Nat Biotechnol , IF:54.908 , 2023 Mar doi: 10.1038/s41587-023-01707-w
Tuning plant phenotypes by precise, graded downregulation of gene expression.
State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.; Qi Biodesign, Beijing, China.; State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. cxgao@genetics.ac.cn.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China. cxgao@genetics.ac.cn.
The ability to control gene expression and generate quantitative phenotypic changes is essential for breeding new and desired traits into crops. Here we report an efficient, facile method for downregulating gene expression to predictable, desired levels by engineering upstream open reading frames (uORFs). We used base editing or prime editing to generate de novo uORFs or to extend existing uORFs by mutating their stop codons. By combining these approaches, we generated a suite of uORFs that incrementally downregulate the translation of primary open reading frames (pORFs) to 2.5-84.9% of the wild-type level. By editing the 5' untranslated region of OsDLT, which encodes a member of the GRAS family and is involved in the brassinosteroid transduction pathway, we obtained, as predicted, a series of rice plants with varied plant heights and tiller numbers. These methods offer an efficient way to obtain genome-edited plants with graded expression of traits.
PMID: 36894598
Nature , IF:49.962 , 2023 Apr doi: 10.1038/s41586-023-06023-6
Reducing brassinosteroid signalling enhances grain yield in semi-dwarf wheat.
Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China.; National Observation and Research Station of Agriculture Green Development (Quzhou, Hebei), China Agricultural University, Beijing, China.; USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA.; Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China. nizf@cau.edu.cn.
Modern green revolution varieties of wheat (Triticum aestivum L.) confer semi-dwarf and lodging-resistant plant architecture owing to the Reduced height-B1b (Rht-B1b) and Rht-D1b alleles(1). However, both Rht-B1b and Rht-D1b are gain-of-function mutant alleles encoding gibberellin signalling repressors that stably repress plant growth and negatively affect nitrogen-use efficiency and grain filling(2-5). Therefore, the green revolution varieties of wheat harbouring Rht-B1b or Rht-D1b usually produce smaller grain and require higher nitrogen fertilizer inputs to maintain their grain yields. Here we describe a strategy to design semi-dwarf wheat varieties without the need for Rht-B1b or Rht-D1b alleles. We discovered that absence of Rht-B1 and ZnF-B (encoding a RING-type E3 ligase) through a natural deletion of a haploblock of about 500 kilobases shaped semi-dwarf plants with more compact plant architecture and substantially improved grain yield (up to 15.2%) in field trials. Further genetic analysis confirmed that the deletion of ZnF-B induced the semi-dwarf trait in the absence of the Rht-B1b and Rht-D1b alleles through attenuating brassinosteroid (BR) perception. ZnF acts as a BR signalling activator to facilitate proteasomal destruction of the BR signalling repressor BRI1 kinase inhibitor 1 (TaBKI1), and loss of ZnF stabilizes TaBKI1 to block BR signalling transduction. Our findings not only identified a pivotal BR signalling modulator but also provided a creative strategy to design high-yield semi-dwarf wheat varieties by manipulating the BR signal pathway to sustain wheat production.
PMID: 37100915
Science , IF:47.728 , 2023 Mar , V379 (6639) : Peadf4721 doi: 10.1126/science.adf4721
Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root.
Department of Biology, Duke University, Durham, NC, USA.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; Center for Plant Systems Biology, VIB, Ghent, Belgium.; Department of Biology, Humboldt Universitat zu Berlin, Berlin, Germany.; The Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany.; Howard Hughes Medical Institute, Duke University, Durham, NC, USA.; Department of Mathematics, University of British Columbia, Vancouver, BC, Canada.; Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.; Department of Computer Science, Humboldt Universitat zu Berlin, Berlin, Germany.
Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and cell elongation, through gene regulatory networks that vary in space and time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive gene expression specific to different cell types and developmental stages of the Arabidopsis root, we identified the elongating cortex as a site where brassinosteroids trigger a shift from proliferation to elongation associated with increased expression of cell wall-related genes. Our analysis revealed HOMEOBOX FROM ARABIDOPSIS THALIANA 7 (HAT7) and GT-2-LIKE 1 (GTL1) as brassinosteroid-responsive transcription factors that regulate cortex cell elongation. These results establish the cortex as a site of brassinosteroid-mediated growth and unveil a brassinosteroid signaling network regulating the transition from proliferation to elongation, which illuminates aspects of spatiotemporal hormone responses.
PMID: 36996230
Trends Plant Sci , IF:18.313 , 2023 Apr , V28 (4) : P399-414 doi: 10.1016/j.tplants.2022.12.006
Mass spectrometric exploration of phytohormone profiles and signaling networks.
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193, Beijing, China. Electronic address: chenym@cau.edu.cn.; State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, 450002, Zhengzhou, China.; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
Phytohormones have crucial roles in plant growth, development, and acclimation to environmental stress; however, measuring phytohormone levels and unraveling their complex signaling networks and interactions remains challenging. Mass spectrometry (MS) has revolutionized the study of complex biological systems, enabling the comprehensive identification and quantification of phytohormones and their related targets. Here, we review recent advances in MS technologies and highlight studies that have used MS to discover and analyze phytohormone-mediated molecular events. In particular, we focus on the application of MS for profiling phytohormones, elucidating phosphorylation signaling, and mapping protein interactions in plants.
PMID: 36585336
Autophagy , IF:16.016 , 2023 Apr , V19 (4) : P1293-1310 doi: 10.1080/15548627.2022.2124501
Brassinosteroids modulate autophagy through phosphorylation of RAPTOR1B by the GSK3-like kinase BIN2 in Arabidopsis.
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.; Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA.
Macroautophagy/autophagy is a conserved recycling process that maintains cellular homeostasis during environmental stress. Autophagy is negatively regulated by TOR (target of rapamycin), a nutrient-regulated protein kinase that in plants is activated by several phytohormones, leading to increased growth. However, the detailed molecular mechanisms by which TOR integrates autophagy and hormone signaling are poorly understood. Here, we show that TOR modulates brassinosteroid (BR)-regulated plant growth and stress-response pathways. Active TOR was required for full BR-mediated growth in Arabidopsis thaliana. Autophagy was constitutively up-regulated upon blocking BR biosynthesis or signaling, and down-regulated by increasing the activity of the BR pathway. BIN2 (brassinosteroid-insensitive 2) kinase, a GSK3-like kinase functioning as a negative regulator in BR signaling, directly phosphorylated RAPTOR1B (regulatory-associated protein of TOR 1B), a substrate-recruiting subunit in the TOR complex, at a conserved serine residue within a typical BIN2 phosphorylation motif. Mutation of RAPTOR1B serine 916 to alanine, to block phosphorylation by BIN2, repressed autophagy and increased phosphorylation of the TOR substrate ATG13a (autophagy-related protein 13a). By contrast, this mutation had only a limited effect on growth. We present a model in which RAPTOR1B is phosphorylated and inhibited by BIN2 when BRs are absent, activating the autophagy pathway. When BRs signal and inhibit BIN2, RAPTOR1B is thus less inhibited by BIN2 phosphorylation. This leads to increased TOR activity and ATG13a phosphorylation, and decreased autophagy activity. Our studies define a new mechanism by which coordination between BR and TOR signaling pathways helps to maintain the balance between plant growth and stress responses.
PMID: 36151786
Plant Cell , IF:11.277 , 2023 Mar doi: 10.1093/plcell/koad060
Brassinosteroids regulate cotton fiber elongation by modulating very-long-chain fatty acid biosynthesis.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, Xinjiang, China.
Brassinosteroid (BR), a growth-promoting phytohormone, regulates many plant growth processes including cell development. However, the mechanism by which BR regulates fiber growth is poorly understood. Cotton (Gossypium hirsutum) fibers are an ideal single-cell model in which to study cell elongation due to their length. Here we report that BR controls cotton fiber elongation by modulating very-long-chain fatty acid (VLCFA) biosynthesis. BR deficiency reduces the expression of 3-ketoacyl-CoA synthases (GhKCSs), the rate-limiting enzymes involved in VLCFA biosynthesis, leading to lower saturated VLCFAs contents in pagoda1 (pag1) mutant fibers. In vitro ovule culture experiments show that BR acts upstream of VLCFAs. Silencing of BRI1-EMS-SUPPRESOR 1.4 (GhBES1.4), encoding a master transcription factor (TF) of the BR signaling pathway, significantly reduces fiber length, whereas GhBES1.4 over-expression produces longer fibers. GhBES1.4 regulates endogenous VLCFA contents and directly binds to BR RESPONSE ELEMENTS (BRREs) in the GhKCS10_At promoter region, which in turn regulates GhKCS10_At expression to increase endogenous VLCFA contents. GhKCS10_At overexpression promotes cotton fiber elongation, whereas GhKCS10_At silencing inhibits cotton fiber growth, supporting a positive regulatory role for GhKCS10_At in fiber elongation. Overall, these results uncover a mechanism of fiber elongation through crosstalk between BR and VLCFAs at the single-cell level.
PMID: 36861340
Plant Cell , IF:11.277 , 2023 Apr , V35 (5) : P1283-1284 doi: 10.1093/plcell/koad040
Don't be blue: Pure green light spurs brassinosteroid signaling.
The Plant Cell, American Society of Plant Biologists, USA.; Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA.
PMID: 36808293
Plant Cell , IF:11.277 , 2023 Apr , V35 (5) : P1455-1473 doi: 10.1093/plcell/koad032
Signaling by the EPFL-ERECTA family coordinates female germline specification through the BZR1 family in Arabidopsis.
College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany.; Tea Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Dafeng Road 6, Tianhe District, Guangzhou 510640, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China.
