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Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24:ijms24033025. [PMID: 36769343 PMCID: PMC9918255 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
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Pons C, Casals J, Palombieri S, Fontanet L, Riccini A, Rambla JL, Ruggiero A, Figás MDR, Plazas M, Koukounaras A, Picarella ME, Sulli M, Fisher J, Ziarsolo P, Blanca J, Cañizares J, Cammareri M, Vitiello A, Batelli G, Kanellis A, Brouwer M, Finkers R, Nikoloudis K, Soler S, Giuliano G, Grillo S, Grandillo S, Zamir D, Mazzucato A, Causse M, Díez MJ, Prohens J, Monforte AJ, Granell A. Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato. HORTICULTURE RESEARCH 2022; 9:uhac112. [PMID: 35795386 PMCID: PMC9252105 DOI: 10.1093/hr/uhac112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.
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Affiliation(s)
- Clara Pons
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Joan Casals
- Department of Agri-Food Engineering and Biotechnology/Miquel Agustí Foundation, Universitat Politècnica de Catalunya, Campus Baix Llobregat, Esteve Terrades 8, 08860 Castelldefels, Spain
| | - Samuela Palombieri
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy
| | - Lilian Fontanet
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allé des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
- HM Clause, Portes-lès-Valence, France
| | - Alessandro Riccini
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Jose Luis Rambla
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Alessandra Ruggiero
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Maria del Rosario Figás
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Athanasios Koukounaras
- Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Vegetable Crops, Thessaloniki, 54124 Greece
| | - Maurizio E Picarella
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Josef Fisher
- Hebrew University of Jerusalem, Robert H Smith Inst Plant Sci & Genet Agr, Rehovot, Israel
| | - Peio Ziarsolo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Jose Blanca
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Joaquin Cañizares
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Maria Cammareri
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Antonella Vitiello
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Giorgia Batelli
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Angelos Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Matthijs Brouwer
- Wageningen Univ & Res, Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands
| | - Richard Finkers
- Wageningen Univ & Res, Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands
| | | | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Stephania Grillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Silvana Grandillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Dani Zamir
- Hebrew University of Jerusalem, Robert H Smith Inst Plant Sci & Genet Agr, Rehovot, Israel
| | - Andrea Mazzucato
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Mathilde Causse
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allé des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Maria José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Antonio Jose Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
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Wang S, Yan J, Hu B, Wang R, Xu J. Advanced epigenomic engineering in crop quality improvement. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Li X, Wang X, Zhang Y, Zhang A, You CX. Regulation of fleshy fruit ripening: From transcription factors to epigenetic modifications. HORTICULTURE RESEARCH 2022; 9:uhac013. [PMID: 35147185 PMCID: PMC9035223 DOI: 10.1093/hr/uhac013] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/01/2021] [Indexed: 05/24/2023]
Abstract
Fleshy fruits undergo a complex ripening process, developing organoleptic fruit traits that attract herbivores and maximize seed dispersal. Ripening is the terminal stage of fruit development and involves a series of physiological and biochemical changes. In fleshy fruits, ripening always involves a drastic color change triggered by the accumulation of pigments and degradation of chlorophyll, softening caused by cell wall remodeling, and flavor formation as acids and sugars accumulate alongside volatile compounds. The mechanisms underlying fruit ripening rely on the orchestration of ripening-related transcription factors, plant hormones, and epigenetic modifications. In this review, we discuss current knowledge of the transcription factors that regulate ripening in conjunction with ethylene and environmental signals (light and temperature) in the model plant tomato (Solanum lycopersicum) and other fleshy fruits. We emphasize the critical roles of epigenetic regulation, including DNA methylation and histone modification as well as RNA m6A modification, which has been studied intensively. This detailed review was compiled to provide a comprehensive description of the regulatory mechanisms of fruit ripening and guide new strategies for its effective manipulation.
