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Huang Y, Yue E, Lian G, Lu J, Ran L, Ma S, Wang K, Bai Y, Han N, Bian H, Guo F. Novel mechanism of MicroRNA408 in callus formation from rice mature embryo. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39265046 DOI: 10.1111/tpj.17019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/14/2024]
Abstract
Mature embryos are the main explants of tissue culture used in rice transgenic technology. However, the mechanism of mature embryo callus formation remains unclear. In this study, a microRNA-mediated gene regulatory network of rice calli was established using degradome sequencing. We identified a microRNA, OsmiR408, that regulates the formation of the callus derived from the mature rice embryo. OsUCLACYANIN 30 (OsUCL 30), a target gene of OsmiR408, was the most abundant cleavage mRNA in rice callus. OsUCL17 was verified as a target gene of OsmiR408 using RNA ligase-mediated 5'-RACE. In analysis of the OsmiR408 promoter reporter line and pri-miR408 transcript level, the promoter activity and transcript level of MIR408 were increased dramatically during callus formation. In phenotypic observations, OsmiR408 knockout caused severe defects in mature embryo callus formation, whereas OsmiR408 overexpression promoted callus formation. Transcriptome analysis demonstrated that OsUCLs and certain genes related to the plant hormone signal transduction and phenylpropanoid-flavonoid biosynthesis pathway had different differential expression patterns between OsmiR408 knockout and overexpression calli. Thus, OsmiR408 may regulate callus formation mainly by affecting plant hormone signal transduction and phenylpropanoid-flavonoid biosynthesis pathway. Our findings provide insight into OsmiR408/UCLs module function in callus formation.
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Affiliation(s)
- Yizi Huang
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Erkui Yue
- Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Guiwei Lian
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinhan Lu
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Le Ran
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Shengyun Ma
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kaiqiang Wang
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Yu Bai
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hongwu Bian
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fu Guo
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Seed Industry Laboratory, Yazhou Bay Science and Technology City, Sanya, 572025, China
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Huang Y, Liu J, Cheng L, Xu D, Liu S, Hu H, Ling Y, Yang R, Zhang Y. Genome-Wide Analysis of the Histone Modification Gene ( HM) Family and Expression Investigation during Anther Development in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2496. [PMID: 39273980 PMCID: PMC11396841 DOI: 10.3390/plants13172496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
Histone modification plays a crucial role in chromatin remodeling and regulating gene expression, and participates in various biological processes, including plant development and responses to stress. Several gene families related to histone modification have been reported in various plant species. However, the identification of members and their functions in the rice (Oryza sativa L.) histone modification gene family (OsHM) at the whole-genome level remains unclear. In this study, a total of 130 OsHMs were identified through a genome-wide analysis. The OsHM gene family can be classified into 11 subfamilies based on a phylogenetic analysis. An analysis of the genes structures and conserved motifs indicates that members of each subfamily share specific conserved protein structures, suggesting their potential conserved functions. Molecular evolutionary analysis reveals that a significant number of OsHMs proteins originated from gene duplication events, particularly segmental duplications. Additionally, transcriptome analysis demonstrates that OsHMs are widely expressed in various tissues of rice and are responsive to multiple abiotic stresses. Fourteen OsHMs exhibit high expression in rice anthers and peaked at different pollen developmental stages. RT-qPCR results further elucidate the expression patterns of these 14 OsHMs during different developmental stages of anthers, highlighting their high expression during the meiosis and tetrad stages, as well as in the late stage of pollen development. Remarkably, OsSDG713 and OsSDG727 were further identified to be nucleus-localized. This study provides a fundamental framework for further exploring the gene functions of HMs in plants, particularly for researching their functions and potential applications in rice anthers' development and male sterility.
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Affiliation(s)
- Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jiawei Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Long Cheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Duo Xu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Sijia Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Hanqiao Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Rongchao Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
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3
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Wójcikowska B, Chwiałkowska K, Nowak K, Citerne S, Morończyk J, Wójcik AM, Kiwior-Wesołowska A, Francikowski J, Kwaśniewski M, Gaj MD. Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana. BMC Genomics 2024; 25:788. [PMID: 39148037 PMCID: PMC11325840 DOI: 10.1186/s12864-024-10623-5] [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: 01/18/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. RESULTS To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. CONCLUSION The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.
