1
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Fontanet-Manzaneque JB, Laibach N, Herrero-García I, Coleto-Alcudia V, Blasco-Escámez D, Zhang C, Orduña L, Alseekh S, Miller S, Bjarnholt N, Fernie AR, Matus JT, Caño-Delgado AI. Untargeted mutagenesis of brassinosteroid receptor SbBRI1 confers drought tolerance by altering phenylpropanoid metabolism in Sorghum bicolor. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39325724 DOI: 10.1111/pbi.14461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/07/2024] [Accepted: 08/22/2024] [Indexed: 09/28/2024]
Abstract
Drought is a critical issue in modern agriculture; therefore, there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signalling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID-INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. Introducing untargeted mutation in the sorghum BRI1 receptor (SbBRI1) effectively enhances the plant's ability to withstand osmotic and drought stress. Through DNA Affinity Purification sequencing (DAP-seq), we show that the sorghum BRI1-EMS-SUPPRESSOR 1 (SbBES1) transcription factor, a downstream player of the BR signalling, binds to a conserved G-box binding motif, and it is responsible for regulating BR homeostasis, as its Arabidopsis ortholog AtBES1. We further characterized the drought tolerance of sorghum bri1 mutants and decipher SbBES1-mediated regulation of phenylpropanoid pathway. Our findings suggest that SbBRI1 signalling serves a dual purpose: under normal conditions, it regulates lignin biosynthesis by SbBES1, but during drought conditions, BES1 becomes less active, allowing the activation of the flavonoid pathway. This adaptive shift improves the photosynthetic rate and photoprotection, reinforcing crop adaptation to drought.
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Affiliation(s)
- Juan B Fontanet-Manzaneque
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Natalie Laibach
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Iván Herrero-García
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Veredas Coleto-Alcudia
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - David Blasco-Escámez
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Sara Miller
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Nanna Bjarnholt
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
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2
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Nuñez M, Wang Y, Russinova E, Estévez-Braun A, Amesty A, Olea AF, Mellado M, Díaz K, Espinoza Catalán L. Synthesis, Biological Activity, and Molecular-Docking Studies of New Brassinosteroid Analogs. Int J Mol Sci 2024; 25:10158. [PMID: 39337642 PMCID: PMC11432311 DOI: 10.3390/ijms251810158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/29/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
Much work has been dedicated to the quest to determine the structure-activity relationship in synthetic brassinosteroid (BR) analogs. Recently, it has been reported that analogs with phenyl or benzoate groups in the alkyl chain present activities comparable to those shown by natural BRs, depending on the nature of the substituent in the aromatic ring. However, as it is well known that the activity depends on the structure of the whole molecule, in this work, we have synthesized a series of compounds with the same substituted benzoate in the alkyl chain and a hydroxyl group at C3. The main goal was to compare the activities with analogs with -OH at C2 and C3. Additionally, a molecular-docking study and molecular dynamics simulations were performed to establish a correlation between the experimental and theoretical results. The synthesis of eight new BR analogs was described. All the analogs were fully characterized by spectroscopical methods. The bioactivity of these analogs was assessed using the rice lamina inclination test (RLIT) and the inhibition of the root and hypocotyl elongation of Arabidopsis thaliana. The results of the RLIT indicate that at the lowest tested concentration (1 × 10-8 M), in the BR analogs in which the aromatic ring was substituted at the para position with methoxy, the I and CN substituents were more active than brassinolide (50-72%) and 2-3 times more active than those analogs in which the substituent group was F, Cl or Br atoms. However, at the highest concentrations, brassinolide was the most active compound, and the structure-activity relationship changed. On the other hand, the results of the A. thaliana root sensitivity assay show that brassinolide and the analogs with I and CN as substituents on the benzoyl group were the most active compounds. These results are in line with those obtained via the RLIT. A comparison of these results with those obtained for similar analogs that had a hydroxyl group at C2 indicates the importance of considering the whole structure. The molecular-docking results indicate that all the analogs adopted a brassinolide-like orientation, while the stabilizing effect of the benzoate group on the interactions with the receptor complex provided energy binding values ranging between -10.17 and -13.17 kcal mol-1, where the analog with a nitrile group was the compound that achieved better contact with the amino acids present in the active site.
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Affiliation(s)
- María Nuñez
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile;
| | - Yaowei Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; (Y.W.); (E.R.)
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; (Y.W.); (E.R.)
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ana Estévez-Braun
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain; (A.E.-B.); (A.A.)
| | - Angel Amesty
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain; (A.E.-B.); (A.A.)
| | - Andrés F. Olea
- Grupo QBAB, Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, Santiago 8900000, Chile;
| | - Marco Mellado
- Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile;
| | - Katy Díaz
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile;
| | - Luis Espinoza Catalán
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile;
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3
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Zebosi B, Vollbrecht E, Best NB. Brassinosteroid biosynthesis and signaling: Conserved and diversified functions of core genes across multiple plant species. PLANT COMMUNICATIONS 2024; 5:100982. [PMID: 38816993 DOI: 10.1016/j.xplc.2024.100982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024]
Abstract
Brassinosteroids (BRs) are important regulators that control myriad aspects of plant growth and development, including biotic and abiotic stress responses, such that modulating BR homeostasis and signaling presents abundant opportunities for plant breeding and crop improvement. Enzymes and other proteins involved in the biosynthesis and signaling of BRs are well understood from molecular genetics and phenotypic analysis in Arabidopsis thaliana; however, knowledge of the molecular functions of these genes in other plant species, especially cereal crop plants, is minimal. In this manuscript, we comprehensively review functional studies of BR genes in Arabidopsis, maize, rice, Setaria, Brachypodium, and soybean to identify conserved and diversified functions across plant species and to highlight cases for which additional research is in order. We performed phylogenetic analysis of gene families involved in the biosynthesis and signaling of BRs and re-analyzed publicly available transcriptomic data. Gene trees coupled with expression data provide a valuable guide to supplement future research on BRs in these important crop species, enabling researchers to identify gene-editing targets for BR-related functional studies.
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Affiliation(s)
- Brian Zebosi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Erik Vollbrecht
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA.
| | - Norman B Best
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65201, USA.
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4
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Marathe S, Grotewold E, Otegui MS. Should I stay or should I go? Trafficking of plant extra-nuclear transcription factors. THE PLANT CELL 2024; 36:1524-1539. [PMID: 38163635 PMCID: PMC11062434 DOI: 10.1093/plcell/koad277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 01/03/2024]
Abstract
At the heart of all biological processes lies the control of nuclear gene expression, which is primarily achieved through the action of transcription factors (TFs) that generally contain a nuclear localization signal (NLS) to facilitate their transport into the nucleus. However, some TFs reside in the cytoplasm in a transcriptionally inactive state and only enter the nucleus in response to specific signals, which in plants include biotic or abiotic stresses. These extra-nuclear TFs can be found in the cytosol or associated with various membrane systems, including the endoplasmic reticulum and plasma membrane. They may be integral proteins with transmembrane domains or associate peripherally with the lipid bilayer via acylation or membrane-binding domains. Although over 30 plant TFs, most of them involved in stress responses, have been experimentally shown to reside outside the nucleus, computational predictions suggest that this number is much larger. Understanding how extra-nuclear TFs are trafficked into the nucleus is essential for reconstructing transcriptional regulatory networks that govern major cellular pathways in response to biotic and abiotic signals. Here, we provide a perspective on what is known on plant extranuclear-nuclear TF retention, nuclear trafficking, and the post-translational modifications that ultimately enable them to regulate gene expression upon entering the nucleus.
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Affiliation(s)
- Sarika Marathe
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
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5
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Kim SH, Lee SH, Park TK, Tian Y, Yu K, Lee BH, Bai MY, Cho SJ, Kim TW. Comparative analysis of BZR1/BES1 family transcription factors in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:747-765. [PMID: 37926922 DOI: 10.1111/tpj.16527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Brassinazole Resistant 1 (BZR1) and bri1 EMS Suppressor 1 (BES1) are key transcription factors that mediate brassinosteroid (BR)-responsive gene expression in Arabidopsis. The BZR1/BES1 family is composed of BZR1, BES1, and four BES1/BZR1 homologs (BEH1-BEH4). However, little is known about whether BEHs are regulated by BR signaling in the same way as BZR1 and BES1. We comparatively analyzed the functional characteristics of six BZR1/BES1 family members and their regulatory mechanisms in BR signaling using genetic and biochemical analyses. We also compared their subcellular localizations regulated by the phosphorylation status, interaction with GSK3-like kinases, and heterodimeric combination. We found that all BZR1/BES1 family members restored the phenotypic defects of bri1-5 by their overexpression. Unexpectedly, BEH2-overexpressing plants showed the most distinct phenotype with enhanced BR responses. RNA-Seq analysis indicated that overexpression of both BZR1 and BEH2 regulates BR-responsive gene expression, but BEH2 has a much greater proportion of BR-independent gene expression than BZR1. Unlike BZR1 and BES1, the BR-regulated subcellular translocation of the four BEHs was not tightly correlated with their phosphorylation status. Notably, BEH1 and BEH2 are predominantly localized in the nucleus, which induces the nuclear accumulation of other BZR1/BES1 family proteins through heterodimerization. Altogether, our comparative analyses suggest that BEH1 and BEH2 play an important role in the functional interaction between BZR1/BES1 family transcription factors.
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Affiliation(s)
- So-Hee Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Se-Hwa Lee
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Tae-Ki Park
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yanchen Tian
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Kyoungjae Yu
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Sung-Jin Cho
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Tae-Wuk Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea
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6
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Zhang Y, Yuan Y, Qu M, Kang C. Brassinosteroid catabolic enzyme CYP734A129 regulates the morphologies of leaves and floral organs in woodland strawberry. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111788. [PMID: 37421982 DOI: 10.1016/j.plantsci.2023.111788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/10/2023]
Abstract
Brassinosteroids (BRs) play critical roles in plant growth and development and regulate many important agronomic traits. However, the functions of BRs in strawberry are unclear. This study identified two mutants, named P6 and R87, in woodland strawberry (Fragaria vesca) from EMS mutagenesis populations that exhibit narrow leaves, petals and sepals. Mapping by sequencing and genetic studies revealed that the F. vesca CYP734A129, encoding a putative BR catabolic enzyme, is the causative gene for both P6 and R87. Overexpression of CYP734A129 in both F. vesca and Arabidopsis causes a severe dwarf phenotype, and the BRI1-EMS-SUPPRESSOR 1 (BES1) protein is less abundant in the CYP734A129-overexpressing Arabidopsis seedlings. This suggests that CYP734A129 is functionally conserved with CYP734A1, as a BR-inactivating enzyme. Transcriptome analysis of young leaves revealed that four BR biosynthetic genes were significantly downregulated in P6 (cyp734a129), and photosynthesis-related genes were highly enriched among the up-regulated genes in P6 compared to the wild type. This further supports that CYP734A129 inactivates BRs in F. vesca. Furthermore, we showed that mutations in CYP734A129 do not affect fruit shape and color during ripening in strawberry. Overall, our results suggest that F. vesca CYP734A129 is a BR catabolic enzyme, and provide insights into the roles of CYP734A129 in strawberry.