In most flowering plants, the female germline is initiated in the subepidermal L2 layer of ovule primordia forming a single megaspore mother cell (MMC). How signaling from the L1 (epidermal) layer could contribute to the gene regulatory network (GRN) restricting MMC formation to a single cell is unclear. We show that EPIDERMAL PATTERNING FACTOR-like (EPFL) peptide ligands are expressed in the L1 layer, together with their ERECTA family (ERf) receptor kinases, to control female germline specification in Arabidopsis thaliana. EPFL-ERf dependent signaling restricts multiple subepidermal cells from acquiring MMC-like cell identity by activating the expression of the major brassinosteroid (BR) receptor kinase BRASSINOSTEROID INSENSITIVE 1 and the BR-responsive transcription factor BRASSINOZOLE RESISTANT 1 (BZR1). Additionally, BZR1 coordinates female germline specification by directly activating the expression of a nucleolar GTP-binding protein, NUCLEOSTEMIN-LIKE 1 (NSN1), which is expressed in early-stage ovules excluding the MMC. Mutants defective in this GRN form multiple MMCs resulting in a strong reduction of seed set. In conclusion, we uncovered a ligand/receptor-like kinase-mediated signaling pathway acting upstream and coordinating BR signaling via NSN1 to restrict MMC differentiation to a single subepidermal cell.
PMID: 36748257
Plant Cell , IF:11.277 , 2023 Apr , V35 (5) : P1304-1317 doi: 10.1093/plcell/koad022
Green means go: Green light promotes hypocotyl elongation via brassinosteroid signaling.
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200031 Shanghai, P. R. China.; University of Chinese Academy of Sciences, Shanghai 200031, P. R. China.; Department of Light Source and Illuminating Engineering, Fudan University, 2005 Songhu Rd, Shanghai 200433, P. R. China.
Although many studies have elucidated the mechanisms by which different wavelengths of light (blue, red, far-red, or ultraviolet-B [UV-B]) regulate plant development, whether and how green light regulates plant development remains largely unknown. Previous studies reported that green light participates in regulating growth and development in land plants, but these studies have reported conflicting results, likely due to technical problems. For example, commercial green light-emitting diode light sources emit a little blue or red light. Here, using a pure green light source, we determined that unlike blue, red, far-red, or UV-B light, which inhibits hypocotyl elongation, green light promotes hypocotyl elongation in Arabidopsis thaliana and several other plants during the first 2-3 d after planting. Phytochromes, cryptochromes, and other known photoreceptors do not mediate green-light-promoted hypocotyl elongation, but the brassinosteroid (BR) signaling pathway is involved in this process. Green light promotes the DNA binding activity of BRI1-EMS-SUPPRESSOR 1 (BES1), a master transcription factor of the BR pathway, thus regulating gene transcription to promote hypocotyl elongation. Our results indicate that pure green light promotes elongation via BR signaling and acts as a shade signal to enable plants to adapt their development to a green-light-dominant environment under a canopy.
PMID: 36724050
Plant Cell , IF:11.277 , 2023 Mar , V35 (3) : P975-993 doi: 10.1093/plcell/koad013
Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics.
Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA.; Department of Life Science, Hanyang University, Seoul 04763, South Korea.; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, South Korea.; Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan.; Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, California 94305, USA.; Department of Biology, Stanford University, Stanford, California 94305, USA.; Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.; Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA.; Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.; Chan Zuckerberg Biohub, San Francisco, California, USA.
Elucidating enzyme-substrate relationships in posttranslational modification (PTM) networks is crucial for understanding signal transduction pathways but is technically difficult because enzyme-substrate interactions tend to be transient. Here, we demonstrate that TurboID-based proximity labeling (TbPL) effectively and specifically captures the substrates of kinases and phosphatases. TbPL-mass spectrometry (TbPL-MS) identified over 400 proximal proteins of Arabidopsis thaliana BRASSINOSTEROID-INSENSITIVE2 (BIN2), a member of the GLYCOGEN SYNTHASE KINASE 3 (GSK3) family that integrates signaling pathways controlling diverse developmental and acclimation processes. A large portion of the BIN2-proximal proteins showed BIN2-dependent phosphorylation in vivo or in vitro, suggesting that these are BIN2 substrates. Protein-protein interaction network analysis showed that the BIN2-proximal proteins include interactors of BIN2 substrates, revealing a high level of interactions among the BIN2-proximal proteins. Our proteomic analysis establishes the BIN2 signaling network and uncovers BIN2 functions in regulating key cellular processes such as transcription, RNA processing, translation initiation, vesicle trafficking, and cytoskeleton organization. We further discovered significant overlap between the GSK3 phosphorylome and the O-GlcNAcylome, suggesting an evolutionarily ancient relationship between GSK3 and the nutrient-sensing O-glycosylation pathway. Our work presents a powerful method for mapping PTM networks, a large dataset of GSK3 kinase substrates, and important insights into the signaling network that controls key cellular functions underlying plant growth and acclimation.
PMID: 36660928
Plant Cell , IF:11.277 , 2023 Mar , V35 (4) : P1241-1258 doi: 10.1093/plcell/koad007
Spatiotemporal formation of the large vacuole regulated by the BIN2-VLG module is required for female gametophyte development in Arabidopsis.
School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.; Shanghai Collaborative Innovation Center of Agri-Seeds/Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200240, China.
In Arabidopsis thaliana, female gametophyte (FG) development is accompanied by the formation and expansion of the large vacuole in the FG; this is essential for FG expansion, nuclear polar localization, and cell fate determination. Arabidopsis VACUOLELESS GAMETOPHYTES (VLG) facilitates vesicular fusion to form large vacuole in the FG, but the regulation of VLG remains largely unknown. Here, we found that gain-of-function mutation of BRASSINOSTEROID INSENSITIVE2 (BIN2) (bin2-1) increases VLG abundance to induce the vacuole formation at stage FG1, and leads to abortion of FG. Loss-of-function mutation of BIN2 and its homologs (bin2-3 bil1 bil2) reduced VLG abundance and mimicked vlg/VLG phenotypes. Knocking down VLG in bin2-1 decreased the ratio of aberrant vacuole formation at stage FG1, whereas FG1-specific overexpression of VLG mimicked the bin2-1 phenotype. VLG partially rescued the bin2-3 bil1 bil2 phenotype, demonstrating that VLG acts downstream of BIN2. Mutation of VLG residues that are phosphorylated by BIN2 altered VLG stability and a phosphorylation mimic of VLG causes similar defects as did bin2-1. Therefore, BIN2 may function by interacting with and phosphorylating VLG in the FG to enhance its stability and abundance, thus facilitating vacuole formation. Our findings provide mechanistic insight into how the BIN2-VLG module regulates the spatiotemporal formation of the large vacuole in FG development.
PMID: 36648110
Plant Cell , IF:11.277 , 2023 Mar , V35 (3) : P1076-1091 doi: 10.1093/plcell/koac364
An endoplasmic reticulum-associated degradation-related E2-E3 enzyme pair controls grain size and weight through the brassinosteroid signaling pathway in rice.
College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China.; College of Tropical Crops Hainan University, Hainan University, Haikou 570288, China.; The Innovative of Seed Design, Chinese Academy of Sciences, Sanya 572025, China.
Grain size is an important agronomic trait, but our knowledge about grain size determination in crops is still limited. Endoplasmic reticulum (ER)-associated degradation (ERAD) is a special ubiquitin proteasome system that is involved in degrading misfolded or incompletely folded proteins in the ER. Here, we report that SMALL GRAIN 3 (SMG3) and DECREASED GRAIN SIZE 1 (DGS1), an ERAD-related E2-E3 enzyme pair, regulate grain size and weight through the brassinosteroid (BR) signaling pathway in rice (Oryza sativa). SMG3 encodes a homolog of Arabidopsis (Arabidopsis thaliana) UBIQUITIN CONJUGATING ENZYME 32, which is a conserved ERAD-associated E2 ubiquitin conjugating enzyme. SMG3 interacts with another grain size regulator, DGS1. Loss of function of SMG3 or DGS1 results in small grains, while overexpression of SMG3 or DGS1 leads to long grains. Further analyses showed that DGS1 is an active E3 ubiquitin ligase and colocates with SMG3 in the ER. SMG3 and DGS1 are involved in BR signaling. DGS1 ubiquitinates the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1) and affects its accumulation. Genetic analysis suggests that SMG3, DGS1, and BRI1 act together to regulate grain size and weight. In summary, our findings identify an ERAD-related E2-E3 pair that regulates grain size and weight, which gives insight into the function of ERAD in grain size control and BR signaling.
PMID: 36519262
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Apr , V120 (16) : Pe2301879120 doi: 10.1073/pnas.2301879120
HY5 functions as a systemic signal by integrating BRC1-dependent hormone signaling in tomato bud outgrowth.
Department of Horticulture, Zijinggang Campus, Zhejiang University, Hangzhou 310058, China.; College of Horticulture, Northwest Agriculture & Forestry University, Xianyang, Shaanxi 712100, China.; School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, B15 2TT Edgbaston, UK.; Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Zhejiang University, Hangzhou 310058, China.
Light plays an important role in determining plant architecture, which greatly influences crop yield. However, the precise mechanisms by which light signaling regulates bud outgrowth remain to be identified. Here, we show that light regulates bud outgrowth via both HY5 and brassinosteroid (BR)-dependent pathways in tomato. Inactivation of the red-light photoreceptor PHYB, or deficiencies in PHYB or the blue-light photoreceptor CRY1a, inhibits bud outgrowth and leads to decreased accumulation of HY5 protein and increased transcript level of BRANCHED1 (BRC1), a central integrator of branching signals. HY5, functioning as a mobile systemic signal from leaves, promotes bud outgrowth by directly suppressing BRC1 transcript and activating the transcript of BR biosynthesis genes within the lateral buds in tomato. Furthermore, BRC1 prevents the accumulation of cytokinin (CK) and gibberellin (GA) by directly inhibiting the transcript of CK synthesis gene LOG4, while increasing the transcript levels of CK and GA degradation genes (CKX7, GA2ox4, and GA2ox5), leading to an arrest of bud outgrowth. Moreover, bud outgrowth occurs predominantly in the day due to the suppression of BRC1 transcript by HY5. These findings demonstrate that light-inducible HY5 acts as a systemic signaling factor in fine-tuning the bud outgrowth of tomato.
PMID: 37036969
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Apr , V120 (15) : Pe2216632120 doi: 10.1073/pnas.2216632120
HD-ZIP III-dependent local promotion of brassinosteroid synthesis suppresses vascular cell division in Arabidopsis root apical meristem.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.; Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.; Department of Bioscience and Biotechnology, Faculty of Environmental Sciences, Kyoto University of Advanced Science, Kyoto 621-8555, Japan.