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Affiliation(s)
- Barbara Wójcikowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Sylvie Citerne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Joanna Morończyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Anna Maria Wójcik
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Agnieszka Kiwior-Wesołowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Jacek Francikowski
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Małgorzata Danuta Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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Li J, Zhang Q, Wang Z, Liu Q. The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions. PLANT PHYSIOLOGY 2024; 194:2022-2038. [PMID: 38290051 PMCID: PMC10980418 DOI: 10.1093/plphys/kiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.
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Affiliation(s)
- Jiawen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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5
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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6
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Pírek P, Kryštofová K, Kováčová I, Kromerová A, Zachová D, Helia O, Panzarová K, Fajkus J, Zdráhal Z, Lochmanová G, Fojtová M. Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors. PLANTS (BASEL, SWITZERLAND) 2023; 12:4177. [PMID: 38140504 PMCID: PMC10747063 DOI: 10.3390/plants12244177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings. Increased levels of the histone H3.3 variant were found to be the major and most prominent feature of 20-day calli, associated with chromatin relaxation. The methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate, and trichostatin A. Each HDACi affected the state of post-translational histone modifications in a specific manner; NaB-treated calli were epigenetically more similar to root-derived calli, and TSA-treated calli resembled shoot-derived calli.
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Affiliation(s)
- Pavlína Pírek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Karolína Kryštofová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Ingrid Kováčová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Anna Kromerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Ondřej Helia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Klára Panzarová
- PSI (Photon Systems Instruments), spol. s.r.o., 66424 Drásov, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
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Guo F, Wang H, Lian G, Cai G, Liu W, Zhang H, Li D, Zhou C, Han N, Zhu M, Su Y, Seo PJ, Xu L, Bian H. Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice. Commun Biol 2023; 6:457. [PMID: 37100819 PMCID: PMC10130139 DOI: 10.1038/s42003-023-04835-w] [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: 10/19/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pathway triggers cell division in the epidermis of the scutellum to form an embryo-like structure, which leads to callus formation. Our transcriptome data show that embryo-, stem cell-, and auxin-related genes are upregulated during scutellum-derived callus initiation. Among those genes, the embryo-specific gene OsLEC1 is activated by auxin and involved in scutellum-derived callus initiation. However, OsLEC1 is not required for vasculature-derived callus initiation from roots. In addition, OsIAA11 and OsCRL1, which are involved in root development, are required for vasculature-derived callus formation but not for scutellum-derived callus formation. Overall, our data indicate that scutellum-derived callus initiation is regulated by an embryo-like development program, and this is different from vasculature-derived callus initiation which borrows a root development program.
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Affiliation(s)
- Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guiwei Lian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Haidao Zhang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Chun Zhou
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Muyuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghua Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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8
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Song X, Xiong Y, Kong X, Huang G. Roles of auxin response factors in rice development and stress responses. PLANT, CELL & ENVIRONMENT 2023; 46:1075-1086. [PMID: 36397176 DOI: 10.1111/pce.14494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Auxin signalling plays a key role in various developmental processes ranging from embryogenesis to senescence in plants. Auxin response factor (ARF), a key component of auxin signalling, functions by binding to auxin response element within promoter of auxin response genes, activating or repressing the target genes. Increasing evidences show that ARFs are crucial for plant response to stresses. This review summarises the recent advance on the functions and their regulatory pathways of rice ARFs in development and responding to stresses. The importance of OsARFs is demonstrated by their roles in triggering various physiological, biochemical and molecular reactions to resist adverse environmental conditions. We also describe the transcriptional and post-transcriptional regulation of OsARFs, and discuss the major challenges in this area.