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Affiliation(s)
- Yunming Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yingxin Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Minghao Qu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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7
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An JP, Li HL, Liu ZY, Wang DR, You CX, Han Y. The E3 ubiquitin ligase SINA1 and the protein kinase BIN2 cooperatively regulate PHR1 in apple anthocyanin biosynthesis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2175-2193. [PMID: 37272713 DOI: 10.1111/jipb.13538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/02/2023] [Indexed: 06/06/2023]
Abstract
PHR1 (PHOSPHATE STARVATION RESPONSE1) plays key roles in the inorganic phosphate (Pi) starvation response and in Pi deficiency-induced anthocyanin biosynthesis in plants. However, the post-translational regulation of PHR1 is unclear, and the molecular basis of PHR1-mediated anthocyanin biosynthesis remains elusive. In this study, we determined that MdPHR1 was essential for Pi deficiency-induced anthocyanin accumulation in apple (Malus × domestica). MdPHR1 interacted with MdWRKY75, a positive regulator of anthocyanin biosynthesis, to enhance the MdWRKY75-activated transcription of MdMYB1, leading to anthocyanin accumulation. In addition, the E3 ubiquitin ligase SEVEN IN ABSENTIA1 (MdSINA1) negatively regulated MdPHR1-promoted anthocyanin biosynthesis via the ubiquitination-mediated degradation of MdPHR1. Moreover, the protein kinase apple BRASSINOSTEROID INSENSITIVE2 (MdBIN2) phosphorylated MdPHR1 and positively regulated MdPHR1-mediated anthocyanin accumulation by attenuating the MdSINA1-mediated ubiquitination degradation of MdPHR1. Taken together, these findings not only demonstrate the regulatory role of MdPHR1 in Pi starvation induced anthocyanin accumulation, but also provide an insight into the post-translational regulation of PHR1.
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Affiliation(s)
- Jian-Ping An
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Hong-Liang Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Zhi-Ying Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Da-Ru Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Chun-Xiang You
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
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8
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Grape BES1 transcription factor gene VvBES1-3 confers salt tolerance in transgenic Arabidopsis. Gene X 2023; 854:147059. [PMID: 36535462 DOI: 10.1016/j.gene.2022.147059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
BRI1-EMS-Suppressor 1 (BES1) regulates plant growth, development, and stress resistance, and plays a pivotal role in the brassinosteroid (BR) signal transduction pathway. In this study, a total of 12 BES1 genes were identified in the grape (Vitis vinifera) genome. Phylogenetic, structure, and motif sequence analyses of these genes provided insights into their evolutionary characteristics. Hormone-, stress-, and light-responsive and organ-specific cis-acting elements were identified in VvBES1 gene promoters. Microarray data analysis showed that VvBES1 family members exhibit diverse expression patterns in different organs. Quantitative real-time PCR (qRT-PCR) analysis showed that the expression levels of VvBES1 genes differed in response to BR, methyl jasmonate (MeJA), cold (4 °C), NaCl, and polyethylene glycol (PEG) treatments. The expression of VvBES1-3 was 29-fold higher under salt stress than control at 12 h. Moreover, VvBES1-3-overexpessing Arabidopsis thaliana plants showed lower malondialdehyde content, higher proline content, enhanced antioxidant enzyme (catalase, superoxide dismutase, peroxidase) activities, and higher salt-responsive gene expression levels than wild-type plants under salt stress, indicating that VvBES1-3 overexpression enhances salt stress tolerance in transgenic Arabidopsis. These results will contribute to further understanding the functions of BES1 transcription factors in the abiotic stress response.
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9
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Lv P, Wan J, Zhang C, Hina A, Al Amin GM, Begum N, Zhao T. Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective. Int J Mol Sci 2023; 24:ijms24044187. [PMID: 36835600 PMCID: PMC9966272 DOI: 10.3390/ijms24044187] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies.
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Affiliation(s)
- Peiyun Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Wan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - G M Al Amin
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
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10
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Niu K, Zhu R, Wang Y, Zhao C, Ma H. 24-epibrassinolide improves cadmium tolerance and lateral root growth associated with regulating endogenous auxin and ethylene in Kentucky bluegrass. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114460. [PMID: 38321679 DOI: 10.1016/j.ecoenv.2022.114460] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 02/08/2024]
Abstract
The application of phytohormones is a viable technique to increase the efficiency of phytoremediation in heavy metal-contaminated soils. The objective of this study was to determine how the application of 24-epibrassinolide (EBR), a brassinosteroid analog, could regulate root growth and tolerance to cadmium (Cd) stress in Kentucky bluegrass. As a result, the number of lateral root primordia and total root length in the Cd-treated seedlings decreased by 33.1 % and 56.5 %, respectively. After the application of EBR, Cd accumulation in roots and leaves, and the negative effect of Cd on root growth were reduced under Cd stress. Additionally, the expression of the brassinosteroid signaling gene PpBRI1 was significantly upregulated by exogenous EBR. Moreover, exogenous EBR upregulated the expression of genes encoding antioxidant enzymes and improved the activity of antioxidant enzymes, thereby reduced oxidative stress in roots. Finally, targeted hormonomics analysis highlighted the utility of the application of EBR to alleviate the effect of Cd on the reduction in auxin (IAA) content and the increase in ethylene (ACC) content. These were known to be associated with the upregulation in the expression of auxin biosynthesis gene PpYUCCA1 and downregulation in the expression of ethylene biosynthesis gene PpACO1 in the roots treated with Cd stress. Overall, the application of EBR alleviated Cd-induced oxidative stress in addition to improving root elongation and lateral root growth crosstalk with auxin and ethylene in Kentucky bluegrass subjected to Cd stress. This study further highlights the potential role of brassinosteroids in improving the efficiency of phytoremediation for Cd-contaminated soils.
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Affiliation(s)
- Kuiju Niu
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China.
| | - Ruiting Zhu
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Yong Wang
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunxu Zhao
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Huiling Ma
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China
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11
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Montes C, Wang P, Liao C, Nolan TM, Song G, Clark NM, Elmore JM, Guo H, Bassham DC, Yin Y, Walley JW. Integration of multi-omics data reveals interplay between brassinosteroid and Target of Rapamycin Complex signaling in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:893-910. [PMID: 35892179 PMCID: PMC9804314 DOI: 10.1111/nph.18404] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/16/2022] [Indexed: 06/01/2023]
Abstract
Brassinosteroids (BRs) and Target of Rapamycin Complex (TORC) are two major actors coordinating plant growth and stress responses. Brassinosteroids function through a signaling pathway to extensively regulate gene expression and TORC is known to regulate translation and autophagy. Recent studies have revealed connections between these two pathways, but a system-wide view of their interplay is still missing. We quantified the level of 23 975 transcripts, 11 183 proteins, and 27 887 phosphorylation sites in wild-type Arabidopsis thaliana and in mutants with altered levels of either BRASSINOSTEROID INSENSITIVE 2 (BIN2) or REGULATORY ASSOCIATED PROTEIN OF TOR 1B (RAPTOR1B), two key players in BR and TORC signaling, respectively. We found that perturbation of BIN2 or RAPTOR1B levels affects a common set of gene-products involved in growth and stress responses. Furthermore, we used the multi-omic data to reconstruct an integrated signaling network. We screened 41 candidate genes identified from the reconstructed network and found that loss of function mutants of many of these proteins led to an altered BR response and/or modulated autophagy activity. Altogether, these results establish a predictive network that defines different layers of molecular interactions between BR- or TORC-regulated growth and autophagy.
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Affiliation(s)
- Christian Montes
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Ping Wang
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Ching‐Yi Liao
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Trevor M. Nolan
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
- Department of BiologyDuke UniversityDurhamNC27708USA
| | - Gaoyuan Song
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Natalie M. Clark
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - J. Mitch Elmore
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
- USDA‐ARS Cereal Disease LaboratoryUniversity of MinnesotaSt PaulMN55108USA
| | - Hongqing Guo
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Diane C. Bassham
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
- Plant Sciences InstituteIowa State UniversityAmesIA50011USA
| | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
- Plant Sciences InstituteIowa State UniversityAmesIA50011USA
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12
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Chen E, Yang X, Liu R, Zhang M, Zhang M, Zhou F, Li D, Hu H, Li C. GhBEE3-Like gene regulated by brassinosteroids is involved in cotton drought tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1019146. [PMID: 36311136 PMCID: PMC9606830 DOI: 10.3389/fpls.2022.1019146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Brassinosteroids (BRs) are important phytohormones that play a vital role in plant drought tolerance, but their mechanisms in cotton (Gossypium hirsutum L.) are poorly understood. Numerous basic helix-loop-helix (bHLH) family genes are involved in the responses to both BRs and drought stress. GhBEE3-Like, a bHLH transcription factor, is repressed by both 24-epi-BL (an active BR substance) and PEG8000 (drought simulation) treatments in cotton. Moreover, GhBZR1, a crucial transcription factor in BR signaling pathway, directly binds to the E-box element in GhBEE3-Like promoter region and inhibits its expression, which has been confirmed by electrophoretic mobility shift assay (EMSA) and dual luciferase reporter assay. Functional analysis revealed that Arabidopsis with GhBEE3-Like overexpression had drought sensitive phenotype, while GhBEE3-Like knock-down cotton plants obtained by virus-induced gene silencing (VIGS) technology were more tolerant to drought stress. Furthermore, the expression levels of three stress-related genes, GhERD10, GhCDPK1 and GhRD26, were significantly higher in GhBEE3-Like knock-down cotton than in control cotton after drought treatment. These results suggest that GhBEE3-Like is inhibited by BRs which elevates the expressions of stress-related genes to enhance plant drought tolerance. This study lays the foundation for understanding the mechanisms of BR-regulated drought tolerance and establishment of drought-resistant cotton lines.
