Biochem Biophys Res Commun , IF:3.575 , 2024 Jun , V714 : P149956 doi: 10.1016/j.bbrc.2024.149956
Function analysis of transcription factor OSR1 regulating osmotic stress resistance in maize.
State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, PR China; School of Physical Education and Health Management, Henan Finance University, Zhengzhou, 450046, Henan, PR China.; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, PR China.; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, PR China. Electronic address: wangpt@henu.edu.cn.
BACKGROUND: Maize is a major cereal crop world widely, however, the yield of maize is frequently limited by dehydration and even death of plants, which resulted from osmotic stress such as drought and salinity. Dissection of molecular mechanisms controlling stress tolerance will enable plant scientists and breeders to increase crops yield by manipulating key regulatory components. METHODS: The candidate OSR1 gene was identified by map-based cloning. The expression level of OSR1 was verified by qRT-PCR and digital PCR in WT and osr1 mutant. Electrophoretic mobility shift assay, transactivation activity assay, subcellular localization, transcriptome analysis and physiological characters measurements were conducted to analyze the function of OSR1 in osmotic stress resistance in maize. RESULTS: The osr1 mutant was significantly less sensitive to osmotic stress than the WT plants and displayed stronger water-holding capacity, and the OSR1 homologous mutant in Arabidopsis showed a phenotype similar with maize osr1 mutant. Differentially expressed genes (DEGs) were identified between WT and osr1 under osmotic stress by transcriptome analysis, the expression levels of many genes, such as LEA, auxin-related factors, PPR family members, and TPR family members, changed notably, which may primarily involve in osmotic stress or promote root development. CONCLUSIONS: OSR1 may serve as a negative regulatory factor in response to osmotic stress in maize. The present study sheds new light on the molecular mechanisms of osmotic stress in maize.
PMID: 38663095
Biochem Biophys Res Commun , IF:3.575 , 2024 Jun , V711 : P149934 doi: 10.1016/j.bbrc.2024.149934
CEPs suppress auxin signaling but promote cytokinin signaling to inhibit root growth in Arabidopsis.
Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: 2018203051@njau.edu.cn.; Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China; Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
C-terminally encoded peptides (CEPs) are peptide hormones that function as mobile signals coordinating crucial developmental programs in plants. Previous studies have revealed that CEPs exert negative regulation on root development through interaction with CEP receptors (CEPRs), CEP DOWNSTREAMs (CEPDs), the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE (AHKs) and the transcriptional repressor Auxin/Indole-3-Acetic Acid (AUX/IAA). However, the precise molecular mechanisms underlying CEPs-mediated regulation of root development via auxin and cytokinin signaling pathways still necessitate further detailed investigation. In this study, we examined prior research and elucidated the underlying molecular mechanisms. The results showed that both synthetic AtCEPs and overexpression of AtCEP5 markedly supressed primary root elongation and lateral root (LR) formation in Arabidopsis. Molecular biology and genetics elucidated how CEPs inhibit root growth by suppressing auxin signaling while promoting cytokinin signaling. In summary, this study elucidated the inhibitory effects of AtCEPs on Arabidopsis root growth and provided insights into their potential molecular mechanisms, thus enhancing our comprehension of CEP-mediated regulation of plant growth and development.
PMID: 38626621
J Plant Physiol , IF:3.549 , 2024 Jun , V297 : P154259 doi: 10.1016/j.jplph.2024.154259
Sucrose supplements modulate the Pseudomonas chlororaphis-Arabidopsis thaliana interaction via decreasing the production of phenazines and enhancing the root auxin response.
Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacan, Mexico.; Red de Estudios Moleculares Avanzados, Cluster BioMimic(R), Instituto de Ecologia, Carretera Antigua a Coatepec 351, El Haya, A.C 91073 Veracruz, Mexico.; Catedratico (IXM) CONAHCYT-Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacan, Mexico. Electronic address: jlopezb@conahcyt.mx.