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Affiliation(s)
- Xiaoyun Song
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Xiong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuzhen Kong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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9
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Liu X, Zhu K, Xiao J. Recent advances in understanding of the epigenetic regulation of plant regeneration. ABIOTECH 2023; 4:31-46. [PMID: 37220541 PMCID: PMC10199984 DOI: 10.1007/s42994-022-00093-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/27/2022] [Indexed: 05/22/2023]
Abstract
Ever since the concept of "plant cell totipotency" was first proposed in the early twentieth century, plant regeneration has been a major focus of study. Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture. Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration. The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation. Here, we summarize how various aspects of epigenetic regulation, including histone modifications and variants, chromatin accessibility dynamics, DNA methylation, and microRNAs, modulate plant regeneration. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in boosting crop breeding, especially if coupled with emerging single-cell omics technologies.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
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Wei Z, Li Y, Ali F, Wang Y, Liu J, Yang Z, Wang Z, Xing Y, Li F. Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton. Cell Biosci 2022; 12:107. [PMID: 35831870 PMCID: PMC9277824 DOI: 10.1186/s13578-022-00840-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/28/2022] [Indexed: 12/04/2022] Open
Abstract
Background Histone deacetylation is one of the most important epigenetic modifications and plays diverse roles in plant development. However, the detailed functions and mechanisms of histone deacetylation in fiber development of cotton are still unclear. HDAC inhibitors (HDACi) have been commonly used to study the molecular mechanism underlying histone deacetylation or to facilitate disease therapy in humans through hindering the histone deacetylase catalytic activity. Trichostatin A (TSA)—the most widely used HDACi has been extensively employed to determine the role of histone deacetylation on different developmental stages of plants. Results Through in vitro culture of ovules, we observed that exogenous application of TSA was able to inhibit the fiber initiation development. Subsequently, we performed a transcriptomic analysis to reveal the underlying mechanisms. The data showed that TSA treatment resulted in 4209 differentially expressed genes, which were mostly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, and carbon metabolism pathways. The phytohormone signal transduction pathways harbor the most differentially expressed genes. Deeper studies showed that some genes promoting auxin, Gibberellic Acid (GA) signaling were down-regulated, while some genes facilitating Abscisic Acid (ABA) and inhibiting Jasmonic Acid (JA) signaling were up-regulated after the TSA treatments. Further analysis of plant hormone contents proved that TSA significantly promoted the accumulation of ABA, JA and GA3. Conclusions Collectively, histone deacetylation can regulate some key genes involved in different phytohormone pathways, and consequently promoting the auxin, GA, and JA signaling, whereas repressing the ABA synthesis and signaling to improve the fiber cell initiation. Moreover, the genes associated with energy metabolism, phenylpropanoid, and glutathione metabolism were also regulated by histone deacetylation. The above results provided novel clues to illuminate the underlying mechanisms of epigenetic modifications as well as related different phytohormones in fiber cell differentiation, which is also very valuable for the molecular breeding of higher quality cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00840-4.
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Xu Y, Miao Y, Cai B, Yi Q, Tian X, Wang Q, Ma D, Luo Q, Tan F, Hu Y. A histone deacetylase inhibitor enhances rice immunity by derepressing the expression of defense-related genes. FRONTIERS IN PLANT SCIENCE 2022; 13:1041095. [PMID: 36407628 PMCID: PMC9667192 DOI: 10.3389/fpls.2022.1041095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Histone deacetylase (HDAC) inhibitors (HDACis) have been widely used in plants to investigate the role of histone acetylation, particularly the function of HDACs, in the regulation of development and stress response. However, how histone acetylation is involved in rice (Oryza sativa L.) disease resistance has hardly been studied. In this paper, four HDACis including Sodium butyrate (NaBT), Suberoylanilide Hydroxamic Acid (SAHA), LBH-589 and Trichostatin A (TSA) were used to treat rice seedlings at different concentrations before inoculation of Magnaporthe oryzae. We found that only 10mM NaBT treatment can significantly enhanced rice blast resistance. However, treatment of the four HDACis all increased global histone acetylation but at different sites, suggesting that the inhibition selectivity of these HDACis is different. Notably, the global H3K9ac level was dramatically elevated after both NaBT and LBH589 treatment although LBH589 could not enhance rice blast resistance. This indicates that the HDACs they inhibit target different genes. In accordance with the phenotype, transcriptomic analysis showed that many defense-related genes were up-regulated by NaBT treatment. Up-regulation of the four genes bsr-d1, PR10B, OsNAC4, OsKS4 were confirmed by RT-qPCR. ChIP-qPCR results revealed that H3K9ac level on these genes was increased after NaBT treatment, suggesting that these defense-related genes were repressed by HDACs. In addition, by promoter motif analysis of the genes that induced by both NaBT treatment and rice blast infection, we found that the motifs bound by ERF and AHL transcription factors (TFs) were the most abundant, which demonstrates that ERF and AHL proteins may act as the candidate TFs that recruit HDACs to defense-related genes to repress their expression when plants are not infected by rice blast.