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Affiliation(s)
- Eryong Chen
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaobei Yang
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Ruie Liu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mengke Zhang
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Meng Zhang
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Feng Zhou
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Dongxiao Li
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Haiyan Hu
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Chengwei Li
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
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13
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Yang Y, Wang B, Wang J, He C, Zhang D, Li P, Zhang J, Li Z. Transcription factors ZmNF-YA1 and ZmNF-YB16 regulate plant growth and drought tolerance in maize. PLANT PHYSIOLOGY 2022; 190:1506-1525. [PMID: 35861438 PMCID: PMC9516732 DOI: 10.1093/plphys/kiac340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/25/2022] [Indexed: 05/26/2023]
Abstract
The identification of drought stress regulatory genes is crucial for the genetic improvement of maize (Zea mays L.) yield. Nuclear factors Y (NF-Ys) are important transcription factors, but their roles in the drought stress tolerance of plants and underlying molecular mechanisms are largely unknown. In this work, we used yeast two-hybrid screening to identify potential interactors of ZmNF-YB16 and confirmed the interaction between ZmNF-YA1 and ZmNF-YB16-YC17 and between ZmNF-YA7 and ZmNF-YB16-YC17. ZmNF-YB16 interacted with ZmNF-YC17 via its histone fold domain to form a heterodimer in the cytoplasm and then entered the nucleus to form a heterotrimer with ZmNF-YA1 or ZmNF-YA7 under osmotic stress. Overexpression of ZmNF-YA1 improved drought and salt stress tolerance and root development of maize, whereas zmnf-ya1 mutants exhibited drought and salt stress sensitivity. ZmNF-YA1-mediated transcriptional regulation, especially in JA signaling, histone modification, and chromatin remodeling, could underlie the altered stress tolerance of zmnf-ya1 mutant plants. ZmNF-YA1 bound to promoter CCAAT motifs and directly regulated the expression of multiple genes that play important roles in stress responses and plant development. Comparison of ZmNF-YB16- and ZmNF-YA1-regulated genes showed that ZmNF-YA1 and ZmNF-YB16 have similar biological functions in stress responses but varied functions in other biological processes. Taken together, ZmNF-YA1 is a positive regulator of plant drought and salt stress responses and is involved in the root development of maize, and ZmNF-Y complexes with different subunits may have discrepant functions.
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Affiliation(s)
| | | | | | - Chunmei He
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peng Li
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Juren Zhang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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14
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Li Y, Zhang H, Zhang Y, Liu Y, Li Y, Tian H, Guo S, Sun M, Qin Z, Dai S. Genome-wide identification and expression analysis reveals spinach brassinosteroid-signaling kinase (BSK) gene family functions in temperature stress response. BMC Genomics 2022; 23:453. [PMID: 35725364 PMCID: PMC9208177 DOI: 10.1186/s12864-022-08684-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/10/2022] [Indexed: 11/14/2022] Open
Abstract
Background Brassinosteroid (BR)- signaling kinase (BSK) is a critical family of receptor-like cytoplasmic kinase for BR signal transduction, which plays important roles in plant development, immunity, and abiotic stress responses. Spinach (Spinacia oleracea) is cold- tolerant but heat- sensitive green leafy vegetable. A study on BSK family members and BSKs- mediated metabolic processes in spinach has not been performed. Results We identified and cloned seven SoBSKs in spinach. Phylogenetic and collinearity analyses suggested that SoBSKs had close relationship with dicotyledonous sugar beet (Beta vulgaris) rather than monocotyledons. The analyses of gene structure and conserved protein domain/ motif indicated that most SoBSKs were relative conserved, while SoBSK6 could be a truncated member. The prediction of post-translation modification (PTM) sites in SoBSKs implied their possible roles in signal transduction, redox regulation, and protein turnover of SoBSKs, especially the N-terminal myristoylation site was critical for BSK localization to cell periphery. Cis-acting elements for their responses to light, drought, temperature (heat and cold), and hormone distributed widely in the promoters of SoBSKs, implying the pivotal roles of SoBSKs in response to diverse abiotic stresses and phytohormone stimuli. Most SoBSKs were highly expressed in leaves, except for SoBSK7 in roots. Many SoBSKs were differentially regulated in spinach heat- sensitive variety Sp73 and heat- tolerant variety Sp75 under the treatments of heat, cold, as well as exogenous brassinolide (BL) and abscisic acid (ABA). The bsk134678 mutant Arabidopsis seedlings exhibited more heat tolerance than wild- type and SoBSK1- overexpressed seedlings. Conclusions A comprehensive genome- wide analysis of the BSK gene family in spinach presented a global identification and functional prediction of SoBSKs. Seven SoBSKs had relatively- conserved gene structure and protein function domains. Except for SoBSK6, all the other SoBSKs had similar motifs and conserved PTM sites. Most SoBSKs participated in the responses to heat, cold, BR, and ABA. These findings paved the way for further functional analysis on BSK- mediated regulatory mechanisms in spinach development and stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08684-5.
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Affiliation(s)
- Yang Li
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Heng Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Yongxue Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yanshuang Liu
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Yueyue Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Haodong Tian
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Meihong Sun
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhi Qin
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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15
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Guo B, Yang H, Dai L, Zhao X, Wang LF. Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree ( Hevea brasiliensis Muell. Arg.). PeerJ 2022; 10:e13189. [PMID: 35586131 PMCID: PMC9109691 DOI: 10.7717/peerj.13189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/08/2022] [Indexed: 01/12/2023] Open
Abstract
Brassinolide (BR) plays an important role in plant growth, development, and the adaptation adversity process. Moreover, BRI1-EMS-SUPPRESSOR 1 (BES1) genes are crucial transcription factors (TFs) in the BR signaling pathway. To realize the function of HbBES1 family is helpful to improve genetic resources for rubber tree breeding. Based on the rubber tree database, we used bioinformatics to characterize physicochemical properties, gene structure, cis-elements, and expression patterns. These results indicated that there were nine BES1 members in rubber tree, which we named HbBES1-1 to HbBES1-9 and divided into two groups (I and II) based on their genetic relationships. HbBES1 genes in the same group shared similar gene structures and motifs. Cis-acting element analysis showed that the promoter sequences of HbBES1 genes contained many regulator elements that were related to hormone and stress, indicating that HbBES1 genes might be involved in the regulation of hormone and stress signal pathways. Our analysis of tissue specificity revealed that all of the nine HbBES1 members expressed highly in branches. Gene expression profiles under different hormone treatments showed that the HbBES1 gene family was induced to varying degrees under different hormones, HbBES1-3 and HbBES1-9 were extremely induced by ethylene (ETH). These results lay the foundation for further exploration of the molecular mechanism of the BES1 gene family, especially HbBES1-3 and HbBES1-9, regulating plant stress tolerance in rubber tree.
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Affiliation(s)
- Bingbing Guo
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Hong Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Longjun Dai
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Xizhu Zhao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Li-feng Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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16
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Guo X, Ding X, Dong J. Dichotomy of the BSL phosphatase signaling spatially regulates MAPK components in stomatal fate determination. Nat Commun 2022; 13:2438. [PMID: 35508457 PMCID: PMC9068801 DOI: 10.1038/s41467-022-30254-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/21/2022] [Indexed: 11/29/2022] Open
Abstract
MAPK signaling modules play crucial roles in regulating numerous biological processes in all eukaryotic cells. How MAPK signaling specificity and strength are tightly controlled remains a major challenging question. In Arabidopsis stomatal development, the MAPKK Kinase YODA (YDA) functions at the cell periphery to inhibit stomatal production by activating MAPK 3 and 6 (MPK3/6) that directly phosphorylate stomatal fate-determining transcription factors for degradation in the nucleus. Recently, we demonstrated that BSL1, one of the four BSL protein phosphatases, localizes to the cell cortex to activate YDA, elevating MPK3/6 activity to suppress stomatal formation. Here, we showed that at the plasma membrane, all four members of BSL proteins contribute to the YDA activation. However, in the nucleus, specific BSL members (BSL2, BSL3, and BSU1) directly deactivate MPK6 to counteract the linear MAPK pathway, thereby promoting stomatal formation. Thus, the pivotal MAPK signaling in stomatal fate determination is spatially modulated by a signaling dichotomy of the BSL protein phosphatases in Arabidopsis, providing a prominent example of how MAPK activities are integrated and specified by signaling compartmentalization at the subcellular level.
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Affiliation(s)
- Xiaoyu Guo
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xue Ding
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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17
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Chai G, Qi G, Wang D, Zhuang Y, Xu H, Bai Z, Bai MY, Hu R, Wang ZY, Zhou G, Kong Y. The CCCH zinc finger protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid signaling. PLANT PHYSIOLOGY 2022; 189:285-300. [PMID: 35139225 PMCID: PMC9070797 DOI: 10.1093/plphys/kiac046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/10/2022] [Indexed: 05/20/2023]
Abstract
Plant CCCH proteins participate in the control of multiple developmental and adaptive processes, but the regulatory mechanisms underlying these processes are not well known. In this study, we showed that the Arabidopsis (Arabidopsis thaliana) CCCH protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid (BR) signaling. Genetic and biochemical evidence showed that C3H15 functions downstream of the receptor BR INSENSITIVE 1 (BRI1) as a negative regulator in the BR pathway. C3H15 is phosphorylated by the GLYCOGEN SYNTHASE KINASE 3 -like kinase BR-INSENSITIVE 2 (BIN2) at Ser111 in the cytoplasm in the absence of BRs. Upon BR perception, C3H15 transcription is enhanced, and the phosphorylation of C3H15 by BIN2 is reduced. The dephosphorylated C3H15 protein accumulates in the nucleus, where C3H15 regulates transcription via G-rich elements (typically GGGAGA). C3H15 and BRASSINAZOLE RESISTANT 1 (BZR1)/BRI1-EMS-SUPPRESSOR 1 (BES1), two central transcriptional regulators of BR signaling, directly suppress each other and share a number of BR-responsive target genes. Moreover, C3H15 antagonizes BZR1 and BES1 to regulate the expression of their shared cell elongation-associated target gene, SMALL AUXIN-UP RNA 15 (SAUR15). This study demonstrates that C3H15-mediated BR signaling may be parallel to, or even attenuate, the dominant BZR1 and BES1 signaling pathways to control cell elongation. This finding expands our understanding of the regulatory mechanisms underlying BR-induced cell elongation in plants.
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Affiliation(s)
| | | | | | | | - Hua Xu
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Zetao Bai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Ming-Yi Bai
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Ruibo Hu
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Zeng-yu Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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18
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Zhao J, Yang G, Jiang L, Zhang S, Miao L, Xu P, Chen H, Chen L, Mao Z, Guo T, Kou S, Yang HQ, Wang W. Phytochromes A and B Mediate Light Stabilization of BIN2 to Regulate Brassinosteroid Signaling and Photomorphogenesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:865019. [PMID: 35432407 PMCID: PMC9005995 DOI: 10.3389/fpls.2022.865019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Phytochromes A and B (phyA and phyB) are the far-red and red lights photoreceptors mediating many light responses in Arabidopsis thaliana. Brassinosteroid (BR) is a pivotal phytohormone regulating a variety of plant developmental processes including photomorphogenesis. It is known that phyB interacts with BES1 to inhibit its DNA-binding activity and repress BR signaling. Here, we show that far-red and red lights modulate BR signaling through phyA and phyB regulation of the stability of BIN2, a glycogen synthase kinase 3 (GSK3)-like kinase that phosphorylates BES1/BZR1 to inhibit BR signaling. The BIN2 gain-of-function mutant bin2-1 displays an enhanced photomorphogenic phenotype in both far-red and red lights. phyA-enhanced accumulation of BIN2 promotes the phosphorylation of BES1 in far-red light. BIN2 acts genetically downstream from PHYA to regulate photomorphogenesis under far-red light. Both phyA and phyB interact directly with BIN2, which may promote the interaction of BIN2 with BES1 and induce the phosphorylation of BES1. Our results suggest that far-red and red lights inhibit BR signaling through phyA and phyB stabilization of BIN2 and promotion of BES1 phosphorylation, which defines a new layer of the regulatory mechanism that allows plants to coordinate light and BR signaling pathways to optimize photomorphogenesis.