Management of the plant microbiome may help support food needs for the human population. Bacteria influence plants through enhancing nutrient uptake, metabolism, photosynthesis, biomass production and/or reinforcing immunity. However, information into how these microbes behave under different growth conditions is missing. In this work, we tested how carbon supplements modulate the interaction of Pseudomonas chlororaphis with Arabidopsis thaliana. P. chlororaphis streaks strongly repressed primary root growth, lateral root formation and ultimately, biomass production. Noteworthy, increasing sucrose availability into the media from 0 to 2.4% restored plant growth and promoted lateral root formation in bacterized seedlings. This effect could not be observed by supplementing sucrose to leaves only, indicating that the interaction was strongly modulated by bacterial access to sugar. Total phenazine content decreased in the bacteria grown in high (2.4%) sucrose medium, and conversely, the expression of phzH and pslA genes were diminished by sugar supply. Pyocyanin antagonized the promoting effects of sucrose in lateral root formation and biomass production in inoculated seedlings, indicating that this virulence factor accounts for growth repression during the plant-bacterial interaction. Defence reporter transgenes PR-1::GUS and LOX2::GUS were induced in leaves, while the expression of the auxin-inducible, synthetic reporter gene DR5::GUS was enhanced in the roots of bacterized seedlings at low and high sucrose treatments, which suggests that growth/defence trade-offs in plants are critically modulated by P. chlororaphis. Collectively, our data suggest that bacterial carbon nutrition controls the outcome of the relation with plants.
PMID: 38705079
J Plant Physiol , IF:3.549 , 2024 Jun , V297 : P154257 doi: 10.1016/j.jplph.2024.154257
Physiological and molecular mechanisms of plant-root responses to iron toxicity.
State Key Laboratory of Nutrient Use and Management, Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences, Jinan, 250100, China. Electronic address: ligjsaas@163.com.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China.; School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia. Electronic address: herbert.kronzucker@unimelb.edu.au.; MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China. Electronic address: bhli@zju.edu.cn.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China; University of the Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China. Electronic address: wmshi@issas.ac.cn.
The chemical form and physiological activity of iron (Fe) in soil are dependent on soil pH and redox potential (Eh), and Fe levels in soils are frequently elevated to the point of causing Fe toxicity in plants, with inhibition of normal physiological activities and of growth and development. In this review, we describe how iron toxicity triggers important physiological changes, including nitric-oxide (NO)-mediated potassium (K(+)) efflux at the tips of roots and accumulation of reactive oxygen species (ROS) and reactive nitrogen (RNS) in roots, resulting in physiological stress. We focus on the root system, as the first point of contact with Fe in soil, and describe the key processes engaged in Fe transport, distribution, binding, and other mechanisms that are drawn upon to defend against high-Fe stress. We describe the root-system regulation of key physiological processes and of morphological development through signaling substances such as ethylene, auxin, reactive oxygen species, and nitric oxide, and discuss gene-expression responses under high Fe. We especially focus on studies on the physiological and molecular mechanisms in rice and Arabidopsis under high Fe, hoping to provide a valuable theoretical basis for improving the ability of crop roots to adapt to soil Fe toxicity.
PMID: 38688043
J Plant Physiol , IF:3.549 , 2024 Jun , V297 : P154242 doi: 10.1016/j.jplph.2024.154242
AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis.
College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China.; London Research and Development Centre, Agriculture and Agri-food Canada, London, Ontario, N5V 4T3, Canada.; College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China. Electronic address: hanzhaofen@nwsuaf.edu.cn.
Roots are essential to terrestrial plants, as their growth and morphology are crucial for plant development. The growth of the roots is affected and regulated by several internal and external environmental signals and metabolic pathways. Among them, chromatin modification plays an important regulatory role. In this study, we explore the potential roles of the histone deacetylase AtHD2D in root development and lay the foundation for further research on the biological processes and molecular mechanisms of AtHD2D in the future. Our study indicates that AtHD2D affects the root tip microenvironment homeostasis by affecting the gene transcription levels required to maintain the root tip microenvironment. In addition, we confirmed that AtHD2D is involved in regulating Arabidopsis lateral root development and further explained the possible role of AtHD2D in auxin-mediated lateral root development. AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. We believe that AtHD2D is involved in coping with abiotic stress by promoting the development of lateral roots. Overexpression of AtHD2D promotes the accumulation of reactive oxygen species (ROS) in roots, indicating that AtHD2D is also involved in developing lateral roots mediated by ROS. Previous studies have shown that the overexpression of AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. Based on our data, we believe that AtHD2D participates in the response to abiotic stress by promoting the development of lateral roots. AtHD2D-mediated lateral root development provides new ideas for studying the mechanism of HDAC protein in regulating root development.
PMID: 38614048
Int J Phytoremediation , IF:3.212 , 2024 Jun , V26 (8) : P1221-1230 doi: 10.1080/15226514.2024.2304562
Changes in microRNAs expression of flax (Linum usitatissimum L.) planted in a cadmium-contaminated soil following the inoculation with root symbiotic fungi.