Spatiotemporal control of cell division in the meristem is vital for plant growth. In the stele of the root apical meristem (RAM), procambial cells divide periclinally to increase the number of vascular cell files. Class III homeodomain leucine zipper (HD-ZIP III) proteins are key transcriptional regulators of RAM development and suppress the periclinal division of vascular cells in the stele; however, the mechanism underlying the regulation of vascular cell division by HD-ZIP III transcription factors (TFs) remains largely unknown. Here, we performed transcriptome analysis to identify downstream genes of HD-ZIP III and found that HD-ZIP III TFs positively regulate brassinosteroid biosynthesis-related genes, such as CONSTITUTIVE PHOTOMORPHOGENIC DWARF (CPD), in vascular cells. Introduction of pREVOLUTA::CPD in a quadruple loss-of-function mutant of HD-ZIP III genes partly rescued the phenotype in terms of the vascular defect in the RAM. Treatment of a quadruple loss-of-function mutant, a gain-of-function mutant of HD-ZIP III, and the wild type with brassinosteroid and a brassinosteroid synthesis inhibitor also indicated that HD-ZIP III TFs act together to suppress vascular cell division by increasing brassinosteroid levels. Furthermore, brassinosteroid application suppressed the cytokinin response in vascular cells. Together, our findings suggest that the suppression of vascular cell division by HD-ZIP III TFs is caused, at least in part, by the increase in brassinosteroid levels through the transcriptional activation of brassinosteroid biosynthesis genes in the vascular cells of the RAM. This elevated brassinosteroid level suppresses cytokinin response in vascular cells, inhibiting vascular cell division in the RAM.
PMID: 37011193
New Phytol , IF:10.151 , 2023 May , V238 (4) : P1516-1533 doi: 10.1111/nph.18779
The regulatory module MdBZR1-MdCOL6 mediates brassinosteroid- and light-regulated anthocyanin synthesis in apple.
College of Horticulture, Shandong Agricultural University, Taian, 271000, Shandong, China.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
The anthocyanin content is an important indicator of the nutritional value of most fruits, including apple (Malus domestica). Anthocyanin synthesis is coordinately regulated by light and various phytohormones. In this study on apple, we revealed the antagonistic relationship between light and brassinosteroid (BR) signaling pathways, which is mediated by BRASSINAZOLE-RESISTANT 1 (MdBZR1) and the B-box protein MdCOL6. The exogenous application of brassinolide inhibited the high-light-induced anthocyanin accumulation in red-fleshed apple seedlings, whereas increases in the light intensity decreased the endogenous BR content. The overexpression of MdBZR1 inhibited the anthocyanin synthesis in apple plants. An exposure to a high-light intensity induced the degradation of dephosphorylated MdBZR1, resulting in functional impairment. MdBZR1 was identified as an upstream repressor of MdCOL6, which promotes anthocyanin synthesis in apple plants. Furthermore, MdBZR1 interacts with MdCOL6 to attenuate its ability to activate MdUFGT and MdANS transcription. Thus, MdBZR1 negatively regulates MdCOL6-mediated anthocyanin accumulation. Our study findings have clarified the molecular basis of the integration of light and BR signals during the regulation of anthocyanin biosynthesis, which is an important process influencing fruit quality.
PMID: 36710519
Plant Biotechnol J , IF:9.803 , 2023 May , V21 (5) : P896-898 doi: 10.1111/pbi.14005
GhPRE1A promotes cotton fibre elongation by activating the DNA-binding bHLH factor GhPAS1.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, 450000, Zhengzhou, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 455000, Anyang, China.; College of Life Sciences and Agronomy, Zhoukou Normal University, 466000, Zhoukou, China.; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, 831100, Changji, China.
PMID: 36609789
Cell Rep , IF:9.423 , 2023 Mar , V42 (4) : P112301 doi: 10.1016/j.celrep.2023.112301
A conserved brassinosteroid-mediated BES1-CERP-EXPA3 signaling cascade controls plant cell elongation.
College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.; College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China. Electronic address: guanghuix@snnu.edu.cn.
Continuous plant growth is achieved by cell division and cell elongation. Brassinosteroids control cell elongation and differentiation throughout plant life. However, signaling cascades underlying BR-mediated cell elongation are unknown. In this study, we introduce cotton fiber, one of the most representative single-celled tissues, to decipher cell-specific BR signaling. We find that gain of function of GhBES1, a key transcriptional activator in BR signaling, enhances fiber elongation. The chromatin immunoprecipitation sequencing analysis identifies a cell-elongation-related protein, GhCERP, whose transcription is directly activated by GhBES1. GhCERP, a downstream target of GhBES1, transmits the GhBES1-mediated BR signaling to its target gene, GhEXPA3-1. Ultimately, GhEXPA3-1 promotes fiber cell elongation. In addition, inter-species functional analysis of the BR-mediated BES1-CERP-EXPA3 signaling cascade also promotes Arabidopsis root and hypocotyl growth. We propose that the BES1-CERP-EXPA3 module may be a broad-spectrum pathway that is universally exploited by diverse plant species to regulate BR-promoted cell elongation.
PMID: 36952343
Cell Rep , IF:9.423 , 2023 Mar , V42 (3) : P112187 doi: 10.1016/j.celrep.2023.112187
Control of grain size in rice by TGW3 phosphorylation of OsIAA10 through potentiation of OsIAA10-OsARF4-mediated auxin signaling.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.; National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: songxj@ibcas.ac.cn.
Grain size is a key component of grain yield and quality in crops. Several core players of auxin signaling have been revealed to modulate grain size; however, to date, few genetically defined pathways have been reported, and whether phosphorylation could boost degradation of Aux/IAA proteins is uncertain. Here, we show that TGW3 (also called OsGSK5) interacts with and phosphorylates OsIAA10. Phosphorylation of OsIAA10 facilitates its interaction with OsTIR1 and subsequent destabilization, but this modification hinders its interaction with OsARF4. Our genetic and molecular evidence identifies an OsTIR1-OsIAA10-OsARF4 axis as key for grain size control. In addition, physiological and molecular studies suggest that TGW3 mediates the brassinosteroid response, the effect of which can be relayed through the regulatory axis. Collectively, these findings define a auxin signaling pathway to regulate grain size, in which phosphorylation of OsIAA10 enhances its proteolysis and potentiates OsIAA10-OsARF4-mediated auxin signaling.
PMID: 36871218
Plant Physiol , IF:8.34 , 2023 Apr doi: 10.1093/plphys/kiad208
PbrBZR1 Interacts with PbrARI2.3 to Mediate Brassinosteroid-Regulated Pollen Tube Growth during Self-Incompatibility Signaling in Pear.
Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China.
S-RNase-mediated self-incompatibility (SI) prevents self-fertilization and promotes outbreeding to ensure genetic diversity in many flowering plants, including pear (Pyrus sp.). Brassinosteroids (BRs) have well-documented functions in cell elongation, but their molecular mechanisms in pollen tube growth, especially in the SI response, remain elusive. Here, exogenously applied brassinolide (BL), an active BR, countered incompatible pollen tube growth inhibition during the SI response in pear. Antisense repression of BRASSINAZOLE-RESISTANT1 (PbrBZR1), a critical component of BR signaling, blocked the positive effect of BL on pollen tube elongation. Further analyses revealed that PbrBZR1 binds to the promoter of EXPANSIN-LIKE A3 (PbrEXLA3) to activate its expression. PbrEXLA3 encodes an expansin that promotes pollen tube elongation in pear. The stability of dephosphorylated PbrBZR1 was substantially reduced in incompatible pollen tubes, where it is targeted by ARIADNE2.3 (PbrARI2.3), an E3 ubiquitin ligase that is strongly expressed in pollen. Our results show that during the SI response, PbrARI2.3 accumulates and negatively regulates pollen tube growth by accelerating the degradation of PbrBZR1 via the 26S proteasome pathway. Together, our results show that a ubiquitin-mediated modification participates in BR signaling in pollen and reveal the molecular mechanism by which BRs regulate S-RNase-based SI.
PMID: 37010117
Plant Physiol , IF:8.34 , 2023 Mar , V191 (3) : P1985-2000 doi: 10.1093/plphys/kiac590
A brassinosteroid transcriptional regulatory network participates in regulating fiber elongation in cotton.
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.; Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA.; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, Xinjiang, China.
Brassinosteroids (BRs) participate in the regulation of plant growth and development through BRI1-EMS-SUPPRESSOR1 (BES1)/BRASSINAZOLE-RESISTANT1 (BZR1) family transcription factors. Cotton (Gossypium hirsutum) fibers are highly elongated single cells, and BRs play a vital role in the regulation of fiber elongation. However, the mode of action on how BR is involved in the regulation of cotton fiber elongation remains unexplored. Here, we generated GhBES1.4 over expression lines and found that overexpression of GhBES1.4 promoted fiber elongation, whereas silencing of GhBES1.4 reduced fiber length. DNA affinity purification and sequencing (DAP-seq) identified 1,531 target genes of GhBES1.4, and five recognition motifs of GhBES1.4 were identified by enrichment analysis. Combined analysis of DAP-seq and RNA-seq data of GhBES1.4-OE/RNAi provided mechanistic insights into GhBES1.4-mediated regulation of cotton fiber development. Further, with the integrated approach of GWAS, RNA-seq, and DAP-seq, we identified seven genes related to fiber elongation that were directly regulated by GhBES1.4. Of them, we showed Cytochrome P450 84A1 (GhCYP84A1) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (GhHMG1) promote cotton fiber elongation. Overall, the present study established the role of GhBES1.4-mediated gene regulation and laid the foundation for further understanding the mechanism of BR participation in regulating fiber development.
PMID: 36542688
Plant Cell Environ , IF:7.228 , 2023 Apr , V46 (4) : P1249-1263 doi: 10.1111/pce.14502
Red-light receptor phytochrome B inhibits BZR1-NAC028-CAD8B signaling to negatively regulate rice resistance to sheath blight.
Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China.; Laboratory of Rice Disease Research, Institution of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, China.; Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China.; Department of Plant Protection, Rice Research Institute, Sichuan Agricultural University, Chengdu, China.; Department of Biological Science, College of Life Science, Yan'an University, Yan'an, Shaanxi, China.; Liaoning Province Shiyan High School, Shenyang, China.; College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China.