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Affiliation(s)
- Jiachen Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guangqiong Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lu Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shilong Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Langxi Miao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Peng Xu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Huiru Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Li Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shuang Kou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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19
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Lohani N, Singh MB, Bhalla PL. Biological Parts for Engineering Abiotic Stress Tolerance in Plants. BIODESIGN RESEARCH 2022; 2022:9819314. [PMID: 37850130 PMCID: PMC10521667 DOI: 10.34133/2022/9819314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2023] Open
Abstract
It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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20
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Clark NM, Nolan TM, Wang P, Song G, Montes C, Valentine CT, Guo H, Sozzani R, Yin Y, Walley JW. Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. Nat Commun 2021; 12:5858. [PMID: 34615886 PMCID: PMC8494934 DOI: 10.1038/s41467-021-26165-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/22/2021] [Indexed: 11/14/2022] Open
Abstract
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time. We then construct a network inference pipeline called Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) to integrate these data. We use our network predictions to identify putative phosphorylation sites on BES1 and experimentally validate their importance. Additionally, we identify BRONTOSAURUS (BRON) as a transcription factor that regulates cell division, and we show that BRON expression is modulated by BR-responsive kinases and transcription factors. This work demonstrates the power of integrative network analysis applied to multi-omic data and provides fundamental insights into the molecular signaling events occurring during BR response.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Trevor M Nolan
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Ping Wang
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Conner T Valentine
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Hongqing Guo
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Yanhai Yin
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
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21
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Yang M, He J, Wan S, Li W, Chen W, Wang Y, Jiang X, Cheng P, Chu P, Shen W, Guan R. Fine mapping of the BnaC04.BIL1 gene controlling plant height in Brassica napus L. BMC PLANT BIOLOGY 2021; 21:359. [PMID: 34353289 PMCID: PMC8340546 DOI: 10.1186/s12870-021-03137-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant height is an important architecture trait which is a fundamental yield-determining trait in crops. Variety with dwarf or semi-dwarf phenotype is a major objective in the breeding because dwarfing architecture can help to increase harvest index, increase planting density, enhance lodging resistance, and thus be suitable for mechanization harvest. Although some germplasm or genes associated with dwarfing plant type have been carried out. The molecular mechanisms underlying dwarfism in oilseed rape (Brassica napus L.) are poorly understood, restricting the progress of breeding dwarf varieties in this species. Here, we report a new dwarf mutant Bndwarf2 from our B. napus germplasm. We studied its inheritance and mapped the dwarf locus BnDWARF2. RESULTS The inheritance analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped in an interval of 787.88 kb on the C04 chromosome of B. napus by Illumina Brassica 60 K Bead Chip Array. To fine-map BnDWARF2, 318 simple sequence repeat (SSR) primers were designed to uniformly cover the mapping interval. Among them, 15 polymorphic primers that narrowed down the BnDWARF2 locus to 34.62 kb were detected using a F2:3 family population with 889 individuals. Protein sequence analysis showed that only BnaC04.BIL1 (BnaC04g41660D) had two amino acid residues substitutions (Thr187Ser and Gln399His) between ZS11 and Bndwarf2, which encoding a GLYCOGEN SYNTHASE KINASE 3 (GSK3-like). The quantitative real-time PCR (qRT-PCR) analysis showed that the BnaC04.BIL1 gene expressed in all tissues of oilseed rape. Subcellular localization experiment showed that BnaC04.BIL1 was localized in the nucleus in tobacco leaf cells. Genetic transformation experiments confirmed that the BnaC04.BIL1 is responsible for the plant dwarf phenotype in the Bndwarf2 mutants. Overexpression of BnaC04.BIL1 reduced plant height, but also resulted in compact plant architecture. CONCLUSIONS A dominant dwarfing gene, BnaC04.BIL1, encodes an GSK3-like that negatively regulates plant height, was mapped and isolated. Our identification of a distinct gene locus may help to improve lodging resistance in oilseed rape.
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Affiliation(s)
- Mao Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weiyan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenjing Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yangming Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiaomei Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Pengfei Cheng
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Pu Chu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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22
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Seyed Rahmani R, Shi T, Zhang D, Gou X, Yi J, Miclotte G, Marchal K, Li J. Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes. BMC Genomics 2021; 22:465. [PMID: 34157989 PMCID: PMC8220701 DOI: 10.1186/s12864-021-07778-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Brassinosteroid (BR) signaling regulates plant growth and development in concert with other signaling pathways. Although many genes have been identified that play a role in BR signaling, the biological and functional consequences of disrupting those key BR genes still require detailed investigation. RESULTS Here we performed phenotypic and transcriptomic comparisons of A. thaliana lines carrying a loss-of-function mutation in BRI1 gene, bri1-5, that exhibits a dwarf phenotype and its three activation-tag suppressor lines that were able to partially revert the bri1-5 mutant phenotype to a WS2 phenotype, namely bri1-5/bri1-1D, bri1-5/brs1-1D, and bri1-5/bak1-1D. From the three investigated bri1-5 suppressors, bri1-5/bak1-1D was the most effective suppressor at the transcriptional level. All three bri1-5 suppressors showed altered expression of the genes in the abscisic acid (ABA signaling) pathway, indicating that ABA likely contributes to the partial recovery of the wild-type phenotype in these bri1-5 suppressors. Network analysis revealed crosstalk between BR and other phytohormone signaling pathways, suggesting that interference with one hormone signaling pathway affects other hormone signaling pathways. In addition, differential expression analysis suggested the existence of a strong negative feedback from BR signaling on BR biosynthesis and also predicted that BRS1, rather than being directly involved in signaling, might be responsible for providing an optimal environment for the interaction between BRI1 and its ligand. CONCLUSIONS Our study provides insights into the molecular mechanisms and functions of key brassinosteroid (BR) signaling genes, especially BRS1.
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Affiliation(s)
- Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, IDLab, imec, Ghent University, Ghent, Belgium
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Dongzhi Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Giles Miclotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, IDLab, imec, Ghent University, Ghent, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Information Technology, IDLab, imec, Ghent University, Ghent, Belgium. .,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Xi L, Schulze WX, Wu XN. Phosphoproteomic Analysis of Plant Membranes. Methods Mol Biol 2021; 2200:441-451. [PMID: 33175392 DOI: 10.1007/978-1-0716-0880-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry (MS) is a powerful tool to investigate plant phosphorylation dynamics on a system-wide scale (phosphoproteomics). Plant membrane phosphoproteomics enables elucidating regulatory patterns in membranes, such as kinase-target relationships in different signaling pathways. Here, we present "ShortPhos," an efficient and simple phosphoproteomics protocol for research on plant membrane proteins, which allows fast and efficient identification and quantification of phosphopeptides from small amounts of starting plant material and/or membrane proteins. This method improves upon the efficiency of plant membrane phosphoproteomics profiling and can be applied to the study of membrane-based signaling networks.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
- School of Life Sciences, Center for Life Sciences, Yunnan University, Kunming, China.
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24
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Lu D, Gao T, Xi L, Krall L, Wu XN. Phosphoproteomics Profiling of Receptor Kinase Mutants. Methods Mol Biol 2021; 2358:73-82. [PMID: 34270046 DOI: 10.1007/978-1-0716-1625-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The transmembrane receptor kinase family is the largest protein kinase family in Arabidopsis. Many members of this family play critical roles in plant signaling pathways. However, many of these kinases have yet uncharacterized functions and very little is known about the direct substrates of these kinases. We have developed the "ShortPhos" method, an efficient and simple mass spectrometry (MS)-based phosphoproteomics protocol to perform comparative phosphopeptide profiling of knockout mutants of receptor-like kinases. Through this method, we are able to better understand the functional roles of plant kinases in the context of their signaling networks.
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Affiliation(s)
- Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Ting Gao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Leonard Krall
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China.
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25
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Song B, Zhao H, Dong K, Wang M, Wu S, Li S, Wang Y, Chen P, Jiang L, Tao Y. Phytochrome A inhibits shade avoidance responses under strong shade through repressing the brassinosteroid pathway in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1520-1534. [PMID: 33037720 DOI: 10.1111/tpj.15018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
In dense canopy, a reduction in red to far-red (R/FR) light ratio triggers shade avoidance responses (SARs) in Arabidopsis thaliana, a shade avoiding plant. Two red/far-red (R/FR) light photoreceptors, PHYB and PHYA, were reported to be key negative regulators of the SARs. PHYB represses the SARs under normal light conditions; however, the role of PHYA in the SARs remains elusive. We set up two shade conditions: Shade and strong Shade (s-Shade) with different R/FR ratios (0.7 and 0.1), which allowed us to observe phenotypes dominated by PHYB- and PHYA-mediated pathway, respectively. By comparing the hypocotyl growth under these two conditions with time, we found PHYA was predominantly activated in the s-Shade after prolonged shade treatment. We further showed that under s-Shade, PHYA inhibits hypocotyl elongation partially through repressing the brassinosteroid (BR) pathway. COP1 and PIF4,5 act downstream of PHYA. After prolonged shade treatment, the nuclear localization of COP1 was reduced, while the PIF4 protein level was much lower in the s-Shade than that in Shade. Both changes occurred in a PHYA-dependent manner. We propose that under deep canopy, the R/FR ratio is extremely low, which promotes the nuclear accumulation of PHYA. Activated PHYA reduces COP1 nuclear speckle, which may lead to changes of downstream targets, such as PIF4,5 and HY5. Together, these proteins regulate the BR pathway through modulating BES1/BZR1 and the expression of BR biosynthesis and BR target genes.