Department of Soil Biology and Biotechnology, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.; Department of Plant Productions and Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
Cadmium is one of the most harmful heavy metals that harm agricultural products. Evaluating microRNAs expression is a new and accurate method to study plant response in various environmental conditions. So this study aimed to evaluate the contribution of two symbiotic fungi in improving flax tolerance in a Cd-polluted soil using microRNAs and their target gene expression. A factorial pot experiment in a completely randomized design was conducted with different levels of Cd (0, 20, and 40 mg kg(-1)) on non-inoculated and inoculated flax with Claroideoglomus etunicatum and Serendipita indica. The results presented that increasing Cd levels caused a constant decline of alkaline phosphatase of soil (from 243 to 210 and 153 mug PNP g(-1) h(-1)), respectively, from control (Cd0) to 20 and 40 mg Cd kg(-1). However, the inoculation of flax with fungi significantly enhanced these properties. A negative correlation was observed between the expression level of microRNA 167 and microRNA 398 with their corresponding target genes, auxin response factor 8 and superoxide dismutase zinc/copper 1, respectively. The expression level of both microRNAs and their targets indicated that the inoculation with symbiont fungi could diminish Cd stress and enhance the growth of flax.
PMID: 38279665
Braz J Microbiol , IF:2.476 , 2024 Jun doi: 10.1007/s42770-024-01399-7
Cladosporium psychrotolerans strain T01 enhances plant biomass and also exhibits antifungal activity against pathogens.
Laboratorio de Biotecnologia Molecular de Plantas, Division de Biologia Molecular, Instituto Potosino de Investigacion Cientifica y Tecnologica A. C, San Luis Potosi, SLP, Mexico.; Laboratorio de Biotecnologia Molecular de Plantas, Division de Biologia Molecular, Instituto Potosino de Investigacion Cientifica y Tecnologica A. C, San Luis Potosi, SLP, Mexico. jbremont@ipicyt.edu.mx.
An increasing number of microorganisms are being identified to enhance plant growth and inhibit phytopathogens. Some Cladosporium species form beneficial associations with plants, either as endophytes or by colonizing the rhizosphere. Herein, we evaluated the influence of the Cladosporium psychrotolerans (T01 strain) fungus on the in vitro growth of Arabidopsis thaliana plantlets through direct and split interactions. After 9 days post-inoculation with C. psychrotolerans, Arabidopsis plantlets exhibited a notable increase in fresh weight and lateral roots, particularly in split interactions. Chlorophyll content increased in both plant-fungus interaction conditions, whereas the primary root was inhibited during direct interaction. We observed an increase in the GUS signal from the Arabidopsis auxin-inducible DR5:uidA marker in lateral root tips in both contact and split fungal interactions, and primary root tips in a split interaction. Arabidopsis and tomato plants cultivated in soil pots and inoculated with C. psychrotolerans (T01 strain) showed a positive effect on biomass production. GC/MS analysis detected that the T01 strain emitted volatile organic compounds (VOCs), predominantly alcohols and aldehydes. These VOCs displayed potent inhibitory effects, with a 60% inhibition against Botrytis cinerea and a 50% inhibition against C. gloeosporioides. Our study demonstrates that C. psychrotolerans T01 has the potential to enhance biomass production and inhibit pathogens, making it a promising candidate for green technology applications.
PMID: 38825649
3 Biotech , IF:2.406 , 2024 Jul , V14 (7) : P174 doi: 10.1007/s13205-024-04019-1
Transcriptomic and metabolomic profiling reveals molecular regulatory network involved in flower development and phenotypic changes in two Lonicera macranthoides varieties.