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Affiliation(s)
- Xiuming Li
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xuemei Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai-An, 271018, China
| | - Aihong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai-An, 271018, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
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Wen YX, Wang JY, Zhu HH, Han GH, Huang RN, Huang L, Hong YG, Zheng SJ, Yang JL, Chen WW. Potential Role of Domains Rearranged Methyltransferase7 in Starch and Chlorophyll Metabolism to Regulate Leaf Senescence in Tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:836015. [PMID: 35211145 PMCID: PMC8860812 DOI: 10.3389/fpls.2022.836015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Deoxyribonucleic acid (DNA) methylation is an important epigenetic mark involved in diverse biological processes. Here, we report the critical function of tomato (Solanum lycopersicum) Domains Rearranged Methyltransferase7 (SlDRM7) in plant growth and development, especially in leaf interveinal chlorosis and senescence. Using a hairpin RNA-mediated RNA interference (RNAi), we generated SlDRM7-RNAi lines and observed pleiotropic developmental defects including small and interveinal chlorosis leaves. Combined analyses of whole genome bisulfite sequence (WGBS) and RNA-seq revealed that silencing of SlDRM7 caused alterations in both methylation levels and transcript levels of 289 genes, which are involved in chlorophyll synthesis, photosynthesis, and starch degradation. Furthermore, the photosynthetic capacity decreased in SlDRM7-RNAi lines, consistent with the reduced chlorophyll content and repression of genes involved in chlorophyll biosynthesis, photosystem, and photosynthesis. In contrast, starch granules were highly accumulated in chloroplasts of SlDRM7-RNAi lines and associated with lowered expression of genes in the starch degradation pathway. In addition, SlDRM7 was activated by aging- and dark-induced senescence. Collectively, these results demonstrate that SlDRM7 acts as an epi-regulator to modulate the expression of genes related to starch and chlorophyll metabolism, thereby affecting leaf chlorosis and senescence in tomatoes.
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Affiliation(s)
- Yu Xin Wen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jia Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hui Hui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guang Hao Han
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ru Nan Huang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Yi Guo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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6
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Zhu F, Wen W, Cheng Y, Fernie AR. The metabolic changes that effect fruit quality during tomato fruit ripening. MOLECULAR HORTICULTURE 2022; 2:2. [PMID: 37789428 PMCID: PMC10515270 DOI: 10.1186/s43897-022-00024-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/12/2022] [Indexed: 10/05/2023]
Abstract
As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany.
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7
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Li S, Chen K, Grierson D. Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening. Cells 2021; 10:1136. [PMID: 34066675 PMCID: PMC8151651 DOI: 10.3390/cells10051136] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.
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Affiliation(s)
- Shan Li
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Donald Grierson
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
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Tang D, Gallusci P, Lang Z. Fruit development and epigenetic modifications. THE NEW PHYTOLOGIST 2020; 228:839-844. [PMID: 32506476 DOI: 10.1111/nph.16724] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/01/2020] [Indexed: 05/26/2023]
Abstract
Fruit development is a complex process that is regulated not only by plant hormones and transcription factors, but also requires epigenetic modifications. Epigenetic modifications include DNA methylation, histone post-translational modifications, chromatin remodeling and noncoding RNAs. Together, these epigenetic modifications, which are controlled during development and in response to the environment, determine the chromatin state of genes and contribute to the transcriptomes of an organism. Recent studies have demonstrated that epigenetic regulation plays an important role in fleshy fruit ripening. Dysfunction of a DNA demethylase delayed ripening in tomato, and the application of a DNA methylation inhibitor altered ripening process in the fruits of several species. These studies indicated that manipulating the epigenome of fruit crops could open new ways for breeding in the future. In this review, we highlight recent progress and address remaining questions and challenges concerning the epigenetic regulation of fruit development and ripening.