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Affiliation(s)
- Bin Song
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Hongli Zhao
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Kangmei Dong
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Meiling Wang
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Shujuan Wu
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Si Li
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Yuxiang Wang
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Peirui Chen
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Liangrong Jiang
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Yi Tao
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
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26
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Ma S, Ji T, Liang M, Li S, Tian Y, Gao L. Genome-Wide Identification, Structural, and Gene Expression Analysis of BRI1-EMS-Suppressor 1 Transcription Factor Family in Cucumis sativus. Front Genet 2020; 11:583996. [PMID: 33133168 PMCID: PMC7573293 DOI: 10.3389/fgene.2020.583996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
BRASSINOSTEROID INSENSITIVE1-EMS-suppressor 1 (BES1) is an essential regulator downstream of brassinosteroid signaling and plays important roles in plant stress response, growth, and development. To date, the regulation mechanisms of BES1 transcription factors have been identified and elucidated in model plants Arabidopsis and rice. However, little information is available regarding the BES1 family in Cucumis sativus. Therefore, this study conducted a genome-wide analysis of BES1 genes in cucumber. In cucumber, a total of six CsBES1 genes were identified, and their phylogenetic relationships, gene structures, and cis-elements in promoters were studied. CsBES1 genes were distributed on four of seven chromosomes. Gene structure analysis showed that the intron–exon model of CsBES1 genes was conserved and the CsBES1 protein contained a DUF822-conserved motif. Promoter cis-element prediction showed that plenty of developmental and stress- and hormone-related elements have been found in promoter regions of CsBES1 genes. Meanwhile, BES1 was divided into three groups (I, II, and III) on the basis of phylogenetic relationship analysis in six plant species. In addition, CsBES1 gene expression patterns were confirmed by transcription database and qRT-PCR analysis; the results showed that the expression of CsBES1 genes had not only tissue-specific expression but also different types of CsBES1 isoform which might respond to specific plant stresses. In summary, genome-wide identification, phylogeny, gene structure, and expression profile analysis of CsBES1 genes in cucumber provided a referable theoretical information for further functional study of CsBES1 genes and further facilitated the molecular breeding of cucumber.
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Affiliation(s)
- Si Ma
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Tingting Ji
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Meiting Liang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Shihui Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Yongqiang Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
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27
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Lv M, Li J. Molecular Mechanisms of Brassinosteroid-Mediated Responses to Changing Environments in Arabidopsis. Int J Mol Sci 2020; 21:ijms21082737. [PMID: 32326491 PMCID: PMC7215551 DOI: 10.3390/ijms21082737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Plant adaptations to changing environments rely on integrating external stimuli into internal responses. Brassinosteroids (BRs), a group of growth-promoting phytohormones, have been reported to act as signal molecules mediating these processes. BRs are perceived by cell surface receptor complex including receptor BRI1 and coreceptor BAK1, which subsequently triggers a signaling cascade that leads to inhibition of BIN2 and activation of BES1/BZR1 transcription factors. BES1/BZR1 can directly regulate the expression of thousands of downstream responsive genes. Recent studies in the model plant Arabidopsis demonstrated that BR biosynthesis and signal transduction, especially the regulatory components BIN2 and BES1/BZR1, are finely tuned by various environmental cues. Here, we summarize these research updates and give a comprehensive review of how BR biosynthesis and signaling are modulated by changing environments and how these changes regulate plant adaptive growth or stress tolerance.
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28
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Wang K, Li MQ, Chang YP, Zhang B, Zhao QZ, Zhao WL. The basic helix-loop-helix transcription factor OsBLR1 regulates leaf angle in rice via brassinosteroid signalling. PLANT MOLECULAR BIOLOGY 2020; 102:589-602. [PMID: 32026326 DOI: 10.1007/s11103-020-00965-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/09/2020] [Indexed: 05/10/2023]
Abstract
Leaf angle is a key factor in plant architecture and crop yield. Brassinosteroids (BRs) regulate many developmental processes, especially the leaf angle in monocots. However, the BR signalling pathway is complex and includes many unknown members. Here, we propose that Oryza sativa BRASSINOSTEROID-RESPONSIVE LEAF ANGLE REGULATOR 1 (OsBLR1) encodes a bHLH transcription factor, and positively regulates BR signalling to increase the leaf angle and grain length in rice (Oryza sativa L.). Lines overexpressing OsBLR1 (blr1-D and BLR1-OE-1/2/3) had similar traits, with increased leaf angle and grain length. Conversely, OsBLR1-knockout mutants (blr1-1/2/3) had erect leaves and shorter grains. Lamina joint inclination, coleoptile elongation, and root elongation assay results indicated that these overexpression lines were more sensitive to BR, while the knockout mutants were less sensitive. There was no significant difference in the endogenous BR contents of blr1-1/2 and wild-type plants. These results suggest that OsBLR1 is involved in BR signal transduction. The blr1-D mutant, with increased cell growth in the lamina joint and smaller leaf midrib, showed significant changes in gene expression related to the cell wall and leaf development compared with wild-type plants; furthermore, the cellulose and protopectin contents in blr1-D were reduced, which resulted in the increased leaf angle and bent leaves. As the potential downstream target gene of OsBLR1, the REGULATOR OF LEAF INCLINATION1 (OsRLI1) gene expression was up-regulated in OsBLR1-overexpression lines and down-regulated in OsBLR1-knockout mutants. Moreover, we screened OsRACK1A as an interaction protein of OsBLR1 using a yeast two-hybrid assay and glutathione-S-transferase pull-down.
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Affiliation(s)
- Kun Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Meng-Qi Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Yan-Peng Chang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Bo Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Quan-Zhi Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Wen-Li Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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29
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Samakovli D, Roka L, Plitsi PK, Kaltsa I, Daras G, Milioni D, Hatzopoulos P. Active BR signalling adjusts the subcellular localisation of BES1/HSP90 complex formation. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:129-133. [PMID: 31469500 DOI: 10.1111/plb.13040] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 05/23/2023]
Abstract
Heat shock proteins 90 (HSP90) are essential and play critical roles in the adaptation of organisms to diverse stimuli. In plants, HSP90 are involved in auxin, jasmonate and brassinosteroid (BR) signalling pathways. The BR-promoted activation of the BES1 transcription factor regulates BR-responsive genes. Using genetic, physiological, fluorescence live cell imaging, molecular and biochemical approaches, such as phenotypic analysis, co-immunoprecipitation assay, yeast-two hybrid and Bimolecular fluorescence complementation (BiFC), we studied complex formation between BES1 and HSP90 under control conditions and active BR signalling. Further, we determined the effect of the pharmacological inhibition of HSP90 ATPase activity on hypocotyl elongation of bes1-D mutant. We determined that HSP90 interact with BES1 in the nucleus and in the cytoplasm. During active BR signalling, nuclear complexes were absent while cytoplasmic HSP90/BES1 complexes were prominent. Our results showed that the hypocotyl length of bes1-D mutants was highly reduced when HSP90 was challenged by the geldanamycin (GDA) inhibitor of the ATPase activity of HSP90. Active BR signalling could not rescue the GDA effect on the hypocotyl elongation of bes1-D. Our results reveal that the constitutively active BES1 in the bes1-D mutant is hypersensitive to GDA. The interaction of HSP90 with BES1 argues that HSP90 facilitate the nuclear metastable conformation of BES1 to regulate BR-dependent gene expression, and our data show that HSP90 assist in the compartmentalised cycle of BES1 during active BR signalling.
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Affiliation(s)
- D Samakovli
- Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece
- Department of Cell Biology Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic
| | - L Roka
- Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece
| | - P-K Plitsi
- Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece
| | - I Kaltsa
- Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece
| | - G Daras
- Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece
| | - D Milioni
- Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece
| | - P Hatzopoulos
- Laboratory of Molecular Biology, Agricultural University of Athens, Athens, Greece
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Song S, Wang H, Sun M, Tang J, Zheng B, Wang X, Tan YW. Reactive oxygen species-mediated BIN2 activity revealed by single-molecule analysis. THE NEW PHYTOLOGIST 2019; 223:692-704. [PMID: 30597572 DOI: 10.1111/nph.15669] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/21/2018] [Indexed: 05/28/2023]
Abstract
Much evidence has shown that reactive oxygen species (ROS) regulate several plant hormone signaling cascades, but little is known about the real-time kinetics and the underlying molecular mechanisms of the target proteins in the brassinosteroid (BR) signaling pathway. In this study, we used single-molecule techniques to investigate the true signaling timescales of the major BR signaling components BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINOSTEROID INSENSITIVE 2 (BIN2) of Arabidopsis thaliana. The rate constants of BIN2 associating with ATP and phosphorylating BES1 were determined to be 0.7 ± 0.4 mM-1 s-1 and 2.3 ± 1.4 s-1 , respectively. Interestingly, we found that the interaction of BIN2 and BES1 was oxygen-dependent, and oxygen can directly modify BIN2. The activity of BIN2 was switched on via modification of specific cysteine (Cys) residues, including C59, C95, C99 and C162. The mutation of these Cys residues inhibited the BR signaling outputs. These findings demonstrate the power of using single-molecule techniques to study the dynamic interactions of signaling components, which is difficult to be discovered by conventional physiological and biochemical methods.
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Affiliation(s)
- Song Song
- State Key Laboratory of Surface Physics, Collaborative Innovation Center for Genetics and Development, Department of Physics, Fudan University, Shanghai, 200433, China
| | - Haijiao Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengyuan Sun
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jie Tang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xuelu Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan-Wen Tan
- State Key Laboratory of Surface Physics, Collaborative Innovation Center for Genetics and Development, Department of Physics, Fudan University, Shanghai, 200433, China
- Multiscale Research Institute for Complex Systems, Fudan University, Shanghai, 200438, China
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Wang W, Sun YQ, Li GL, Zhang SY. Genome-wide identification, characterization, and expression patterns of the BZR transcription factor family in sugar beet (Beta vulgaris L.). BMC PLANT BIOLOGY 2019; 19:191. [PMID: 31072335 PMCID: PMC6506937 DOI: 10.1186/s12870-019-1783-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/16/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND BRASSINAZOLE-RESISTANT (BZR) family genes encode plant-specific transcription factors (TFs) that participate in brassinosteroid signal transduction. BZR TFs have vital roles in plant growth, including cell elongation. However, little is known about BZR genes in sugar beet (Beta vulgaris L.). RESULTS Therefore, we performed a genome-wide investigation of BvBZR genes in sugar beet. Through an analysis of the BES1_N conserved domain, six BvBZR gene family members were identified in the sugar beet genome, which clustered into three subgroups according to a phylogenetic analysis. Each clade was well defined by the conserved motifs, implying that close genetic relationships could be identified among the members of each subfamily. According to chromosomal distribution mapping, 2, 1, 1, 1, and 1 genes were located on chromosomes 1, 4, 5, 6, and 8, respectively. The cis-acting elements related to taproot growth were randomly distributed in the promoter sequences of the BvBZR genes. Tissue-specific expression analyses indicated that all BvBZR genes were expressed in all three major tissue types (roots, stems, and leaves), with significantly higher expression in leaves. Subcellular localization analysis revealed that Bv1_fxre and Bv6_nyuw are localized in the nuclei, consistent with the prediction of Wolf PSORT. CONCLUSION These findings offer a basis to predict the functions of BZR genes in sugar beet, and lay a foundation for further research of the biological functions of BZR genes in sugar beet.