College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China. GRID: grid.488482.a. ISNI: 0000 0004 1765 5169; Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China.; Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China. ROR: https://ror.org/05ckg3w11. GRID: grid.454772.7. ISNI: 0000 0004 5901 2284
Due to the medicinal importance of the flowers of Xianglei type (XL) Lonicera macranthoides, it is important to understand the molecular mechanisms that underlie their development. In this study, we elucidated the transcriptomic and metabolomic mechanisms that underlie the flower development mechanism of two L. macranthoides varieties. In this study, 3435 common differentially expressed unigenes (DEGs) and 1138 metabolites were identified. These common DEGs were mainly enriched in plant hormone signal transduction pathways. Metabolomic analysis showed that amino acids were the main metabolites of differential accumulation in wild-type (WT) L. macranthoides, whereas in XL, they were flavonoids and phenylalanine metabolites. Genes and transcription factors (TFs), such as MYB340, histone deacetylase 1 (HDT1), small auxin-up RNA 32 (SAUR32), auxin response factor 6 (ARF6), PIN-LIKES 7 (PILS7), and WRKY6, likely drive metabolite accumulation. Plant hormone signals, especially auxin signals, and various TFs induce downstream flower organ recognition genes, resulting in a differentiation of the two L. macranthoides varieties in terms of their developmental trajectories. In addition, photoperiodic, autonomous, and plant hormone pathways jointly regulated the L. macranthoides corolla opening. SAUR32, Arabidopsis response regulator 9 (ARR9), Gibberellin receptor (GID1B), and Constans-like 10 (COL10) were closely related to the unfolding of the L. macranthoides corolla. These findings offer valuable understanding of the flower growth process of L. macranthoides and the excellent XL phenotypes at the molecular level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-024-04019-1.
PMID: 38855147
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2348917 doi: 10.1080/15592324.2024.2348917
Investigation of Arabidopsis root skototropism with different distance settings.
Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany.
Plants can activate protective and defense mechanisms under biotic and abiotic stresses. Their roots naturally grow in the soil, but when they encounter sunlight in the top-soil layers, they may move away from the light source to seek darkness. Here we investigate the skototropic behavior of roots, which promotes their fitness and survival. Glutamate-like receptors (GLRs) of plants play roles in sensing and responding to signals, but their role in root skototropism is not yet understood. Light-induced tropisms are known to be affected by auxin distribution, mainly determined by auxin efflux proteins (PIN proteins) at the root tip. However, the role of PIN proteins in root skototropism has not been investigated yet. To better understand root skototropism and its connection to the distance between roots and light, we established five distance settings between seedlings and darkness to investigate the variations in root bending tendencies. We compared differences in root skototropic behavior across different expression lines of Arabidopsis thaliana seedlings (atglr3.7 ko, AtGLR3.7 OE, and pin2 knockout) to comprehend their functions. Our research shows that as the distance between roots and darkness increases, the root's positive skototropism noticeably weakens. Our findings highlight the involvement of GLR3.7 and PIN2 in root skototropism.
PMID: 38704856
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2341506 doi: 10.1080/15592324.2024.2341506
Complex genetic interaction between glucose sensor HXK1 and E3 SUMO ligase SIZ1 in regulating plant morphogenesis.
National Institute of Plant Genome Research, New Delhi, India.
Sugar signaling forms the basis of metabolic activities crucial for an organism to perform essential life activities. In plants, sugars like glucose, mediate a wide range of physiological responses ranging from seed germination to cell senescence. This has led to the elucidation of cell signaling pathways involving glucose and its counterparts and the mechanism of how these sugars take control over major hormonal pathways such as auxin, ethylene, abscisic acid and cytokinin in Arabidopsis. Plants use HXK1(Hexokinase) as a glucose sensor to modulate changes in photosynthetic gene expression in response to high glucose levels. Other proteins such as SIZ1, a major SUMO E3 ligase have recently been implicated in controlling sugar responses via transcriptional and translational regulation of a wide array of sugar metabolic genes. Here, we show that these two genes work antagonistically and are epistatic in controlling responsiveness toward high glucose conditions.
PMID: 38607960
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2331358 doi: 10.1080/15592324.2024.2331358
Plant hormone profiling of scion and rootstock incision sites and intra- and inter-family graft junctions in Nicotiana benthamiana.
Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.; RIKEN Center for Sustainable Resource Science, Plant Productivity Systems Research Group, Yokohama, Japan.
Many previous studies have suggested that various plant hormones play essential roles in the grafting process. In this study, to understand the plant hormones that accumulate in the graft junctions, whether these are supplied from the scion or rootstock, and how these hormones play a role in the grafting process, we performed a hormonome analysis that accumulated in the incision site of the upper plants from the incision as "ungrafted scion" and lower plants from the incision as "ungrafted rootstock" in Nicotiana benthamiana. The results revealed that indole-3-acetic acid (IAA) and gibberellic acid (GA), which regulate cell division; abscisic acid (ABA) and jasmonic acid (JA), which regulate xylem formation; cytokinin (CK), which regulates callus formation, show different accumulation patterns in the incision sites of the ungrafted scion and rootstock. In addition, to try discussing the differences in the degree and speed of each event during the grafting process between intra- and inter-family grafting by determining the concentration and accumulation timing of plant hormones in the graft junctions, we performed hormonome analysis of graft junctions of intra-family grafted plants with N. benthamiana as scion and Solanum lycopersicum as rootstock (Nb/Sl) and inter-family grafted plants with N. benthamiana as scion and Arabidopsis thaliana as rootstock (Nb/At), using the ability of Nicotiana species to graft with many plant species. The results revealed that ABA and CK showed different accumulation timings; IAA, JA, and salicylic acid (SA) showed similar accumulation timings, while different accumulated concentrations in the graft junctions of Nb/Sl and Nb/At. This information is important for understanding the molecular mechanisms of plant hormones in the grafting process and the differences in molecular mechanisms between intra- and inter-family grafting.