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Affiliation(s)
- Yan Xu
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Yuanxin Miao
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Botao Cai
- Center for Science Popularization Jingmen, Science and Technology Museum, Jingmen, China
| | - Qingping Yi
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Xuejun Tian
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Qihai Wang
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Dan Ma
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Feng Tan
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, China
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Guo F, Zhang P, Wu Y, Lian G, Yang Z, Liu W, Buerte B, Zhou C, Zhang W, Li D, Han N, Tong Z, Zhu M, Xu L, Chen M, Bian H. Rice LEAFY COTYLEDON1 Hinders Embryo Greening During the Seed Development. FRONTIERS IN PLANT SCIENCE 2022; 13:887980. [PMID: 35620685 PMCID: PMC9128838 DOI: 10.3389/fpls.2022.887980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
LEAFY COTYLEDON1 (LEC1) is the central regulator of seed development in Arabidopsis, while its function in monocots is largely elusive. We generated Oslec1 mutants using CRISPR/Cas9 technology. Oslec1 mutant seeds lost desiccation tolerance and triggered embryo greening at the early development stage. Transcriptome analysis demonstrated that Oslec1 mutation altered diverse hormonal pathways and stress response in seed maturation, and promoted a series of photosynthesis-related genes. Further, genome-wide identification of OsLEC1-binding sites demonstrated that OsLEC1 bound to genes involved in photosynthesis, photomorphogenesis, as well as abscisic acid (ABA) and gibberellin (GA) pathways, involved in seed maturation. We illustrated an OsLEC1-regulating gene network during seed development, including the interconnection between photosynthesis and ABA/GA biosynthesis/signaling. Our findings suggested that OsLEC1 acts as not only a central regulator of seed maturation but also an inhibitor of embryo greening during rice seed development. This study would provide new understanding for the OsLEC1 regulatory mechanisms on photosynthesis in the monocot seed development.
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Affiliation(s)
- Fu Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Peijing Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Centre, Hangzhou, China
| | - Yan Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guiwei Lian
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhengfei Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - B. Buerte
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chun Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wenqian Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Ning Han
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, China
| | - Muyuan Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hongwu Bian
- College of Life Sciences, Zhejiang University, Hangzhou, China
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Morończyk J, Brąszewska A, Wójcikowska B, Chwiałkowska K, Nowak K, Wójcik AM, Kwaśniewski M, Gaj MD. Insights into the Histone Acetylation-Mediated Regulation of the Transcription Factor Genes That Control the Embryogenic Transition in the Somatic Cells of Arabidopsis. Cells 2022; 11:863. [PMID: 35269485 PMCID: PMC8909028 DOI: 10.3390/cells11050863] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Somatic embryogenesis (SE), which is a process that involves the in vitro-induced embryogenic reprogramming of plant somatic cells, requires dynamic changes in the cell transcriptome. These changes are fine-tuned by many genetic and epigenetic factors, including posttranslational histone modifications such as histone acetylation. Antagonistically acting enzymes, histone acetyltransferases (HATs) and deacetylases (HDACs), which control histone acetylation in many developmental processes, are believed to control SE. However, the function of specific HAT/HDACs and the genes that are subjected to histone acetylation-mediated regulation during SE have yet to be revealed. Here, we present the global and gene-specific changes in histone acetylation in Arabidopsis explants that are undergoing SE. In the TSA (trichostatin A)-induced SE, we demonstrate that H3 and H4 acetylation might control the expression of the critical transcription factor (TF) genes of a vital role in SE, including LEC1, LEC2 (LEAFY COTYLEDON 1; 2), FUS3 (FUSCA 3) and MYB118 (MYB DOMAIN PROTEIN 118). Within the HATs and HDACs, which mainly positively regulate SE, we identified HDA19 as negatively affecting SE by regulating LEC1, LEC2 and BBM. Finally, we provide some evidence on the role of HDA19 in the histone acetylation-mediated regulation of LEC2 during SE. Our results reveal an essential function of histone acetylation in the epigenetic mechanisms that control the TF genes that play critical roles in the embryogenic reprogramming of plant somatic cells. The results implicate the complexity of Hac-related gene regulation in embryogenic induction and point to differences in the regulatory mechanisms that are involved in auxin- and TSA-induced SE.