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Affiliation(s)
- Wei Wang
- Sugar Beet Physiological Research Institute, Inner Mongolia Agricultural University, Hohhot, China
| | - Ya-Qing Sun
- Sugar Beet Physiological Research Institute, Inner Mongolia Agricultural University, Hohhot, China
| | - Guo-Long Li
- Sugar Beet Physiological Research Institute, Inner Mongolia Agricultural University, Hohhot, China
| | - Shao-Ying Zhang
- Sugar Beet Physiological Research Institute, Inner Mongolia Agricultural University, Hohhot, China.
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Peres ALGL, Soares JS, Tavares RG, Righetto G, Zullo MAT, Mandava NB, Menossi M. Brassinosteroids, the Sixth Class of Phytohormones: A Molecular View from the Discovery to Hormonal Interactions in Plant Development and Stress Adaptation. Int J Mol Sci 2019; 20:ijms20020331. [PMID: 30650539 PMCID: PMC6359644 DOI: 10.3390/ijms20020331] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 12/23/2022] Open
Abstract
Phytohormones are natural chemical messengers that play critical roles in the regulation of plant growth and development as well as responses to biotic and abiotic stress factors, maintaining plant homeostasis, and allowing adaptation to environmental changes. The discovery of a new class of phytohormones, the brassinosteroids (BRs), almost 40 years ago opened a new era for the studies of plant growth and development and introduced new perspectives in the regulation of agronomic traits through their use in agriculture. BRs are a group of hormones with significant growth regulatory activity that act independently and in conjunction with other phytohormones to control different BR-regulated activities. Genetic and molecular research has increased our understanding of how BRs and their cross-talk with other phytohormones control several physiological and developmental processes. The present article provides an overview of BRs' discovery as well as recent findings on their interactions with other phytohormones at the transcriptional and post-transcriptional levels, in addition to clarifying how their network works to modulate plant growth, development, and responses to biotic and abiotic stresses.
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Affiliation(s)
- Ana Laura G L Peres
- Functional Genome Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas 13083-970, Brazil.
| | - José Sérgio Soares
- Functional Genome Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas 13083-970, Brazil.
| | - Rafael G Tavares
- Center for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 400, Australia.
| | - Germanna Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas 13083-970, Brazil.
| | - Marco A T Zullo
- Laboratory of Phytochemistry, Agronomic Institute, Campinas 13020-902, Brazil.
| | - N Bhushan Mandava
- Mandava Associates, LLC, 1050 Connecticut Avenue, N.W. Suite 500, Washington, DC 20036, USA.
| | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas 13083-970, Brazil.
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Martínez C, Espinosa-Ruíz A, de Lucas M, Bernardo-García S, Franco-Zorrilla JM, Prat S. PIF4-induced BR synthesis is critical to diurnal and thermomorphogenic growth. EMBO J 2018; 37:embj.201899552. [PMID: 30389669 DOI: 10.15252/embj.201899552] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/19/2022] Open
Abstract
The Arabidopsis PIF4 and BES1/BZR1 transcription factors antagonize light signaling by facilitating co-activated expression of a large number of cell wall-loosening and auxin-related genes. While PIF4 directly activates expression of these targets, BES1 and BZR1 activity switch from a repressive to an activator function, depending on interaction with TOPLESS and other families of regulators including PIFs. However, the complexity of this regulation and its role in diurnal control of plant growth and brassinosteroid (BR) levels is little understood. We show by using a protein array that BES1, PIF4, and the BES1-PIF4 complex recognize different DNA elements, thus revealing a distinctive cis-regulatory code beneath BES1-repressive and PIF4 co-activation function. BES1 homodimers bind to conserved BRRE- and G-box elements in the BR biosynthetic promoters and inhibit their expression during the day, while elevated PIF4 competes for BES1 homodimer formation, resulting in de-repressed BR biosynthesis at dawn and in response to warmth. Our findings demonstrate a central role of PIF4 in BR synthesis activation, increased BR levels being essential to thermomorphogenic hypocotyl growth.
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Affiliation(s)
- Cristina Martínez
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Ana Espinosa-Ruíz
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Miguel de Lucas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Stella Bernardo-García
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | | | - Salomé Prat
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
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Bhandary P, Seetharam AS, Arendsee ZW, Hur M, Wurtele ES. Raising orphans from a metadata morass: A researcher's guide to re-use of public 'omics data. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:32-47. [PMID: 29362097 DOI: 10.1016/j.plantsci.2017.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/07/2017] [Accepted: 10/15/2017] [Indexed: 05/19/2023]
Abstract
More than 15 petabases of raw RNAseq data is now accessible through public repositories. Acquisition of other 'omics data types is expanding, though most lack a centralized archival repository. Data-reuse provides tremendous opportunity to extract new knowledge from existing experiments, and offers a unique opportunity for robust, multi-'omics analyses by merging metadata (information about experimental design, biological samples, protocols) and data from multiple experiments. We illustrate how predictive research can be accelerated by meta-analysis with a study of orphan (species-specific) genes. Computational predictions are critical to infer orphan function because their coding sequences provide very few clues. The metadata in public databases is often confusing; a test case with Zea mays mRNA seq data reveals a high proportion of missing, misleading or incomplete metadata. This metadata morass significantly diminishes the insight that can be extracted from these data. We provide tips for data submitters and users, including specific recommendations to improve metadata quality by more use of controlled vocabulary and by metadata reviews. Finally, we advocate for a unified, straightforward metadata submission and retrieval system.
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Affiliation(s)
- Priyanka Bhandary
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Zebulun W Arendsee
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA.
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35
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Allen HR, Ptashnyk M. Mathematical modelling and analysis of the brassinosteroid and gibberellin signalling pathways and their interactions. J Theor Biol 2017; 432:109-131. [PMID: 28818467 DOI: 10.1016/j.jtbi.2017.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/28/2017] [Accepted: 08/13/2017] [Indexed: 01/08/2023]
Abstract
The plant hormones brassinosteroid (BR) and gibberellin (GA) have important roles in a wide range of processes involved in plant growth and development. In this paper we derive and analyse new mathematical models for the BR signalling pathway and for the crosstalk between the BR and GA signalling pathways. To analyse the effects of spatial heterogeneity of the signalling processes, along with spatially-homogeneous ODE models we derive coupled PDE-ODE systems modelling the temporal and spatial dynamics of molecules involved in the signalling pathways. The values of the parameters in the model for the BR signalling pathway are determined using experimental data on the gene expression of BR biosynthetic enzymes. The stability of steady state solutions of our mathematical model, shown for a wide range of parameters, can be related to the BR homeostasis which is essential for proper function of plant cells. Solutions of the mathematical model for the BR signalling pathway can exhibit oscillatory behaviour only for relatively large values of parameters associated with transcription factor brassinazole-resistant1's (BZR) phosphorylation state, suggesting that this process may be important in governing the stability of signalling processes. Comparison between ODE and PDE-ODE models demonstrates distinct spatial distribution in the level of BR in the cell cytoplasm, however the spatial heterogeneity has significant effect on the dynamics of the averaged solutions only in the case when we have oscillations in solutions for at least one of the models, i.e. for possibly biologically not relevant parameter values. Our results for the crosstalk model suggest that the interaction between transcription factors BZR and DELLA exerts more influence on the dynamics of the signalling pathways than BZR-mediated biosynthesis of GA, suggesting that the interaction between transcription factors may constitute the principal mechanism of the crosstalk between the BR and GA signalling pathways. In general, perturbations in the GA signalling pathway have larger effects on the dynamics of components of the BR signalling pathway than perturbations in the BR signalling pathway on the dynamics of the GA pathway. The perturbation in the crosstalk mechanism also has a larger effect on the dynamics of the BR pathway than of the GA pathway. Large changes in the dynamics of the GA signalling processes can be observed only in the case where there are disturbances in both the BR signalling pathway and the crosstalk mechanism. Those results highlight the robustness of the GA signalling pathway.
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Affiliation(s)
- Henry R Allen
- Department of Mathematics, Fulton Building, University of Dundee, Dundee, DD1 4HN, United Kingdom
| | - Mariya Ptashnyk
- Department of Mathematics, Fulton Building, University of Dundee, Dundee, DD1 4HN, United Kingdom; Department of Mathematics, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom.
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36
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Lu X, Xiong Q, Cheng T, Li QT, Liu XL, Bi YD, Li W, Zhang WK, Ma B, Lai YC, Du WG, Man WQ, Chen SY, Zhang JS. A PP2C-1 Allele Underlying a Quantitative Trait Locus Enhances Soybean 100-Seed Weight. MOLECULAR PLANT 2017; 10:670-684. [PMID: 28363587 DOI: 10.1016/j.molp.2017.03.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 05/21/2023]
Abstract
Cultivated soybeans may lose some useful genetic loci during domestication. Introgression of genes from wild soybeans could broaden the genetic background and improve soybean agronomic traits. In this study, through whole-genome sequencing of a recombinant inbred line population derived from a cross between a wild soybean ZYD7 and a cultivated soybean HN44, and mapping of quantitative trait loci for seed weight, we discovered that a phosphatase 2C-1 (PP2C-1) allele from wild soybean ZYD7 contributes to the increase in seed weight/size. PP2C-1 may achieve this function by enhancing cell size of integument and activating a subset of seed trait-related genes. We found that PP2C-1 is associated with GmBZR1, a soybean ortholog of Arabidopsis BZR1, one of key transcription factors in brassinosteroid (BR) signaling, and facilitate accumulation of dephosphorylated GmBZR1. In contrast, the PP2C-2 allele with variations of a few amino acids at the N-terminus did not exhibit this function. Moreover, we showed that GmBZR1 could promote seed weight/size in transgenic plants. Through analysis of cultivated soybean accessions, we found that 40% of the examined accessions do not have the PP2C-1 allele, suggesting that these accessions can be improved by introduction of this allele. Taken together, our study identifies an elite allele PP2C-1, which can enhance seed weight and/or size in soybean, and pinpoints that manipulation of this allele by molecular-assisted breeding may increase production in soybean and other legumes/crops.
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Affiliation(s)
- Xiang Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Xiong
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Tian Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Lei Liu
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Ying-Dong Bi
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Wei Li
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Biao Ma
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Cai Lai
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Wei-Guang Du
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Wei-Qun Man
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China.