Phytochrome (Phy)-regulated light signalling plays important roles in plant growth, development, and stress responses. However, its function in rice defence against sheath blight disease (ShB) remains unclear. Here, we found that PhyB mutation or shade treatment promoted rice resistance to ShB, while resistance was reduced by PhyB overexpression. Further analysis showed that PhyB interacts with phytochrome-interacting factor-like 15 (PIL15), brassinazole resistant 1 (BZR1), and vascular plant one-zinc-finger 2 (VOZ2). Plants overexpressing PIL15 were more susceptible to ShB in contrast to bzr1-D-overexpressing plants compared with the wild-type, suggesting that PhyB may inhibit BZR1 to negatively regulate rice resistance to ShB. Although BZR1 is known to regulate brassinosteroid (BR) signalling, the observation that BR signalling negatively regulated resistance to ShB indicated an independent role for BZR1 in controlling rice resistance. It was also found that the BZR1 ligand NAC028 positively regulated resistance to ShB. RNA sequencing showed that cinnamyl alcohol dehydrogenase 8B (CAD8B), involved in lignin biosynthesis was upregulated in both bzr1-D- and NAC028-overexpressing plants compared with the wild-type. Yeast-one hybrid, ChIP, and transactivation assays demonstrated that BZR1 and NAC028 activate CAD8B directly. Taken together, the analyses demonstrated that PhyB-mediated light signalling inhibits the BZR1-NAC028-CAD8B pathway to regulate rice resistance to ShB.
PMID: 36457051
J Integr Plant Biol , IF:7.061 , 2023 Apr doi: 10.1111/jipb.13491
The brassinosteroid signaling component SlBZR1 promotes tomato fruit ripening and carotenoid accumulation.
Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China.; College of Plant Science, Jilin University, Changchun, 130062, China.
The plant hormone ethylene is essential for climacteric fruit ripening, although it is unclear how other phytohormones and their interactions with ethylene might affect fruit ripening. Here, we explored how brassinosteroids (BRs) regulate fruit ripening in tomato (Solanum lycopersicum) and how they interact with ethylene. Exogenous BR treatment and increased endogenous BR contents in tomato plants overexpressing the BR biosynthetic gene SlCYP90B3 promoted ethylene production and fruit ripening. Genetic analysis indicated that the BR signaling regulators Brassinazole-resistant1 (SlBZR1) and BRI1-EMS-suppressor1 (SlBES1) act redundantly in fruit softening. Knocking out SlBZR1 inhibited ripening through transcriptome reprogramming at the onset of ripening. Combined transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing identified 73 SlBZR1-repressed targets and 203 SlBZR1-induced targets involving major ripening-related genes, suggesting that SlBZR1 positively regulates tomato fruit ripening. SlBZR1 directly targeted several ethylene and carotenoid biosynthetic genes to contribute to the ethylene burst and carotenoid accumulation to ensure normal ripening and quality formation. Furthermore, knockout of Brassinosteroid-insensitive2 (SlBIN2), a negative regulator of BR signaling upstream of SlBZR1, promoted fruit ripening and carotenoid accumulation. Taken together, our results highlight the role of SlBZR1 as a master regulator of tomato fruit ripening with potential for tomato quality improvement and carotenoid biofortification. This article is protected by copyright. All rights reserved.
PMID: 37009849
Plant J , IF:6.417 , 2023 Mar doi: 10.1111/tpj.16203
Brassinosteroid transcription factor BES1 modulates nitrate deficiency by promoting NRT2.1 and NRT2.2 transcription in Arabidopsis.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.; High Latitude Crops Institute of Shanxi Agriculture University, Datong, Shanxi, 037008, China.; College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Nitrogen (N) is one of the most essential mineral elements for plants. Brassinosteroids (BRs) play key roles in plant growth and development. Emerging evidence indicates that BRs participate in the responses to nitrate deficiency. However, the precise molecular mechanism underlying the BR signaling pathway in regulating nitrate deficiency remains largely unknown. The transcription factor BES1 regulates the expression of many genes in response to BRs. Root length, nitrate uptake and N concentration of bes1-D mutants were higher than those of wild-type under nitrate deficiency. BES1 levels strongly increased under low nitrate conditions, especially in the non-phosphorylated (active) form. Furthermore, BES1 directly bound to the promoters of NRT2.1 and NRT2.2 to promote their expression under nitrate deficiency. Taken together, BES1 is a key mediator that links BR signaling under nitrate deficiency by modulating high affinity nitrate transporters in plants.
PMID: 36948884
Sci China Life Sci , IF:6.038 , 2023 Mar doi: 10.1007/s11427-022-2319-0
Crosstalk between brassinosteroid signaling and variable nutrient environments.
Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, China.; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. tonghongning@caas.cn.; Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China. ccchu@scau.edu.cn.; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. ccchu@scau.edu.cn.; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, China. ccchu@scau.edu.cn.
Brassinosteroid (BR) represents a group of steroid hormones that regulate plant growth and development as well as environmental adaptation. The fluctuation of external nutrient elements is a situation that plants frequently face in the natural environment, in which nitrogen (N) and phosphorus (P) are two of the most critical nutrients restraint of the early growth of plants. As the macronutrients, N and P are highly required by plants, but their availability or solubility in the soil is relatively low. Since iron (Fe) and P always modulate each other's content and function in plants mutually antagonistically, the regulatory mechanisms of Fe and P are inextricably linked. Recently, BR has emerged as a critical regulator in nutrient acquisition and phenotypic plasticity in response to the variable nutrient levels in Arabidopsis and rice. Here, we review the current understanding of the crosstalk between BR and the three major nutrients (N, P, and Fe), highlighting how nutrient signaling regulates BR synthesis and signaling to accommodate plant growth and development in Arabidopsis and rice.
PMID: 36907968
Int J Mol Sci , IF:5.923 , 2023 Apr , V24 (8) doi: 10.3390/ijms24087227
Bacillus paralicheniformis RP01 Enhances the Expression of Growth-Related Genes in Cotton and Promotes Plant Growth by Altering Microbiota inside and outside the Root.
College of Pharmacy, Chengdu University, Chengdu 610052, China.; Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610052, China.; College of Resources and Environment, Southwest University, Chongqing 400715, China.
Plant growth-promoting bacteria (PGPB) can promote plant growth in various ways, allowing PGPB to replace chemical fertilizers to avoid environmental pollution. PGPB is also used for bioremediation and in plant pathogen control. The isolation and evaluation of PGPB are essential not only for practical applications, but also for basic research. Currently, the known PGPB strains are limited, and their functions are not fully understood. Therefore, the growth-promoting mechanism needs to be further explored and improved. The Bacillus paralicheniformis RP01 strain with beneficial growth-promoting activity was screened from the root surface of Brassica chinensis using a phosphate-solubilizing medium. RP01 inoculation significantly increased plant root length and brassinosteroid content and upregulated the expression of growth-related genes. Simultaneously, it increased the number of beneficial bacteria that promoted plant growth and reduced the number of detrimental bacteria. The genome annotation findings also revealed that RP01 possesses a variety of growth-promoting mechanisms and a tremendous growth-promoting potential. This study isolated a highly potential PGPB and elucidated its possible direct and indirect growth-promoting mechanisms. Our study results will help enrich the PGPB library and provide a reference for plant-microbe interactions.
PMID: 37108389
Front Plant Sci , IF:5.753 , 2023 , V14 : P1136884 doi: 10.3389/fpls.2023.1136884
Transcriptome and functional analysis revealed the intervention of brassinosteroid in regulation of cold induced early flowering in tobacco.
College of Agronomy and Biotechnology, Southwest University, Chongqing, China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China.; Chongqing Tobacco Science Research Institute, Chongqing, China.
Cold environmental conditions may often lead to the early flowering of plants, and the mechanism by cold-induced flowering remains poorly understood. Microscopy analysis in this study demonstrated that cold conditioning led to early flower bud differentiation in two tobacco strains and an Agilent Tobacco Gene Expression microarray was adapted for transcriptomic analysis on the stem tips of cold treated tobacco to gain insight into the molecular process underlying flowering in tobacco. The transcriptomic analysis showed that cold treatment of two flue-cured tobacco varieties (Xingyan 1 and YunYan 85) yielded 4176 and 5773 genes that were differentially expressed, respectively, with 2623 being commonly detected. Functional distribution revealed that the differentially expressed genes (DEGs) were mainly enriched in protein metabolism, RNA, stress, transport, and secondary metabolism. Genes involved in secondary metabolism, cell wall, and redox were nearly all up-regulated in response to the cold conditioning. Further analysis demonstrated that the central genes related to brassinosteroid biosynthetic pathway, circadian system, and flowering pathway were significantly enhanced in the cold treated tobacco. Phytochemical measurement and qRT-PCR revealed an increased accumulation of brassinolide and a decreased expression of the flowering locus c gene. Furthermore, we found that overexpression of NtBRI1 could induce early flowering in tobacco under normal condition. And low-temperature-induced early flowering in NtBRI1 overexpression plants were similar to that of normal condition. Consistently, low-temperature-induced early flowering is partially suppressed in NtBRI1 mutant. Together, the results suggest that cold could induce early flowering of tobacco by activating brassinosteroid signaling.
PMID: 37063233
Front Plant Sci , IF:5.753 , 2023 , V14 : P1152196 doi: 10.3389/fpls.2023.1152196
The identification and characterization of a plant height and grain length related gene hfr131 in rice.
State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Fudan University, Shanghai, China.; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.; Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China.; Ministry of Education, Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, China.