PMID: 38513064
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2305030 doi: 10.1080/15592324.2024.2305030
Cytokinin signaling is involved in root hair elongation in response to phosphate starvation.
School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan.; Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan.
Root hair, single-celled tubular structures originating from the epidermis, plays a vital role in the uptake of nutrients from the soil by increasing the root surface area. Therefore, optimizing root hair growth is crucial for plants to survive in fluctuating environments. Root hair length is determined by the action of various plant hormones, among which the roles of auxin and ethylene have been extensively studied. However, evidence for the involvement of cytokinins has remained elusive. We recently reported that the cytokinin-activated B-type response regulators, ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) and ARR12 directly upregulate the expression of ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4), which encodes a key transcription factor that controls root hair elongation. However, depending on the nutrient availability, it is unknown whether the ARR1/12-RSL4 pathway controls root hair elongation. This study shows that phosphate deficiency induced the expression of RSL4 and increased the root hair length through ARR1/12, though the transcript and protein levels of ARR1/12 did not change. These results indicate that cytokinins, together with other hormones, regulate root hair growth under phosphate starvation conditions.
PMID: 38267225
Biosci Biotechnol Biochem , IF:2.043 , 2024 Jun doi: 10.1093/bbb/zbae080
A mature liquid fertilizer derived from cattle urine promotes Arabidopsis thaliana growth via hormone-like responses.
Kankyo Daizen Co., Ltd., 438-7, Tanno-cho 3-ku, Kitami, Hokkaido, Japan.; Cold Regions, Environmental and Energy Engineering Course, Graduate School of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido, Japan.; Department of Applied Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido, Japan.
To understand the fertilization effects of liquid fertilizer (LF) produced by aerobic microbial processing of cattle urine, we investigated the influence of LF on growth and shoot genetic responses of the model plant Arabidopsis thaliana. LF significantly enhanced both shoot and root growth under aseptic conditions. Although filtrate from ultrafiltration (molecular weight cutoff: 10 000) also promoted shoot growth and root elongation, the concentrate only promoted root growth. Multiple growth-promoting factors were therefore associated with the growth promotion. Transcriptome analysis of shoots following LF addition identified 353 up-regulated and 512 down-regulated genes. According to gene ontology and KEGG enrichment analyses, signal transduction of a phytohormone cytokinins was influenced by LF addition. Cytochrome P450 induction triggered the following signal transitions, and would introduce the growth promotion for shoot. Primary auxin responses and abscisic acid signaling responses were also observed in the presence of the LF. Ethylene signaling seemed to be insensitive.
PMID: 38849314
Mol Breed , 2024 Jul , V44 (7) : P47 doi: 10.1007/s11032-024-01484-7
A novel regulator of wheat tillering LT1 identified by using an upgraded BSA method, uni-BSA.