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Affiliation(s)
- Joanna Morończyk
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland; (J.M.); (A.B.); (B.W.); (K.N.); (A.M.W.)
| | - Agnieszka Brąszewska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland; (J.M.); (A.B.); (B.W.); (K.N.); (A.M.W.)
| | - Barbara Wójcikowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland; (J.M.); (A.B.); (B.W.); (K.N.); (A.M.W.)
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-269 Bialystok, Poland; (K.C.); (M.K.)
| | - Katarzyna Nowak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland; (J.M.); (A.B.); (B.W.); (K.N.); (A.M.W.)
| | - Anna M. Wójcik
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland; (J.M.); (A.B.); (B.W.); (K.N.); (A.M.W.)
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-269 Bialystok, Poland; (K.C.); (M.K.)
| | - Małgorzata D. Gaj
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland; (J.M.); (A.B.); (B.W.); (K.N.); (A.M.W.)
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Zhang Y, Yang X, Nvsvrot T, Huang L, Cai G, Ding Y, Ren W, Wang N. The transcription factor WRKY75 regulates the development of adventitious roots, lateral buds and callus by modulating hydrogen peroxide content in poplar. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1483-1498. [PMID: 34791155 DOI: 10.1093/jxb/erab501] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Hydrogen peroxide (H2O2) plays important roles in plant development. Adventitious roots (AR), lateral buds (LB) and callus formation are important traits for plants. Here, a gene encoding RESPIRATORY BURST OXIDASE HOMOLOG B (PdeRBOHB) from poplar line 'NL895' (Populus. deltoides × P. euramericana) was predicted to be involved in H2O2 accumulation, and lines with reduced expression were generated. H2O2 content was decreased, and the development of adventitious roots, lateral buds, and callus was inhibited in reduced expression PdeRBOHB lines. A gene encoding PdeWRKY75 was identified as the upstream transcription factor positively regulating PdeRBOHB. This regulation was confirmed by dual luciferase reporter assay, GUS transient expression analysis and electrophoretic mobility shift assay. In the reduced expression PdeWRKY75 lines, H2O2 content was decreased and the development of adventitious roots, lateral buds, and callus development was inhibited, while in the overexpression lines, H2O2 content was increased and the development of adventitious roots and lateral buds was inhibited, but callus formation was enhanced. Additionally, reduced expression PdeRBOHB lines showed lowered expression of PdeWRKY75, while exogenous application of H2O2 showed the opposite effect. Together, these results suggest that PdeWRKY75 and PdeRBOHB are part of a regulatory module in H2O2 accumulation, which is involved in the regulation of multiple biological processes.
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Affiliation(s)
- Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqing Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tashbek Nvsvrot
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liyu Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanghua Cai
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiwei Ding
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenyu Ren
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
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15
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Sai CB, Chidambaranathan P, Samantaray S. Role of histone deacetylase inhibitors in androgenic callus induction of Oryza sativa sub indica, in sight into evolution and mode of action of histone deacetylase genes. Mol Biol Rep 2022; 49:2169-2183. [PMID: 34985645 DOI: 10.1007/s11033-021-07036-y] [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: 06/25/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The potential of paddy breeding has reached its pinnacle, and hybrids have been the principal research outcome. Hence, our hypothesis was based on improvising the callus induction efficiency of recalcitrant Oryza sativa sub. indica hybrids by intervening into their cellular functions like cell division and histone regulation for the production of doubled haploids, a better output compared to hybrids. METHODOLOGY AND RESULTS Insight into the mechanism of cell division is the foremost concern in altering the same and hence studies on evolution, expression and action of histone deacetylase and its 12 genes (9 HDA and 3 HD-tunin genes) were chosen in the hypothesis. Expression of HDA genes at three stages (anther dehiscence, 1st callusing and second callusing stages) with inhibitor (trichostatin-A) interventions indicated 1st callusing stage as the most important in influencing callus induction and also the genes HDA19, 6, 15 and 5 were the most important. TSA alone had a significant impact on the regulation of the genes HDT 702, HDA19, HDA9, and HDA6. Higher expression of HDA19 and HDA6 was involved in maximizing callus induction; HDA15 had an antagonistic expression compared to HDA19/6 and might be involved in chlorophyll regulation during regeneration. Results of evolutionary analysis on histone deacetylases indicated a long and single lineage of origin denoting its importance in the basic cellular functions. The tubulin deacetylation gene HDA5, which was exclusively found in dicotyledons, had a recent evolutionary history only from terrestrial plants, and also had significant conservation in its motifs and NLS region. CONCLUSION By combating the recalcitrant nature of Indica cultivars, molecular editing on a combination of HDA genes will enhance the callus induction and regeneration efficiency of the next generation of doubled haploids, therby improving the total yield.