Plant height and grain size are important agronomic traits affecting rice yield. Various plant hormones participate in the regulation of plant height and grain size in rice. However, how these hormones cooperate to regulate plant height and grain size is poorly understood. In this study, we identified a brassinosteroid-related gene, hfr131, from an introgression line constructed using Oryza longistaminata, that caused brassinosteroid insensitivity and reduced plant height and grain length in rice. Further study showed that hfr131 is a new allele of OsBRI1 with a single-nucleotide polymorphism (G to A) in the coding region, leading to a T988I conversion at a conserved site of the kinase domain. By combining yeast one-hybrid assays, chromatin immunoprecipitation-quantitative PCR and gene expression quantification, we demonstrated that OsARF17, an auxin response factor, could bind to the promoter region of HFR131 and positively regulated HFR131 expression, thereby regulating the plant height and grain length, and influencing brassinosteroid sensitivity. Haplotype analysis showed that the consociation of OsAFR17(Hap1) /HFR131(Hap6) conferred an increase in grain length. Overall, this study identified hfr131 as a new allele of OsBRI1 that regulates plant height and grain length in rice, revealed that brassinosteroid and auxin might coordinate through OsARF17-HFR131 interaction, and provided a potential breeding target for improvement of rice yield.
PMID: 37035088
Front Plant Sci , IF:5.753 , 2023 , V14 : P1116078 doi: 10.3389/fpls.2023.1116078
Comprehensive transcriptomic profiling reveals complex molecular mechanisms in the regulation of style-length dimorphism in Guettarda speciosa (Rubiaceae), a species with "anomalous" distyly.
School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China.; Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.; Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China.
BACKGROUND: The evolution of heterostyly, a genetically controlled floral polymorphism, has been a hotspot of research since the 19th century. In recent years, studies on the molecular mechanism of distyly (the most common form of heterostyly) revealed an evolutionary convergence in genes for brassinosteroids (BR) degradation in different angiosperm groups. This floral polymorphism often exhibits considerable variability that some taxa have significant stylar dimorphism, but anther height differs less. This phenomenon has been termed "anomalous" distyly, which is usually regarded as a transitional stage in evolution. Compared to "typical" distyly, the genetic regulation of "anomalous" distyly is almost unknown, leaving a big gap in our understanding of this special floral adaptation strategy. METHODS: Here we performed the first molecular-level study focusing on this floral polymorphism in Guettarda speciosa (Rubiaceae), a tropical tree with "anomalous" distyly. Comprehensive transcriptomic profiling was conducted to examine which genes and metabolic pathways were involved in the genetic control of style dimorphism and if they exhibit similar convergence with "typical" distylous species. RESULTS: "Brassinosteroid homeostasis" and "plant hormone signal transduction" was the most significantly enriched GO term and KEGG pathway in the comparisons between L- and S-morph styles, respectively. Interestingly, homologs of all the reported S-locus genes either showed very similar expressions between L- and S-morph styles or no hits were found in G. speciosa. BKI1, a negative regulator of brassinosteroid signaling directly repressing BRI1 signal transduction, was identified as a potential gene regulating style length, which significantly up-regulated in the styles of S-morph. DISCUSSION: These findings supported the hypothesis that style length in G. speciosa was regulated through a BR-related signaling network in which BKI1 may be one key gene. Our data suggested, in species with "anomalous" distyly, style length was regulated by gene differential expressions, instead of the "hemizygous" S-locus genes in "typical" distylous flowers such as Primula and Gelsemium, representing an "intermediate" stage in the evolution of distyly. Genome-level analysis and functional studies in more species with "typical" and "anomalous" distyly would further decipher this "most complex marriage arrangement" in angiosperms and improve our knowledge of floral evolution.
PMID: 37008460
Theor Appl Genet , IF:5.699 , 2023 Mar , V136 (3) : P29 doi: 10.1007/s00122-023-04325-x
BnaC01.BIN2, a GSK3-like kinase, modulates plant height and yield potential in Brassica napus.
Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.; Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China.; Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China. limei1230@126.com.; Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China. limei1230@126.com.; Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China. wangtonghua2014@163.com.; Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China. wangtonghua2014@163.com.
Using map-based cloning and transgenic transformation, we revealed that glycogen kinase synthase 3-like kinase, BnaC01.BIN2, modulates plant height and yield in rapeseed. The modification of plant height is one of the most important goals in rapeseed breeding. Although several genes that regulate rapeseed plant height have been identified, the genetics mechanisms underlying rapeseed plant height regulation remain poorly understood, and desirable genetic resources for rapeseed ideotype breeding are scarce. Here, we map-based cloned and functionally verified that the rapeseed semi-dominant gene, BnDF4, greatly affects rapeseed plant height. Specifically, BnDF4 encodes brassinosteroid (BR)-insensitive 2, a glycogen synthase kinase 3 primarily expressed in the lower internodes to modulate rapeseed plant height by blocking basal internode-cell elongation. Transcriptome data showed that several cell expansion-related genes involving auxin and BRs pathways were significantly downregulated in the semi-dwarf mutant. Heterozygosity in the BnDF4 allele results in small stature with no marked differences in other agronomic traits. Using BnDF4 in the heterozygous condition, the hybrid displayed strong yield heterosis through optimum intermediate plant height. Our results provide a desirable genetic resource for breeding semi-dwarf rapeseed phenotypes and support an effective strategy for breeding rapeseed hybrid varieties with strong yield heterosis.
PMID: 36867248
Plant Sci , IF:4.729 , 2023 Jun , V331 : P111673 doi: 10.1016/j.plantsci.2023.111673
The receptor-like kinase EMS1 and BRI1 coordinately regulate stamen elongation via the transcription factors BES1/BZR1 in Arabidopsis.
College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.; College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China. Electronic address: zhengbowen365@163.com.
Plants possess a large family of receptor kinase proteins to mediate cell-to-cell and cell-to-environment communication, and these regulations are essential for plant growth and development as well as resistance to biotic or abiotic stresses. EMS1 is a receptor kinase which involved in tapetum cell fate determination during anther development, while brassinosteroid (BR) receptor, BRI1, controls most aspects of plant growth and development. Although EMS1 and BRI1 are known to regulate independent biological processes, they interact with identical components of the downstream signaling pathways. However, the biological processes other than the tapetum development controlled by the EMS1 signal are not clear. Here, we report that EMS1 signaling-related mutants exhibited an insufficient stamen elongation phenotype, similar to BR signaling mutants. Transgenic expression of BRI1 restored the short filament phenotype of ems1. Conversely, co-expression of EMS1 and TPD1 also restored the short filaments of BRI1 mutants, bri1. Genetic experiments confirmed that EMS1 and BRI1 regulate filament elongation through their downstream transcription factors BES1/BZR1. Molecular analysis suggested that the decrease in BR signaling output in filaments of the ems1 mutant caused deficient filament development. Moreover, in vitro and in vivo experiments proved BES1 interacts with filament-specific transcription factor MYB21. Together, we found that the two receptor-like kinases (RLKs) EMS1 and BRI1 are cooperatively involved in the regulation of filament elongation via the transcription factors BES1/BZR1. These results indicated that the biological processes regulated by EMS1 and BRI1 in plants are both independent and interactive, which provides us with insights into multidimensional molecular control of the RLK pathway.
PMID: 36931564
Plant Cell Rep , IF:4.57 , 2023 Apr doi: 10.1007/s00299-023-03016-7
The putative myristoylome of Physcomitrium patens reveals conserved features of myristoylation in basal land plants.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Wuhou District, Chengdu, Sichuan, 610064, People's Republic of China.; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Wuhou District, Chengdu, Sichuan, 610064, People's Republic of China. yipeishan@scu.edu.cn.
The putative myristoylome of moss P. patens opens an avenue for studying myristoylation substrates in non-canonical model plants. A myristoylation signal was shown sufficient for membrane targeting and useful for membrane dynamics visualization during cell growth. N-myristoylation (MYR) is one form of lipid modification catalyzed by N-myristoyltransferase that enables protein-membrane association. MYR is highly conserved in all eukaryotes. However, the study of MYR is limited to a few models such as yeasts, humans, and Arabidopsis. Here, using prediction tools, we report the characterization of the putative myristoylome of the moss Physcomitrium patens. We show that basal land plants display a similar signature of MYR to Arabidopsis and may have organism-specific substrates. Phylogenetically, MYR signals have mostly co-evolved with protein function but also exhibit variability in an organism-specific manner. We also demonstrate that the MYR motif of a moss brassinosteroid-signaling kinase is an efficient plasma membrane targeting signal and labels lipid-rich domains in tip-growing cells. Our results provide insights into the myristoylome in a basal land plant and lay the foundation for future studies on MYR and its roles in plant evolution.
PMID: 37052714
Plant Cell Rep , IF:4.57 , 2023 Apr doi: 10.1007/s00299-023-03001-0
Comparative transcriptome analysis reveals the function of SlPRE2 in multiple phytohormones biosynthesis, signal transduction and stomatal development in tomato.
Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang, 332000, Jiangxi, China. zhuzhiguo@jju.edu.cn.; College of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, 332000, Jiangxi, China. zhuzhiguo@jju.edu.cn.; Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang, 332000, Jiangxi, China.; College of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, 332000, Jiangxi, China.; College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, Guizhou, China.
Transcriptomic, physiological, and qRT-PCR analysis revealed the potential mechanism by which SlPRE2 regulates plant growth and stomatal size via multiple phytohormone pathways in tomato. Paclobutrazol resistance proteins (PREs) are atypical members of the basic/helix-loop-helix (bHLH) transcription factor family that regulate plant morphology, cell size, pigment metabolism and abiotic stress in response to different phytohormones. However, little is known about the network regulatory mechanisms of PREs in plant growth and development in tomato. In this study, the function and mechanism of SlPRE2 in tomato plant growth and development were investigated. The quantitative RT-PCR results showed that the expression of SlPRE2 was regulated by multiple phytohormones and abiotic stresses. It showed light-repressed expression during the photoperiod. The RNA-seq results revealed that SlPRE2 regulated many genes involved in photosynthesis, chlorophyll metabolism, phytohormone metabolism and signaling, and carbohydrate metabolism, suggesting the role of SlPRE2 in gibberellin, brassinosteroid, auxin, cytokinin, abscisic acid and salicylic acid regulated plant development processes. Moreover, SlPRE2 overexpression plants showed widely opened stomata in young leaves, and four genes involved in stomatal development showed altered expression. Overall, the results demonstrated the mechanism by which SlPRE2 regulates phytohormone and stress responses and revealed the function of SlPRE2 in stomatal development in tomato. These findings provide useful clues for understanding the molecular mechanisms of SlPRE2-regulated plant growth and development in tomato.