National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018 China. ROR: https://ror.org/02ke8fw32. GRID: grid.440622.6. ISNI: 0000 0000 9482 4676; Plant Sciences, Gembloux Agro-Bio Tech, University of Liege, Liege, Belgium. GRID: grid.4861.b. ISNI: 0000 0001 0805 7253
Branching/tillering is a critical process for plant architecture and grain yield. However, Branching is intricately controlled by both endogenous and environmental factors. The underlying mechanisms of tillering in wheat remain poorly understood. In this study, we identified Less Tiller 1 (LT1) as a novel regulator of wheat tillering using an enhanced bulked segregant analysis (BSA) method, uni-BSA. This method effectively reduces alignment noise caused by the high repetitive sequence content in the wheat genome. Loss-of-function of LT1 results in fewer tillers due to defects in axillary meristem initiation and bud outgrowth. We mapped LT1 to a 6 Mb region on the chromosome 2D short arm and validated a nucleotide-binding (NB) domain encoding gene as LT1 using CRISPR/Cas9. Furthermore, the lower sucrose concentration in the shoot bases of lt1 might result in inadequate bud outgrowth due to disturbances in the sucrose biosynthesis pathways. Co-expression analysis suggests that LT1 controls tillering by regulating TaROX/TaLAX1, the ortholog of the Arabidopsis tiller regulator REGULATOR OF AXILLARY MERISTEM FORMATION (ROX) or the rice axillary meristem regulator LAX PANICLE1 (LAX1). This study not only offers a novel genetic resource for cultivating optimal plant architecture but also underscores the importance of our innovative BSA method. This uni-BSA method enables the swift and precise identification of pivotal genes associated with significant agronomic traits, thereby hastening gene cloning and crop breeding processes in wheat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-024-01484-7.
PMID: 38939116
Plant Commun , 2024 Jun : P100943 doi: 10.1016/j.xplc.2024.100943
LAZY4 acts additively with the starch-statolith-dependent gravity-sensing pathway to regulate shoot gravitropism and tiller angle in rice.
National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China.; College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China.; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China; Yazhouwan National Laboratory, Sanya 572024, China.; National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China. Electronic address: yhwang@genetics.ac.cn.
Rice tiller angle is a key agronomic trait that has significant effects on the establishment of a high-yield rice population. However, the molecular mechanism underlying the control of rice tiller angle remains to be clarified. Here, we characterized the novel tiller-angle gene LAZY4 (LA4) in rice through map-based cloning. LA4 encodes a C3H2C3-type RING zinc-finger E3 ligase localized in the nucleus, and an in vitro ubiquitination assay revealed that the conserved RING finger domain is essential for its E3 ligase activity. We found that expression of LA4 can be induced by gravistimulation and that loss of LA4 function leads to defective shoot gravitropism caused by impaired asymmetric auxin redistribution upon gravistimulation. Genetic analysis demonstrated that LA4 acts in a distinct pathway from the starch biosynthesis regulators LA2 and LA3, which function in the starch-statolith-dependent pathway. Further genetic analysis showed that LA4 regulates shoot gravitropism and tiller angle by acting upstream of LA1 to mediate lateral auxin transport upon gravistimulation. Our studies reveal that LA4 regulates shoot gravitropism and tiller angle upstream of LA1 through a novel pathway independent of the LA2-LA3-mediated gravity-sensing mechanism, providing new insights into the rice tiller-angle regulatory network.
PMID: 38897199
J Genet Genomics , 2024 Jun doi: 10.1016/j.jgg.2024.05.011
Genome-editing of a circadian clock gene TaPRR95 facilitates wheat peduncle growth and heading date.
State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, China.; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 610106, China.; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China.; School of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China.; State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Electronic address: gengshuaifeng@caas.cn.; State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Electronic address: liaili@caas.cn.; State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Electronic address: maolong@caas.cn.
Plant height and heading date are important agronomic traits in wheat (Triticum aestivum L.) that affect final grain yield. In wheat, knowledge of pseudo-response regulator (PRR) genes on agronomic traits is limited. Here, we identify a wheat TaPRR95 gene by genome-wide association study (GWAS) to be associated with plant height. Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height, particularly at the peduncle, with an earlier heading date. The longer peduncle is mainly caused by the increased cell elongation at its upper section, whilst the early heading date is accompanied with elevated expression of flowering genes, such as TaFT and TaCO1. A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAA/Aux genes for auxin signaling in prr95(aabbdd) plants that may act as a regulatory mechanism to promote robust plant growth. A haplotype analysis identifies a TaPRR95-B haplotype (Hap2) to be closely associated with reduced plant height and increased thousand-grain weight. Moreover, the Hap2 frequency is higher in cultivars than that in landraces, suggesting the artificial selection on the allele during wheat breeding. These findings suggest that TaPRR95 is a new regulator for plant height and heading date, thereby providing an important target for wheat yield improvement.
PMID: 38849110
bioRxiv , 2024 May doi: 10.1101/2023.11.30.569401
Tradeoff Between Speed and Robustness in Primordium Initiation Mediated by Auxin-CUC1 Interaction.
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.; Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.; Present address: Department of Biology, Duke University, Durham, NC 27708, USA.; Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK.; Lead Contact.
Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we found that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases auxin maxima intensity and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we found that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validated experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.
PMID: 38076982