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Affiliation(s)
- Cayalvizhi B Sai
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India.
| | - Parameswaran Chidambaranathan
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India
| | - Sangamitra Samantaray
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India
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Kumar V, Thakur JK, Prasad M. Histone acetylation dynamics regulating plant development and stress responses. Cell Mol Life Sci 2021; 78:4467-4486. [PMID: 33638653 PMCID: PMC11072255 DOI: 10.1007/s00018-021-03794-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022]
Abstract
Crop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Suo J, Zhou C, Zeng Z, Li X, Bian H, Wang J, Zhu M, Han N. Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis. BMC PLANT BIOLOGY 2021; 21:145. [PMID: 33740900 PMCID: PMC7980361 DOI: 10.1186/s12870-021-02922-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/08/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Barley is known to be recalcitrant to tissue culture, which hinders genetic transformation and its biotechnological application. To date, the ideal explant for transformation remains limited to immature embryos; the mechanism underlying embryonic callus formation is elusive. RESULTS This study aimed to uncover the different transcription regulation pathways between calli formed from immature (IME) and mature (ME) embryos through transcriptome sequencing. We showed that incubation of embryos in an auxin-rich medium caused dramatic changes in gene expression profiles within 48 h. Overall, 9330 and 11,318 differentially expressed genes (DEGs) were found in the IME and ME systems, respectively. 3880 DEGs were found to be specific to IME_0h/IME_48h, and protein phosphorylation, regulation of transcription, and oxidative-reduction processes were the most common gene ontology categories of this group. Twenty-three IAA, fourteen ARF, eight SAUR, three YUC, and four PIN genes were found to be differentially expressed during callus formation. The effect of callus-inducing medium (CIM) on IAA genes was broader in the IME system than in the ME system, indicating that auxin response participates in regulating cell reprogramming during callus formation. BBM, LEC1, and PLT2 exhibited a significant increase in expression levels in the IME system but were not activated in the ME system. WUS showed a more substantial growth trend in the IME system than in the ME system, suggesting that these embryonic, shoot, and root meristem genes play crucial roles in determining the acquisition of competency. Moreover, epigenetic regulators, including SUVH3A, SUVH2A, and HDA19B/703, exhibited differential expression patterns between the two induction systems, indicating that epigenetic reprogramming might contribute to gene expression activation/suppression in this process. Furthermore, we examined the effect of ectopic expression of HvBBM and HvWUS on Agrobacterium-mediated barley transformation. The transformation efficiency in the group expressing the PLTPpro:HvBBM + Axig1pro:HvWUS construct was increased by three times that in the control (empty vector) because of enhanced plant regeneration capacity. CONCLUSIONS We identified some regulatory factors that might contribute to the differential responses of the two explants to callus induction and provide a promising strategy to improve transformation efficiency in barley.
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Affiliation(s)
- Jingqi Suo
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
| | - Chenlu Zhou
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
| | - Zhanghui Zeng
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
| | - Xipu Li
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
| | - Hongwu Bian
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
| | - Junhui Wang
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
| | - Muyuan Zhu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
| | - Ning Han
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, 310058 Hangzhou China
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