PMID: 37010556
Plant Cell Rep , IF:4.57 , 2023 Mar , V42 (3) : P587-598 doi: 10.1007/s00299-023-02981-3
Propiconazole-induced brassinosteroid deficiency reduces female fertility by inhibiting female gametophyte development in woodland strawberry.
Yokohama City University, Kihara Institute for Biological Research, Maioka 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan.; Advanced Instrumental Analysis Center, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 321-8505, Japan.; Faculty of Agriculture, Utsunomiya University, 350 Mine, Utsunomiya, Tochigi, 321-8505, Japan.; Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan.; Yokohama City University, Kihara Institute for Biological Research, Maioka 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan. aynakamu@yokohama-cu.ac.jp.
In woodland strawberry, a brassinosteroid biosynthesis inhibitor propiconazole induced typical brassinosteroid-deficient phenotypes and decreased female fertility due to attenuated female gametophyte development. Brassinosteroids (BRs) play roles in various aspects of plant development. We investigated the physiological roles of BRs in the woodland strawberry, Fragaria vesca. BR-level-dependent phenotypes were observed using a BR biosynthetic inhibitor, propiconazole (PCZ), and the most active natural BR, brassinolide (BL). Endogenous BL and castasterone, the active BRs, were below detectable levels in PCZ-treated woodland strawberry. The plants were typical BR-deficient phenotypes, and all phenotypes were restored by treatment with BL. These observations indicate that PCZ is an effective inhibitor of BR in woodland strawberry. Only one gene for each major step of BR biosynthesis in Arabidopsis is encoded in the woodland strawberry genome. BR biosynthetic genes are highly expressed during the early stage of fruit development. Emasculated flowers treated with BL failed to develop fruit, implying that BR is not involved in parthenocarpic fruit development. Similar to BR-deficient and BR-insensitive Arabidopsis mutants, female fertility was lower in PCZ-treated plants than in mock-treated plants due to failed attraction of the pollen tube to the ovule. In PCZ-treated plants, expression of FveMYB98, the homologous gene for Arabidopsis MYB98 (a marker for synergid cells), was downregulated. Ovules were smaller in PCZ-treated plants than in mock-treated plants, and histological analysis implied that the development of more than half of female gametophytes was arrested at the early stage in PCZ-treated plants. Our findings explain how BRs function during female gametophyte development in woodland strawberry.
PMID: 36629883
Physiol Plant , IF:4.5 , 2023 Mar , V175 (2) : Pe13875 doi: 10.1111/ppl.13875
Transcriptome analysis of drought-responsive and drought-tolerant mechanisms in maize leaves under drought stress.
Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China.
Maize is a major crop essential for food and feed, but its production is threatened by various biotic and abiotic stresses. Drought is one of the most common abiotic stresses, causing severe crop yield reduction. Although several studies have been devoted to selecting drought-tolerant maize lines and detecting the drought-responsive mechanism of maize, the transcriptomic differences between drought-tolerant and drought-susceptible maize lines are still largely unknown. In our study, RNA-seq was performed on leaves of the drought-tolerant line W9706 and the drought-susceptible line B73 after drought treatment. We identified 3147 differentially expressed genes (DEGs) between these two lines. The upregulated DEGs in W9706 were enriched in specific processes, including ABA signaling, wax biosynthesis, CHO metabolism, signal transduction and brassinosteroid biosynthesis-related processes, while the downregulated DEGs were enriched in specific processes, such as stomatal movement. Altogether, transcriptomic analysis suggests that the different drought resistances were correlated with the differential expression of genes, while the drought tolerance of W9706 is due to the more rapid response to stimulus, higher water retention capacity and stable cellular environment under water deficit conditions.
PMID: 36775906
Plant Physiol Biochem , IF:4.27 , 2023 Apr , V198 : P107695 doi: 10.1016/j.plaphy.2023.107695
Integrating transcriptome and phytohormones analysis provided insights into plant height development in sesame.
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China. Electronic address: junyou@caas.cn.; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China. Electronic address: wanglinhai@caas.cn.
Plant height is a key agronomic trait influencing crops yield. The height of sesame plants is important for yield performance, lodging resistance and plant architecture. Although plant height is significantly distinct among sesame varieties, the genetic basis of plant height remains largely unknown. In this study, in order to tackle genetic insights into the sesame plant height development, a comprehensive transcriptome analysis was conducted using the stem tips from two sesame varieties with distinct plant height, Zhongzhi13 and ZZM2748, at five time points by BGI MGIseq2000 sequencing platform. A total of 16,952 genes were differentially expressed between Zhongzhi13 and ZZM2748 at five time points. KEGG and MapMan enrichment analyses and quantitative analysis of phytohormones indicated that hormones biosynthesis and signaling pathways were associated with sesame plant height development. Plenty of candidate genes involved in biosynthesis and signaling of brassinosteroid (BR), cytokinin (CK) and gibberellin (GA) which were major differential hormones between two varieties were identified, suggesting their critical roles in plant height regulation. WGCNA revealed a module which was significantly positively associated with the plant height trait and founded SiSCL9 was the hub gene involved in plant height development in our network. Further overexpression in transgenic Arabidopsis validated the function of SiSCL9 in the increase of plant height by 26.86%. Collectively, these results increase our understanding of the regulatory network controlling the development of plant height and provide a valuable genetic resource for improvement of plant architecture in sesame.
PMID: 37058966
Plant Physiol Biochem , IF:4.27 , 2023 Mar , V196 : P993-1001 doi: 10.1016/j.plaphy.2023.02.052
Grape cytochrome P450 CYP90D1 regulates brassinosteroid biosynthesis and increases vegetative growth.
Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, 1-13-1 Kofu, Yamanashi, 400-0005, Japan. Electronic address: senoki@yamanashi.ac.jp.; NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Setagaya, Tokyo, 156-8502, Japan.; Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, 1-13-1 Kofu, Yamanashi, 400-0005, Japan.
Vine vigor or vegetative growth is an important factor related to berry quality and vinicultural training management, but brassinosteroid (BR)-induced molecular mechanisms underlying vine growth remain unclear. In this study, the hypothesis that the Vitis vinifera CYP90D1 gene VvCYP90D1, one of the genes for BR biosynthesis, plays a critical role in shoot elongation was tested. RNA sequencing analysis of shoots collected from the vigorous cultivar Koshu (KO) and the reference cultivar Pinot Noir (PN) 7 days after bud break showed higher expression levels of various genes in the BR biosynthesis pathway in KO than in PN. The VvCYP90D1 expression level in KO was highest in meristems, followed by internodes and leaves. Cluster analysis of amino acid sequences including those in other plant species showed that the isolated gene belonged to the CYP90D1 group. The vegetative growth and the endogenous BR (brassinolide; BL) content were significantly higher in VvCYP90D1-overexpressing Arabidopsis than in wild type. VvCYP90D1-overexpressing Arabidopsis treated with brassinazole (Brz), a BR biosynthesis inhibitor, showed recovery of vegetative growth. These results indicate that VvCYP90D1 in grapevine has a vegetative growth promoting effect via BR biosynthesis. Our findings on the mechanism of BR-induced grape shoot growth will contribute to the development of new shoot control techniques for grapevine.
PMID: 36898216
Plant Physiol Biochem , IF:4.27 , 2023 Mar , V196 : P281-290 doi: 10.1016/j.plaphy.2023.01.056
Cadmium treatment induces endoplasmic reticulum stress and unfolded protein response in Arabidopsisthaliana.
Institute of Sciences of Food Production, C.N.R., Unit of Lecce, Lecce, Italy.; Laboratory of General and Inorganic Chemistry, Di.S.Te.B.A. (Dipartimento di Scienze e Technologie Biologic e Ambientali), University of Salento, Lecce, Italy.; Institute of Agricultural Biology and Biotechnology, C.N.R., Unit of Milan, Milano, Italy; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.; Institute of Sciences of Food Production, C.N.R., Unit of Lecce, Lecce, Italy. Electronic address: angelo.santino@ispa.cnr.it.
We report about the response of Arabidopsis thaliana to chronic and temporary Cd(2+) stress, and the Cd(2+) induced activation of ER stress and unfolded protein response (UPR). Cd(2+)-induced UPR proceeds mainly through the bZIP60 arm, which in turn activates relevant ER stress marker genes such as BiP3, CNX, PDI5 and ERdj3B in a concentration- (chronic stress) or time- (temporary stress) dependent manner. A more severe Cd-stress triggers programmed cell death (PCD) through the activation of the NAC089 transcription factor. Toxic effects of Cd(2+) exposure are reduced in the Atbzip28/bzip60 double mutant in terms of primary root length and fresh shoot weight, likely due to reduced UPR and PCD activation. We also hypothesised that the enhanced Cd(2+) tolerance of the Atbzip28/bzip60 double mutant is due to an increase in brassinosteroids signaling, since the amount of the brassinosteroid insensitive1 receptor (BRI1) protein decreases under Cd(2+) stress only in Wt plants. These data highlight the complexity of the UPR pathway, since the ER stress response is strictly related to the type of the treatment applied and the multifaceted connections of ER signaling. The reduced sensing of Cd(2+) stress in plants with UPR defects can be used as a novel strategy for phytoremediation.
PMID: 36736010
BMC Plant Biol , IF:4.215 , 2023 Apr , V23 (1) : P214 doi: 10.1186/s12870-023-04216-9
Genome-wide identification and expression analysis of BZR gene family and associated responses to abiotic stresses in cucumber (Cucumis sativus L.).
State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China.; College of Horticulture, Gansu Agricultural University, Lanzhou, China.; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China. yujihuagg@163.com.; College of Horticulture, Gansu Agricultural University, Lanzhou, China. yujihuagg@163.com.