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Li H, Ye K, Shi Y, Cheng J, Zhang X, Yang S. BZR1 Positively Regulates Freezing Tolerance via CBF-Dependent and CBF-Independent Pathways in Arabidopsis. MOLECULAR PLANT 2017; 10:545-559. [PMID: 28089951 DOI: 10.1016/j.molp.2017.01.004] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 01/03/2017] [Accepted: 01/09/2017] [Indexed: 05/20/2023]
Abstract
Cold stress is a major environmental factor that adversely affects plant growth and development. The C-repeat binding factor/DRE binding factor 1 (CBF/DREB1) transcriptional regulatory cascade has been shown to play important roles in plant response to cold. Here we demonstrate that two key components of brassinosteroid (BR) signaling modulate freezing tolerance of Arabidopsis plants. The loss-of-function mutant of the GSK3-like kinases involved in BR signaling, bin2-3 bil1 bil2, showed increased freezing tolerance, whereas overexpression of BIN2 resulted in hypersensitivity to freezing stress under both non-acclimated and acclimated conditions. By contrast, gain-of-function mutants of the transcription factors BZR1 and BES1 displayed enhanced freezing tolerance, and consistently cold treatment could induce the accumulation of dephosphorylated BZR1. Biochemical and genetic analyses showed that BZR1 acts upstream of CBF1 and CBF2 to directly regulate their expression. Moreover, we found that BZR1 also regulated other COR genes uncoupled with CBFs, such as WKRY6, PYL6, SOC1, JMT, and SAG21, to modulate plant response to cold stress. Consistently, wrky6 mutants showed decreased freezing tolerance. Taken together, our results indicate that BZR1 positively modulates plant freezing tolerance through CBF-dependent and CBF-independent pathways.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Keyi Ye
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Nie S, Huang S, Wang S, Cheng D, Liu J, Lv S, Li Q, Wang X. Enhancing Brassinosteroid Signaling via Overexpression of Tomato ( Solanum lycopersicum) SlBRI1 Improves Major Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2017; 8:1386. [PMID: 28848587 PMCID: PMC5554372 DOI: 10.3389/fpls.2017.01386] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
Brassinosteroids (BRs) play important roles in plant growth, development, and stress responses through the receptor, Brassinosteroid-insensitive 1 (BRI1), which perceives BRs and initiates BR signaling. There is considerable potential agricultural value in regulating BR signaling in crops. In this study, we investigated the effects of overexpressing the tomato (Solanum lycopersicum) BRI1 gene, SlBRI1, on major agronomic traits, such as seed germination, vegetative growth, fruit ethylene production, carotenoid accumulation, yield, and quality attributes. SlBRI1 overexpression enhanced the endogenous BR signaling intensity thereby increasing the seed germination rate, lateral root number, hypocotyl length, CO2 assimilation, plant height, and flower size. The transgenic plants also showed an increase in fruit yield and fruit number per plant, although the mean weight of individual fruit was reduced, compared with wild type. SlBRI1 overexpression also promoted fruit ripening and ethylene production, and caused an increase in levels of carotenoids, ascorbic acid, soluble solids, and soluble sugars during fruit ripening. An increased BR signaling intensity mediated by SlBRI1 overexpression was therefore positively correlated with carotenoid accumulation and fruit nutritional quality. Our results indicate that enhancing BR signaling by overexpression of SlBRI1 in tomato has the potential to improve multiple major agronomic traits.
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Affiliation(s)
- Shuming Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- Qinghai Key Laboratory of Vegetable Genetics and PhysiologyXining, China
| | - Shuhua Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Shufen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Dandan Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Jianwei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Siqi Lv
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Qi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Xiaofeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- *Correspondence: Xiaofeng Wang,
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39
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Wu Z, Liang S, Song W, Lin G, Wang W, Zhang H, Han Z, Chai J. Functional and Structural Characterization of a Receptor-Like Kinase Involved in Germination and Cell Expansion in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:1999. [PMID: 29213277 PMCID: PMC5702872 DOI: 10.3389/fpls.2017.01999] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/08/2017] [Indexed: 05/22/2023]
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) are widespread in different plant species and play important roles in growth and development. Germination inhibition is vital for the completion of seed maturation and cell expansion is a fundamental cellular process driving plant growth. Here, we report genetic and structural characterizations of a functionally uncharacterized LRR-RLK, named GRACE (Germination Repression and Cell Expansion receptor-like kinase). Overexpression of GRACE in Arabidopsis exhibited delayed germination, enlarged cotyledons, rosette leaves and stubbier petioles. Conversely, these phenotypes were reversed in the T-DNA insertion knock-down mutant grace-1 plants. A crystal structure of the extracellular domain of GRACE (GRACE-LRR) determined at the resolution of 3.0 Å revealed that GRACE-LRR assumed a right-handed super-helical structure with an island domain (ID). Structural comparison showed that structure of the ID in GRACE-LRR is strikingly different from those observed in other LRR-RLKs. This structural observation implies that GRACE might perceive a new ligand for signaling. Collectively, our data support roles of GRACE in repressing seed germination and promoting cell expansion of Arabidopsis, presumably by perception of unknown ligand(s).
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Affiliation(s)
- Zhen Wu
- School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Shan Liang
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, China
| | - Wen Song
- School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Guangzhong Lin
- School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Weiguang Wang
- School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Heqiao Zhang
- School of Life Scienses and Thechology, Shanghai Tech University, Shanghai, China
| | - Zhifu Han
- School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jijie Chai
- School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
- *Correspondence: Jijie Chai
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Zhang G, Song X, Guo H, Wu Y, Chen X, Fang R. A Small G Protein as a Novel Component of the Rice Brassinosteroid Signal Transduction. MOLECULAR PLANT 2016; 9:1260-1271. [PMID: 27375203 DOI: 10.1016/j.molp.2016.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 06/11/2016] [Accepted: 06/22/2016] [Indexed: 05/10/2023]
Abstract
Brassinosteroids (BRs) are a class of steroid hormones that are essential for plant growth and development. The BR signal transduction pathway in the dicot model plant Arabidopsis is well established, but the components connecting the BR signaling steps in rice have not been fully explored. For example, how the BR signaling is fine-tuned in rice, especially at the BR receptor level, is largely unknown. Here we show that OsPRA2, a rice small G protein, plays a repressive role in the BR signaling pathway. Lamina inclination, coleoptile elongation, and root inhibition assays indicated that rice plants with suppressed expression of OsPRA2 were more sensitive to exogenously applied brassinolide than the wild-type plants. Conversely, rice overexpressing OsPRA2 was less sensitive to exogenous brassinolide. Further study uncovered that OsPRA2 inhibited the dephosphorylation of, and thus inactivated the transcription factor BRASSINAZOLE-RESISTANT 1 (OsBZR1). More importantly, OsPRA2 was found to co-localize with and directly bind to rice BR receptor BRASSINOSTEROID-INSENSITIVE 1 (OsBRI1) at the plasma membrane. Additionally, the in vitro assays showed that OsPRA2 inhibits its autophosphorylation. This OsPRA2-OsBRI1 interaction led to the dissociation of OsBRI1 from its co-receptor OsBAK1, and abolished OsBRI1-mediated phosphorylation of OsBAK1. Together, these results reveal a possible working mechanism of OsPRA2 as a novel negative regulator on OsBRI1 and OsBZR1 and extend the knowledge about the regulatory mechanism of rice BR signaling.
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Affiliation(s)
- Ge Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Center for Plant Gene Research (Beijing), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoguang Song
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Center for Plant Gene Research (Beijing), Beijing 100101, China
| | - Hongyan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Center for Plant Gene Research (Beijing), Beijing 100101, China
| | - Yao Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Center for Plant Gene Research (Beijing), Beijing 100101, China
| | - Xiaoying Chen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Center for Plant Gene Research (Beijing), Beijing 100101, China.
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Center for Plant Gene Research (Beijing), Beijing 100101, China.
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Hill K. Post-translational modifications of hormone-responsive transcription factors: the next level of regulation. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4933-45. [PMID: 26041319 DOI: 10.1093/jxb/erv273] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants exhibit a high level of developmental plasticity and growth is responsive to multiple developmental and environmental cues. Hormones are small endogenous signalling molecules which are fundamental to this phenotypic plasticity. Post-translational modifications of proteins are a central feature of the signal transduction pathways that regulate gene transcription in response to hormones. Modifications that affect the function of transcriptional regulators may also serve as a mechanism to incorporate multiple signals, mediate cross-talk, and modulate specific responses. This review discusses recent research that suggests hormone-responsive transcription factors are subject to multiple modifications which imply an additional level of regulation conferred by enzymes that mediate specific modifications, such as phosphorylation, ubiquitination, SUMOylation, and S-nitrosylation. These modifications can affect protein stability, sub-cellular localization, interactions with co-repressors and activators, and DNA binding. The focus here is on direct cross-talk involving transcription factors downstream of auxin, brassinosteroid, and gibberellin signalling. However, many of the concepts discussed are more broadly relevant to questions of how plants can modify their growth by regulating subsets of genes in response to multiple cues.
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Affiliation(s)
- Kristine Hill
- Plant Sciences Division and Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Youn JH, Kim TW. Functional insights of plant GSK3-like kinases: multi-taskers in diverse cellular signal transduction pathways. MOLECULAR PLANT 2015; 8:552-65. [PMID: 25655825 DOI: 10.1016/j.molp.2014.12.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/15/2014] [Accepted: 12/02/2014] [Indexed: 05/03/2023]
Abstract
The physiological importance of GSK3-like kinases in plants emerged when the functional role of plant GSK3-like kinases represented by BIN2 was first elucidated in the brassinosteroid (BR)-regulated signal transduction pathway. While early studies focused more on understanding how GSK3-like kinases regulate BR signaling, recent studies have implicated many novel substrates of GSK3-like kinases that are involved in a variety of cellular processes as well as BR signaling. Plant GSK3-like kinases play diverse roles in physiological and developmental processes such as cell growth, root and stomatal cell development, flower development, xylem differentiation, light response, and stress responses. Here, we review the progress made in recent years in understanding the versatile functions of plant GSK3-like kinases. Based on the relationship between GSK3-like kinases and their newly identified substrates, we discuss the physiological and biochemical relevance of various cellular signaling mediated by GSK3-like kinases in plants.
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Affiliation(s)
- Ji-Hyun Youn
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea
| | - Tae-Wuk Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea; Natural Science Institute, Hanyang University, Seoul 133-791, Korea.
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Wang M, Yang K, Le J. Organ-specific effects of brassinosteroids on stomatal production coordinate with the action of Too Many Mouths. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:247-255. [PMID: 25234048 DOI: 10.1111/jipb.12285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/17/2014] [Indexed: 06/03/2023]
Abstract
In Arabidopsis, stomatal development initiates after protodermal cells acquire stomatal lineage cell fate. Stomata or their precursors communicate with their neighbor epidermal cells to ensure the "one cell spacing" rule. The signals from EPF/EPFL peptide ligands received by Too Many Mouths (TMM) and ERECTA-family receptors are supposed to be transduced by YODA MAPK cascade. A basic helix-loop-helix transcription factor SPEECHLESS (SPCH) is another key regulator of stomatal cell fate determination and asymmetric entry divisions, and SPCH activity is regulated by YODA MAPK cascade. Brassinosteroid (BR) signaling, one of the most well characterized signal transduction pathways in plants, contributes to the control of stomatal production. But opposite organ-specific effects of BR on stomatal production were reported. Here we confirm that stomatal production in hypocotyls is controlled by BR levels. YODA and CYCD4 are not essential for BR stomata-promoting function. Furthermore, we found that BR could confer tmm hypocotyls clustered stomatal phenotype, indicating that the BR organ-specific effects on stomatal production might coordinate with the TMM organ-specific actions.