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Affiliation(s)
- Dengguo Tang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Philippe Gallusci
- Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRAE, Bordeaux Science Agro, Villenave d'Ormon, 33140, France
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Vachon G, Engelhorn J, Carles CC. Interactions between transcription factors and chromatin regulators in the control of flower development. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2461-2471. [PMID: 29506187 DOI: 10.1093/jxb/ery079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/22/2018] [Indexed: 06/08/2023]
Abstract
Chromatin modifiers and remodelers are involved in generating dynamic changes at the chromatin, which allow differential and specific readouts of the genome. While genetic evidence indicates that several chromatin factors play a key role in controlling basic developmental programs for inflorescence and flower morphogenesis, it remained unknown until recently how they exert their specificity toward gene expression, both temporally and spatially. An emerging topic is the recruitment or eviction of chromatin factors through the activity of sequence-specific DNA-binding domains, present in the chromatin factors themselves or in partnering transcription factors. Here we summarize recent progress that has been made in this regard in the model plant Arabidopsis thaliana. We further outline the different possible modes through which chromatin complexes specifically target genes involved in flower development.
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Affiliation(s)
- Gilles Vachon
- LPCV, CNRS, CEA, INRA, Université Grenoble Alpes, BIG, Grenoble, France
| | - Julia Engelhorn
- LPCV, CNRS, CEA, INRA, Université Grenoble Alpes, BIG, Grenoble, France
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Gallusci P, Dai Z, Génard M, Gauffretau A, Leblanc-Fournier N, Richard-Molard C, Vile D, Brunel-Muguet S. Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues. TRENDS IN PLANT SCIENCE 2017; 22:610-623. [PMID: 28587758 DOI: 10.1016/j.tplants.2017.04.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/12/2017] [Accepted: 04/28/2017] [Indexed: 05/21/2023]
Abstract
Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits.
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Affiliation(s)
- Philippe Gallusci
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | | | - Arnaud Gauffretau
- UMR Agronomie, AgroParisTech, INRA, 78850, Thiverval-Grignon, France
| | | | - Céline Richard-Molard
- UMR ECOSYS, INRA AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Denis Vile
- LEPSE, INRA-SupAgro, 34060, Montpellier, France
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Farinati S, Rasori A, Varotto S, Bonghi C. Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective. FRONTIERS IN PLANT SCIENCE 2017; 8:1247. [PMID: 28769956 PMCID: PMC5511831 DOI: 10.3389/fpls.2017.01247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/30/2017] [Indexed: 05/06/2023]
Abstract
Rosaceae is a family with an extraordinary spectrum of fruit types, including fleshy peach, apple, and strawberry that provide unique contributions to a healthy diet for consumers, and represent an excellent model for studying fruit patterning and development. In recent years, many efforts have been made to unravel regulatory mechanism underlying the hormonal, transcriptomic, proteomic and metabolomic changes occurring during Rosaceae fruit development. More recently, several studies on fleshy (tomato) and dry (Arabidopsis) fruit model have contributed to a better understanding of epigenetic mechanisms underlying important heritable crop traits, such as ripening and stress response. In this context and summing up the results obtained so far, this review aims to collect the available information on epigenetic mechanisms that may provide an additional level in gene transcription regulation, thus influencing and driving the entire Rosaceae fruit developmental process. The whole body of information suggests that Rosaceae fruit could become also a model for studying the epigenetic basis of economically important phenotypes, allowing for their more efficient exploitation in plant breeding.