BACKGROUND: BRASSINAZOLE-RESISTANT (BZR) is a class of specific transcription factor (TFs) involved in brassinosteroid (BR) signal transduction. The regulatory mechanism of target genes mediated by BZR has become one of the key research areas in plant BR signaling networks. However, the functions of the BZR gene family in cucumber have not been well characterized. RESULTS: In this study, six CsBZR gene family members were identified by analyzing the conserved domain of BES1 N in the cucumber genome. The size of CsBZR proteins ranges from 311 to 698 amino acids and are mostly located in the nucleus. Phylogenetic analysis divided CsBZR genes into three subgroups. The gene structure and conserved domain showed that the BZR genes domain in the same group was conserved. Cis-acting element analysis showed that cucumber BZR genes were mainly involved in hormone response, stress response and growth regulation. The qRT-PCR results also confirmed CsBZR response to hormones and abiotic stress. CONCLUSION: Collectively, the CsBZR gene is involved in regulating cucumber growth and development, particularly in hormone response and response to abiotic stress. These findings provide valuable information for understanding the structure and expression patterns of BZR genes.
PMID: 37095428
Tree Physiol , IF:4.196 , 2023 Feb doi: 10.1093/treephys/tpad022
Transcriptional reprogramming during recovery from drought stress in Eucalyptus grandis.
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.; Department of Agriculture, University of Zululand, KwaDlangezwa, South Africa.; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
The importance of drought as a constraint to agriculture and forestry is increasing with climate change. Genetic improvement of plants' resilience is one of the mitigation strategies to curb this threat. Although recovery from drought stress is important to long term drought adaptation and has been considered as an indicator of dehydration tolerance in annual crops, this has not been well-explored in forest trees. Thus, we aimed to investigate the physiological and transcriptional changes during drought stress and rewatering in Eucalyptus grandis. We set up a greenhouse experiment where we imposed drought stress on two-year-old seedlings and rewatered the recovery group after 17 days of drought. Our measurement of leaf stomatal conductance (gs) showed that, while gs was reduced by drought stress, it fully recovered after 5 days of rewatering. RNA-seq analysis from stem samples revealed that genes related to known stress responses such as phytohormone and reactive oxygen species signaling were upregulated while genes involved in metabolism and growth were downregulated due to drought stress. We observed reprogramming of signal transduction pathways and metabolic processes at 1 day of rewatering, indicating a quick response to rewatering. Our results suggest that recovery from drought stress may entail alterations in the jasmonic acid, salicylic acid, ethylene, and brassinosteroid signaling pathways. Using co-expression network analysis, we identified hub genes including the putative orthologs of ABI1, ABF2, ABF3, HAI2, BAM1, GolS2, and SIP1 during drought and CAT2, G6PD1, ADG1, and FD-1 during recovery. Taken together, by highlighting the molecular processes and identifying key genes, this study gives an overview of the mechanisms underlying the response of E. grandis to drought stress and recovery that trees may face repeatedly throughout their long-life cycle. This provides a useful reference to the identification and further investigation of signaling pathways and target genes for future tree improvement.
PMID: 36851855
Genes (Basel) , IF:4.096 , 2023 Apr , V14 (4) doi: 10.3390/genes14040884
Integrative Transcriptomics Data Mining to Explore the Functions of TDP1alpha and TDP1beta Genes in the Arabidopsis thaliana Model Plant.
Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3'-phosphate of DNA in the DNA-topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small TDP1 gene subfamily is present in plants, where TDP1alpha has been linked to genome stability maintenance, while TDP1beta has unknown functions. This work aimed to comparatively investigate the function of the TDP1 genes by taking advantage of the rich transcriptomics databases available for the Arabidopsis thaliana model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, TDP1beta seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas TDP1alpha is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to Arabidopsis seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the TDP1 genes expression profiles.
PMID: 37107642
Plants (Basel) , IF:3.935 , 2023 Apr , V12 (7) doi: 10.3390/plants12071555
Transcriptional Profile of Soybean Seeds with Contrasting Seed Coat Color.
Biotechnology Department, Londrina State University, Londrina 86057-970, PR, Brazil.; Arthur Bernardes Foundation, Embrapa Soja, Londrina 86085-981, PR, Brazil.; Embrapa Soja, Londrina 86085-981, PR, Brazil.; Agronomy Department, State University of Maringa, Maringa 87020-900, PR, Brazil.
Soybean is the primary source of vegetable protein and is used for various purposes, mainly to feed animals. This crop can have diverse seed coat colors, varying from yellow, black, brown, and green to bicolor. Black seed coat cultivars have already been assigned as favorable for both seed and grain production. Thus, this work aimed to identify genes associated with soybean seed quality by comparing the transcriptomes of soybean seeds with contrasting seed coat colors. The results from RNA-seq analyses were validated with real-time PCR using the cultivar BRS 715A (black seed coat) and the cultivars BRS 413 RR and DM 6563 IPRO (yellow seed coat). We found 318 genes differentially expressed in all cultivars (freshly harvested seeds and seeds stored in cold chamber). From the in silico analysis of the transcriptomes, the following genes were selected and validated with RT-qPCR: ACS1, ACSF3, CYP90A1, CYP710A1, HCT, CBL, and SAHH. These genes are genes induced in the black seed coat cultivar and are part of pathways responsible for ethylene, lipid, brassinosteroid, lignin, and sulfur amino acid biosynthesis. The BRSMG 715A gene has almost 4times more lignin than the yellow seed coat cultivars. These attributes are related to the BRSMG 715A cultivar's higher seed quality, which translates to more longevity and resistance to moisture and mechanical damage. Future silencing studies may evaluate the knockout of these genes to better understand the biology of soybean seeds with black seed coat.
PMID: 37050181
Plants (Basel) , IF:3.935 , 2023 Mar , V12 (6) doi: 10.3390/plants12061290
Integrative Analysis of Transcriptome, Proteome, and Phosphoproteome Reveals Potential Roles of Photosynthesis Antenna Proteins in Response to Brassinosteroids Signaling in Maize.
Institute of Quality Standard and Testing Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 611130, China.; College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
Brassinosteroids are a recently discovered group of substances that promote plant growth and productivity. Photosynthesis, which is vital for plant growth and high productivity, is strongly influenced by brassinosteroid signaling. However, the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize remains obscure. Here, we performed integrated transcriptome, proteome, and phosphoproteomic analyses to identify the key photosynthesis pathway that responds to brassinosteroid signaling. Transcriptome analysis suggested that photosynthesis antenna proteins and carotenoid biosynthesis, plant hormone signal transduction, and MAPK signaling in CK VS EBR and CK VS Brz were significantly enriched in the list of differentially expressed genes upon brassinosteroids treatment. Consistently, proteome and phosphoproteomic analyses indicated that photosynthesis antenna and photosynthesis proteins were significantly enriched in the list of differentially expressed proteins. Thus, transcriptome, proteome, and phosphoproteome analyses showed that major genes and proteins related to photosynthesis antenna proteins were upregulated by brassinosteroids treatment in a dose-dependent manner. Meanwhile, 42 and 186 transcription factor (TF) responses to brassinosteroid signals in maize leaves were identified in the CK VS EBR and CK VS Brz groups, respectively. Our study provides valuable information for a better understanding of the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize.
PMID: 36986978
Chem Biodivers , IF:2.408 , 2023 Apr : Pe202201243 doi: 10.1002/cbdv.202201243
22-OXOCHOLESTANES SPGP4 AND SPGP8: IN SILICO AND IN VITRO STUDY AS ACTIVATORS OF PLANT GROWTH PROMOTION.
BUAP: Benemerita Universidad Autonoma de Puebla, Laboratorio de Elucidacion y Sintesis en Quimica Organica, Avenida San Claudio S/N, 72530, Puebla, MEXICO.; CIBA: Centro de Ingenieria Genetica y Biotecnologia, Centro de Investigacion en Biotecnologia Aplicada-IPN, N/A, Tlaxcala, MEXICO.; BUAP: Benemerita Universidad Autonoma de Puebla, Facultad de Ciencias Quimicas, Avenida San Claudio S/N, 72530, Puebla, MEXICO.; Benemerita Universidad Autonoma de Puebla, Instituto de Ciencias, PRIV 37 ORIENTE 610 302, 72530, PUEBLA, MEXICO.; BUAP: Benemerita Universidad Autonoma de Puebla, Facultad de Ciencias Quimicas, Av San Claudio, 72530, PUEBLA, MEXICO.
The 22-oxocholestanes compounds have shown an outstanding plant growth promoting activity; they have similar bioactivity as brassinosteroids, so they are normally named as brassinosteroid analogues thinking that they also impact on the known receptor BRI1. However, in silico studies allow us to predict interactions with other receptors and thus it's possible to evaluate them, through receptors of gibberellins, auxins, jasmonates, strigolactones and the protein associated with the BRI1 gene. This paper describes the bioactivity of structures SPGP4 and SPGP8 as plant growth-promoting compounds. Both structures present coupling energies and interactions at the same level as epibrassinolide in the protein associated with BRI1 gene. Additionally, interactions through the auxin pathway and to strigolactone receptor were found using selected tests. In the rice lamina tilt, a higher effect was obtained when SPGP4 and SPGP8 were compared to epibrassinolide, although in a lesser level vis a vis to homobrassinolide. In the same way, when SPGP4 and SPGP8 were tested in the Growth Root Model an activity as strigonolactones was observed, enhancing the relationship between the main and secondary roots. However, the growth of coleptiles, when applying auxins, compounds SPGP4 and SPGP8 did not reach the same level as controls.
PMID: 37062704
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2186640 doi: 10.1080/15592324.2023.2186640
Exogenous Brassinosteroid Enhances Zinc tolerance by activating the Phenylpropanoid Biosynthesis pathway in Citrullus lanatus L.
College of Resources and Environmental Engineering, Yangzhou Polytechnic College, Yangzhou, China.; Jiangsu Safety & Environment Technology and Equipment for Planting and Breeding Industry Engineering Research Center, Yangzhou, China.
Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. The phytohormone brassinosteroids (BRs) play a key role in regulating plant growth, development, and response to stress. However, the role of BRs in watermelon (Citrullus lanatus L.) under Zn stress, one of the most important horticultural crops, remains largely unknown. In this study, we revealed that 24-epibrassinolide (EBR), a bioactive BR enhanced Zn tolerance in watermelon plants, which was related to the EBR-induced increase in the fresh weight, chlorophyll content, and net photosynthetic rate (Pn) and decrease in the content of hydrogen peroxide (H(2)O(2)), malondialdehyde (MDA), and Zn in watermelon leaves. Through RNA deep sequencing (RNA-seq), 350 different expressed genes (DEG) were found to be involved in the response to Zn stress after EBR treatment, including 175 up-regulated DEGs and 175 down-regulated DEGs. The up-regulated DEGs were significantly enriched in 'phenylpropanoid biosynthesis' pathway (map00940) using KEGG enrichment analysis. The gene expression levels of PAL, 4CL, CCR, and CCoAOMT, key genes involved in phenylpropanoid pathway, were significantly induced after EBR treatment. In addition, compared with Zn stress alone, EBR treatment significantly promoted the activities of PAL, 4CL, and POD by 30.90%, 20.69%, and 47.28%, respectively, and increased the content of total phenolic compounds, total flavonoids, and lignin by 23.02%, 40.37%, and 29.26%, respectively. The present research indicates that EBR plays an active role in strengthening Zn tolerance, thus providing new insights into the mechanism of BRs enhancing heavy metal tolerance.
PMID: 37083111
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2163337 doi: 10.1080/15592324.2022.2163337
Arabidopsis clathrin adaptor EPSIN1 but not MODIFIED TRANSPORT TO THE VACOULE1 contributes to effective plant immunity against pathogenic Pseudomonas bacteria.
University of Missouri-Columbia, Division of Biochemistry, Interdisciplinary Plant Group (IPG), Columbia, MO, USA.; Department of Plant Physiology, University of Potsdam, Potsdam, Germany.
In eukaryotes, EPSINs are Epsin N-terminal Homology (ENTH) domain-containing proteins that serve as monomeric clathrin adaptors at the plasma membrane (PM) or the trans-Golgi Network (TGN)/early endosomes (EE). The model plant Arabidopsis thaliana encodes for seven ENTH proteins, of which so far, only AtEPSIN1 (AtEPS1) and MODIFIED TRANSPORT TO THE VACUOLE1 (AtMTV1) localize to the TGN/EE and contribute to cargo trafficking to both the cell surface and the vacuole. However, relatively little is known about role(s) of any plant EPSIN in governing physiological responses. We have recently shown that AtEPS1 is a positive modulator of plant immune signaling and pattern-triggered immunity against flagellated Pseudomonas syringae pv. tomato (Pto) DC3000 bacteria. In eps1 mutants, impaired immune responses correlate with reduced accumulation of the receptor FLAGELLIN SENSING2 (AtFLS2) and the convergent immune co-receptor BRASSINOSTEROID INSENTIVE1-ASSOCIATED RECEPTOR KINASE1 (AtBAK1) in the PM. Here, we report that in contrast to AtEPS1, the TGN/EE-localized AtMTV1 did not contribute significantly to immunity against pathogenic Pto DC3000 bacteria. We also compared the amino acid sequences, peptide motif structures and in silico tertiary structures of the ENTH domains of AtEPS1 and AtMTV1 in more detail. We conclude that despite sharing the classical tertiary alpha helical ENTH-domain structure and clathrin-binding motifs, the overall low amino acid identity and differences in peptide motifs may explain their role(s) in trafficking of some of the same as well as distinct cargo components to their site of function, with the latter potentially contributing to differences in physiological responses.
PMID: 36603596
Plant Commun , 2023 Apr : P100604 doi: 10.1016/j.xplc.2023.100604
The miR167-OsARF12 module regulates grain filling and grain size downstream of miR159.
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China; Henan Engineering Laboratory of Rice, Henan Agricultural University, Zhengzhou 450002, China.; Joint Center for Single Cell Biology/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; Department of Biotechnology, Sharda University, Greater Noida, 201306, India.; Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China.; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA.; Joint Center for Single Cell Biology/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address: lypengting@163.com.; Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China; Henan Engineering Laboratory of Rice, Henan Agricultural University, Zhengzhou 450002, China; College of Agriculture, Guizhou University, 550025, China. Electronic address: lypengting@163.com.; Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China; Henan Engineering Laboratory of Rice, Henan Agricultural University, Zhengzhou 450002, China. Electronic address: lypengting@163.com.
Grain weight and quality are always determined by the grain filling. Plant miRNAs have drawn attention as key targets for regulating grain size and yield. Yet the mechanisms underlying the regulation of grain size are largely unclear due to the complex networks controlling this trait. Our earlier studies proved that the suppressed expression of miR167 (STTM/MIM167) substantially increased grain weight. In a field test, the increased yield up to 12.90%-21.94% due to the significantly enhanced grain filling rate. Biochemical and genetic analyses reveal the regulatory effects of miR159 on miR167 expression. Further analysis indicates that OsARF12 is the major mediator of miR167 in regulating rice grain filling. Expectedly, over expressing OsARF12 could resemble the phenotype of STTM/MIM167 plants with respect to grain weight and grain filling rate. Upon in-depth analysis, we found that OsARF12 activates OsCDKF;2 expressions by directly binding to the TGTCGG motif in the promoter region. Flow cytometric analysis in young panicles of plants overexpressing OsARF12 and cell number examination of cdkf;2 mutants verify that OsARF12 positively regulates grain filling and grain size by targeting OsCDKF;2. Moreover, RNA-seq result suggests that miR167-OsARF12 module is involved in the cell development process and hormone pathways. Additionally, plants overexpressing OsARF12 or cdkf;2 mutants present enhanced or reduced sensitivity to exogenous auxin and brassinosteroid (BR) treatments, confirming that OsCDKF;2 targeting by OsARF12 mediates auxin and BR signaling. Our results reveal that miR167-OsARF12 module works downstream of miR159 to regulate rice grain filling and grain size by OsCDKF;2 through controlling cell division and mediating auxin and BR signals.
PMID: 37085993
Zhongguo Zhong Yao Za Zhi , 2023 Mar , V48 (6) : P1483-1490 doi: 10.19540/j.cnki.cjcmm.20221210.104
[Physiological and biochemical mechanisms of brassinosteroid in improving anti-cadmium stress ability of Panax notoginseng].
Faculty of Life Science and Technology,Kunming University of Science and Technology Kunming 650500,China Yunnan Provincial Panax notoginseng Key Laboratory Kunming 650500,China.; National Resource Center for Chinese Materia Medica,China Academy of Chinese Medical Sciences Beijing 100700,China.
In this study, the effect of brassinosteroid(BR) on the physiological and biochemical conditions of 2-year-old Panax notoginseng under the cadmium stress was investigated by the pot experiments. The results showed that cadmium treatment at 10 mg.kg~(-1) inhibited the root viability of P. notoginseng, significantly increased the content of H_2O_2 and MDA in the leaves and roots of P. noto-ginseng, caused oxidative damage of P. notoginseng, and reduced the activities of SOD and CAT. Cadmium stress reduced the chlorophyll content of P. notoginseng, increased leaf F_o, reduced F_m, F_v/F_m, and PIABS, and damaged the photosynthesis system of P. notoginseng. Cadmium treatment increased the soluble sugar content of P. notoginseng leaves and roots, inhibited the synthesis of soluble proteins, reduced the fresh weight and dry weight, and inhibited the growth of P. notoginseng. External spray application of 0.1 mg.L~(-1) BR reduced the H_2O_2 and MDA content in P. notoginseng leaves and roots under the cadmium stress, alleviated cadmium-induced oxidative damage to P. notoginseng, improved the antioxidant enzyme activity and root activity of P. notoginseng, increased the content of chlorophyll, reduced the F_o of P. notoginseng leaves, increased F_m, F_v/F_m, and PIABS, alleviated the cadmium-induced damage to the photosynthesis system, and improved the synthesis ability of soluble proteins. In summary, BR can enhance the anti-cadmium stress ability of P. notoginseng by regulating the antioxidant enzyme system and photosynthesis system of P. notoginseng under the cadmium stress. In the context of 0.1 mg.L~(-1) BR, P. notoginseng can better absorb and utilize light energy and synthesize more nutrients, which is more suitable for the growth and development of P. notoginseng.
PMID: 37005835
J Genet Genomics , 2023 Mar doi: 10.1016/j.jgg.2023.03.004
Brassinosteroid signaling and molecular crosstalk with nutrients in plants.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.; The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China. Electronic address: baimingyi@sdu.edu.cn.
As sessile organisms, plants have evolved sophisticated mechanisms to optimize their growth and development in response to fluctuating nutrient levels. Brassinosteroids (BRs) are a group of plant steroid hormones that play critical roles in plant growth and developmental processes as well as plant responses to environmental stimuli. Recently, multiple molecular mechanisms have been proposed to explain the integration of BRs with different nutrient signaling processes to coordinate gene expression, metabolism, growth, and survival. Here, we review recent advances in understanding the molecular regulatory mechanisms of the BR signaling pathway and the multifaceted roles of BR in the intertwined sensing, signaling, and metabolic processes of sugar, nitrogen, phosphorus, and iron. Further understanding and exploring these BR-related processes and mechanisms will facilitate advances in crop breeding for higher resource efficiency.
PMID: 36914050
Plant Commun , 2023 Mar , V4 (2) : P100450 doi: 10.1016/j.xplc.2022.100450
The U-box ubiquitin ligase TUD1 promotes brassinosteroid-induced GSK2 degradation in rice.
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China. Electronic address: tonghongning@caas.cn.
Brassinosteroids (BRs) are a class of steroid hormones with great potential for use in crop improvement. De-repression is usually one of the key events in hormone signaling. However, how the stability of GSK2, the central negative regulator of BR signaling in rice (Oryza sativa), is regulated by BRs remains elusive. Here, we identify the U-box ubiquitin ligase TUD1 as a GSK2-interacting protein by yeast two-hybrid screening. We show that TUD1 is able to directly interact with GSK2 and ubiquitinate the protein. Phenotypes of the tud1 mutant are highly similar to those of plants with constitutively activated GSK2. Consistent with this finding, GSK2 protein accumulates in the tud1 mutant compared with the wild type. In addition, inhibition of BR synthesis promotes GSK2 accumulation and suppresses TUD1 stability. By contrast, BRs can induce GSK2 degradation but promote TUD1 accumulation. Furthermore, the GSK2 degradation process is largely impaired in tud1 in response to BR. In conclusion, our study demonstrates the role of TUD1 in BR-induced GSK2 degradation, thereby advancing our understanding of a critical step in the BR signaling pathway of rice.
PMID: 36127877