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Affiliation(s)
- Ming Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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Mantilla Perez MB, Zhao J, Yin Y, Hu J, Salas Fernandez MG. Association mapping of brassinosteroid candidate genes and plant architecture in a diverse panel of Sorghum bicolor. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2645-62. [PMID: 25326721 DOI: 10.1007/s00122-014-2405-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 09/27/2014] [Indexed: 05/09/2023]
Abstract
This first association analysis between plant architecture and BR candidate genes in sorghum suggests that natural allelic variation has significant and pleiotropic effects on plant architecture phenotypes. Sorghum bicolor (L) Moench is a self-pollinated species traditionally used as a staple crop for human consumption and as a forage crop for livestock feed. Recently, sorghum has received attention as a bioenergy crop due to its water use efficiency and biomass yield potential. Breeding for superior bioenergy-type lines requires knowledge of the genetic mechanisms controlling plant architecture. Brassinosteroids (BRs) are a group of hormones that determine plant growth, development, and architecture. Biochemical and genetic information on BRs are available from model species but the application of that knowledge to crop species has been very limited. A candidate gene association mapping approach and a diverse sorghum collection of 315 accessions were used to assess marker-trait associations between BR biosynthesis and signaling genes and six plant architecture traits. A total of 263 single nucleotide polymorphisms (SNPs) from 26 BR genes were tested, 73 SNPs were significantly associated with the phenotypes of interest and 18 of those were associated with more than one trait. An analysis of the phenotypic variation explained by each BR pathway revealed that the signaling pathway had a larger effect for most phenotypes (R (2) = 0.05-0.23). This study constitutes the first association analysis between plant architecture and BR genes in sorghum and the first LD mapping for leaf angle, stem circumference, panicle exsertion and panicle length. Markers on or close to BKI1 associated with all phenotypes and thus, they are the most important outcomes of this study and will be further validated for their future application in breeding programs.
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45
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Serna L. The role of brassinosteroids and abscisic acid in stomatal development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 225:95-101. [PMID: 25017164 DOI: 10.1016/j.plantsci.2014.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/15/2014] [Accepted: 05/24/2014] [Indexed: 06/03/2023]
Abstract
Gas exchange with the atmosphere is regulated through the stomata. This process relies on both the degree and duration of stomatal opening, and the number and patterning of these structures in the plant surface. Recent work has revealed that brassinosteroids and abscisic acid (ABA), which control stomatal opening, also repress stomatal development in cotyledons and leaves of at least some plants. It is speculated that, in Arabidopsis, these phytohormones control the same steps of this developmental process, most probably, through the regulation of the same mitogen-activated protein (MAP) kinase module. The conservation, in seeds plants, of components downstream of this module with MAP kinase target domains, suggests that these proteins are also regulated by these cascades, which, in turn, may be regulated by brassinosteroids and/or ABA.
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Affiliation(s)
- Laura Serna
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, E-45071 Toledo, Spain.
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Wang X, Chen J, Xie Z, Liu S, Nolan T, Ye H, Zhang M, Guo H, Schnable PS, Li Z, Yin Y. Histone lysine methyltransferase SDG8 is involved in brassinosteroid-regulated gene expression in Arabidopsis thaliana. MOLECULAR PLANT 2014; 7:1303-1315. [PMID: 24838002 DOI: 10.1093/mp/ssu056] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The plant steroid hormones, brassinosteroids (BRs), play important roles in plant growth, development, and responses to environmental stresses. BRs signal through receptors localized to the plasma membrane and other signaling components to regulate the BES1/BZR1 family of transcription factors, which modulates the expression of thousands of genes. How BES1/BZR1 and their interacting proteins function to regulate the large number of genes are not completely understood. Here we report that histone lysine methyltransferase SDG8, implicated in histone 3 lysine 36 di- and trimethylation (H3K36me2 and me3), is involved in BR-regulated gene expression. BES1 interacts with SDG8, directly or indirectly through IWS1, a transcription elongation factor involved in BR-regulated gene expression. The knockout mutant sdg8 displays a reduced growth phenotype with compromised BR responses. Global gene expression studies demonstrated that, while BR regulates about 5000 genes in wild-type plants, the hormone regulates fewer than 700 genes in sdg8 mutant. In addition, more than half of BR-regulated genes are differentially affected in sdg8 mutant. A Chromatin Immunoprecipitation (ChIP) experiment showed that H3K36me3 is reduced in BR-regulated genes in the sdg8 mutant. Based on these results, we propose that SDG8 plays an essential role in mediating BR-regulated gene expression. Our results thus reveal a major mechanism by which histone modifications dictate hormonal regulation of gene expression.
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Affiliation(s)
- Xiaolei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P.R. China; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Jiani Chen
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhouli Xie
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; Present address: Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA
| | - Trevor Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Huaxun Ye
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; Present address: Du Pont Pioneer Inc., Johnston, IA, USA
| | - Mingcai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P.R. China
| | - Hongqing Guo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; Data2Bio LLC, Ames, IA 50011-3650, USA
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P.R. China.
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
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Ryu H, Cho H, Bae W, Hwang I. Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3. Nat Commun 2014; 5:4138. [PMID: 24938150 DOI: 10.1038/ncomms5138] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/16/2014] [Indexed: 12/23/2022] Open
Abstract
Seed germination and young seedling establishment should be tightly regulated to maximize plant survival and thereby enable successful propagation. Plants have evolved developmental signalling networks to integrate environmental cues for proper control of these critical processes, in which brassinosteroids are known to attenuate ABA-mediated arrest of early seedling development; however, the underlying regulatory mechanism remains elusive. Here we reveal that a BES1/TPL/HDA19 repressor complex mediates the inhibitory action of brassinosteroids on ABA responses during early seedling development. BR-activated BES1 forms a transcriptional repressor complex with TPL-HDA19, which directly facilitates the histone deacetylation of ABI3 chromatin. This event leads to the transcriptional repression of ABI3 and consequently ABI5, major ABA signalling regulators in early seedling development. Our data reveal that the BR-activated BES1-TPL-HDA19 repressor complex controls epigenetic silencing of ABI3 and thereby suppresses the ABA signalling output during early seedling development.
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Affiliation(s)
- Hojin Ryu
- 1] Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea [2] Division of Agricultural Microbiology, National Academy of Agricultural Science, RDA, Suwon 441-707, South Korea
| | - Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Wonsil Bae
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea
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He X, Fang J, Li J, Qu B, Ren Y, Ma W, Zhao X, Li B, Wang D, Li Z, Tong Y. A genotypic difference in primary root length is associated with the inhibitory role of transforming growth factor-beta receptor-interacting protein-1 on root meristem size in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:931-43. [PMID: 24467344 DOI: 10.1111/tpj.12449] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 01/07/2014] [Accepted: 01/14/2014] [Indexed: 05/24/2023]
Abstract
Previously we identified a major quantitative trait locus (QTL) qTaLRO-B1 for primary root length (PRL) in wheat. Here we compare proteomics in the roots of the qTaLRO-B1 QTL isolines 178A, with short PRL and small meristem size, and 178B, with long PRL and large meristem size. A total of 16 differentially expressed proteins were identified: one, transforming growth factor (TGF)-beta receptor-interacting protein-1 (TaTRIP1), was enriched in 178A, while various peroxidases (PODs) were more abundantly expressed in 178B. The 178A roots showed higher TaTRIP1 expression and lower levels of the unphosphorylated form of the brassinosteroid (BR) signaling component BZR1, lower expression of POD genes and reduced POD activity and accumulation of the superoxide anion O2(-) in the root elongation zone compared with the 178B roots. Low levels of 24-epibrassinolide increased POD gene expression and root meristem size, and rescued the short PRL phenotype of 178A. TaTRIP1 directly interacted with the BR receptor TaBRI1 of wheat. Moreover, overexpressing TaTRIP1 in Arabidopsis reduced the abundance of unphosphorylated BZR1 protein, altered the expression of BR-responsive genes, inhibited POD activity and accumulation of the O2(-) in the root tip and inhibited root meristem size. Our data suggested that TaTRIP1 is involved in BR signaling and inhibited root meristem size, possibly by reducing POD activity and accumulation of O2(-) in the root tip. We further demonstrated a negative correlation between the level of TaTRIP1 mRNA and PRL of landraces and modern wheat varieties, providing a valuable insight for better understanding of the molecular mechanism underlying the genotypic differences in root morphology of wheat in the future.
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Affiliation(s)
- Xue He
- State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
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Maselli GA, Slamovits CH, Bianchi JI, Vilarrasa-Blasi J, Caño-Delgado AI, Mora-García S. Revisiting the evolutionary history and roles of protein phosphatases with Kelch-like domains in plants. PLANT PHYSIOLOGY 2014; 164:1527-41. [PMID: 24492333 PMCID: PMC3938638 DOI: 10.1104/pp.113.233627] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/28/2014] [Indexed: 05/20/2023]
Abstract
Protein phosphatases with Kelch-like domains (PPKL) are members of the phosphoprotein phosphatases family present only in plants and alveolates. PPKL have been described as positive effectors of brassinosteroid (BR) signaling in plants. Most of the evidence supporting this role has been gathered using one of the four homologs in Arabidopsis (Arabidopsis thaliana), brassinosteroid-insensitive1 suppressor (BSU1). We reappraised the roles of the other three members of the family, BSL1, BSL2, and BSL3, through phylogenetic, functional, and genetic analyses. We show that BSL1 and BSL2/BSL3 belong to two ancient evolutionary clades that have been highly conserved in land plants. In contrast, BSU1-type genes are exclusively found in the Brassicaceae and display a remarkable sequence divergence, even among closely related species. Simultaneous loss of function of the close paralogs BSL2 and BSL3 brings about a peculiar array of phenotypic alterations, but with marginal effects on BR signaling; loss of function of BSL1 is, in turn, phenotypically silent. Still, the products of these three genes account for the bulk of PPKL-related activity in Arabidopsis and together have an essential role in the early stages of development that BSU1 is unable to supplement. Our results underline the functional relevance of BSL phosphatases in plants and suggest that BSL2/BSL3 and BSU1 may have contrasting effects on BR signaling. Given that BSU1-type genes have likely undergone a functional shift and are phylogenetically restricted, we caution that inferences based on these genes to the whole family or to other species may be misleading.
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50
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Cho H, Ryu H, Rho S, Hill K, Smith S, Audenaert D, Park J, Han S, Beeckman T, Bennett MJ, Hwang D, De Smet I, Hwang I. A secreted peptide acts on BIN2-mediated phosphorylation of ARFs to potentiate auxin response during lateral root development. Nat Cell Biol 2013; 16:66-76. [DOI: 10.1038/ncb2893] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/11/2013] [Indexed: 01/01/2023]
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