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Affiliation(s)
- Silvia Farinati
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
| | - Angela Rasori
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
| | - Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura e Enologia, University of PadovaConegliano, Italy
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova AgripolisLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura e Enologia, University of PadovaConegliano, Italy
- *Correspondence: Claudio Bonghi,
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12
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Liu DD, Zhou LJ, Fang MJ, Dong QL, An XH, You CX, Hao YJ. Polycomb-group protein SlMSI1 represses the expression of fruit-ripening genes to prolong shelf life in tomato. Sci Rep 2016; 6:31806. [PMID: 27558543 PMCID: PMC4997261 DOI: 10.1038/srep31806] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/26/2016] [Indexed: 12/18/2022] Open
Abstract
Polycomb-group (PcG) protein MULTICOPY SUPPRESSOR OF IRA1 (MSI1) protein is an evolutionarily conserved developmental suppressor and plays a crucial role in regulating epigenetic modulations. However, the potential role and function of MSI1 in fleshy fruits remain unknown. In this study, SlMSI1 was cloned and transformed into tomato to explore its function. The quantitative real-time PCR results showed that SlMSI1 was highly expressed in flowers and fruits and that its transcript and protein levels were significantly decreased in fruits after the breaker stage. Additionally, SlMSI1-overexpressing transgenic tomatoes displayed abnormal non-ripening fruit formation, whereas its suppression promoted fruit ripening in transgenic tomatoes. Quantitative real-time PCR assays also showed that RIN and its regulons were decreased in SlMSI1 overexpression transgenic tomato fruits. Furthermore, RNA-seq analysis demonstrated that SlMSI1 inhibits fruit ripening by negatively regulating a large set of fruit-ripening genes in addition to RIN and its regulons. Finally, genetic manipulation of SlMSI1 and RIN successfully prolonged the fruit shelf life by regulating the fruit-ripening genes in tomato. Our findings reveal a novel regulatory function of SlMSI1 in fruit ripening and provide a new regulator that may be useful for genetic engineering and modification of fruit shelf life.
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Affiliation(s)
- Dan-Dan Liu
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Agriculture, Yunnan University, Kunming, Yunnan 650091, China
| | - Li-Jie Zhou
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Mou-Jing Fang
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Qing-Long Dong
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xiu-Hong An
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
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Berthelot K, Estevez Y, Quiliano M, Baldera-Aguayo PA, Zimic M, Pribat A, Bakleh ME, Teyssier E, Gallusci P, Gardrat C, Lecomte S, Peruch F. HbIDI, SlIDI and EcIDI: A comparative study of isopentenyl diphosphate isomerase activity and structure. Biochimie 2016; 127:133-43. [PMID: 27163845 DOI: 10.1016/j.biochi.2016.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
In this study, we cloned, expressed and purified the isopentenyl diphosphate isomerases (IDIs) from two plants, Hevea brasiliensis and Solanum lycopersicum, and compared them to the already well characterized Escherichia coli IDI. Phylogenetic analysis showed high homology between the three enzymes. Their catalytic activity was investigated in vitro with recombinant purified enzymes and in vivo by complementation colorimetric tests. The three enzymes displayed consistent activities both in vitro and in vivo. In term of structure, studied by ATR-FTIR and molecular modeling, it is clear that both plant enzymes are more related to their human homologue than to E. coli IDI. But it is assumed that EcIDI represent the minimalistic part of the catalytic core, as both plant enzymes present a supplementary sequence forming an extra α-helice surrounding the catalytic site that could facilitate the biocatalysis. New potential biotechnological applications may be envisaged.
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Affiliation(s)
- Karine Berthelot
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France; CNRS, CBMN, UMR 5248, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France.
| | - Yannick Estevez
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Miguel Quiliano
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia y Nutrición, Universidad de Navarra, C/. Irunlarrea 1, 31008, Pamplona, Navarra, Spain
| | - Pedro A Baldera-Aguayo
- Department of Systems Biology and Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University in the City of New York, NY, 10032, USA; Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, 31, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, 31, Peru
| | - Anne Pribat
- INRA Bordeaux-Aquitaine, UMR 1332 Biologie du Fruit et Pathologie, F-33882, Villenave d'Ornon, France
| | - Marc-Elias Bakleh
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Emeline Teyssier
- Univ. Bordeaux, Grape Ecophysiology and Functional Biology Laboratory, ISVV, F-33882, Villenave d'Ornon, France
| | - Philippe Gallusci
- Univ. Bordeaux, Grape Ecophysiology and Functional Biology Laboratory, ISVV, F-33882, Villenave d'Ornon, France
| | - Christian Gardrat
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Sophie Lecomte
- CNRS, CBMN, UMR 5248, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Frédéric Peruch
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France.
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14
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Boureau L, How-Kit A, Teyssier E, Drevensek S, Rainieri M, Joubès J, Stammitti L, Pribat A, Bowler C, Hong Y, Gallusci P. A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants. PLANT MOLECULAR BIOLOGY 2016; 90:485-501. [PMID: 26846417 DOI: 10.1007/s11103-016-0436-0] [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: 05/21/2015] [Accepted: 01/08/2016] [Indexed: 05/21/2023]
Abstract
The Enhancer of Zeste Polycomb group proteins, which are encoded by a small gene family in Arabidopsis thaliana, participate to the control of plant development. In the tomato (Solanum lycopersicum), these proteins are encoded by three genes (SlEZ1, SlEZ2 and SlEZ3) that display specific expression profiles. Using a gene specific RNAi strategy, we demonstrate that repression of SlEZ2 correlates with a general reduction of H3K27me3 levels, indicating that SlEZ2 is part of an active PRC2 complex. Reduction of SlEZ2 gene expression impacts the vegetative development of tomato plants, consistent with SlEZ2 having retained at least some of the functions of the Arabidopsis CURLY LEAF (CLF) protein. Notwithstanding, we observed significant differences between transgenic SlEZ2 RNAi tomato plants and Arabidopsis clf mutants. First, we found that reduced SlEZ2 expression has dramatic effects on tomato fruit development and ripening, functions not described in Arabidopsis for the CLF protein. In addition, repression of SlEZ2 has no significant effect on the flowering time or the control of flower organ identity, in contrast to the Arabidopsis clf mutation. Taken together, our results are consistent with a diversification of the function of CLF orthologues in plants, and indicate that although partly conserved amongst plants, the function of EZ proteins need to be newly investigated for non-model plants because they might have been recruited to specific developmental processes.
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Affiliation(s)
- L Boureau
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Laboratory of Hematology, Centre Hospitalier Universitaire de Bordeaux - Hopital Haut Leveque, 5 Avenue Magellan, 33600, Pessac, France
| | - A How-Kit
- Laboratory for Functional Genomics, Foundation Jean Dausset - CEPH, 75010, Paris, France
| | - E Teyssier
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France
| | - S Drevensek
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, Université, Paris-Sud, Université d'Evry, Université Paris-Diderot, Bâtiment 630, 91405, Orsay, France
| | - M Rainieri
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
| | - J Joubès
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Bâtiment A3, INRA, 71 Avenue Edouard Bourlaux, 33140, Villenave d'Ornon, France
- Laboratoire de Biogenèse Membranaire, UMR5200, CNRS, Bâtiment A3, INRA, 71 Avenue Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - L Stammitti
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France
| | - A Pribat
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
| | - C Bowler
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
| | - Y Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.
| | - P Gallusci
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France.
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France.
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15
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Gallusci P, Hodgman C, Teyssier E, Seymour GB. DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:807. [PMID: 27379113 PMCID: PMC4905957 DOI: 10.3389/fpls.2016.00807] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/23/2016] [Indexed: 05/19/2023]
Abstract
Fruit ripening is a developmental process that results in the leaf-like carpel organ of the flower becoming a mature ovary primed for dispersal of the seeds. Ripening in fleshy fruits involves a profound metabolic phase change that is under strict hormonal and genetic control. This work reviews recent developments in our understanding of the epigenetic regulation of fruit ripening. We start by describing the current state of the art about processes involved in histone post-translational modifications and the remodeling of chromatin structure and their impact on fruit development and ripening. However, the focus of the review is the consequences of changes in DNA methylation levels on the expression of ripening-related genes. This includes those changes that result in heritable phenotypic variation in the absence of DNA sequence alterations, and the mechanisms for their initiation and maintenance. The majority of the studies described in the literature involve work on tomato, but evidence is emerging that ripening in other fruit species may also be under epigenetic control. We discuss how epigenetic differences may provide new targets for breeding and crop improvement.
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Affiliation(s)
- Philippe Gallusci
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d’Ornon, France
- *Correspondence: Philippe Gallusci,
| | - Charlie Hodgman
- School of Biosciences, University of Nottingham Sutton Bonington, UK
| | - Emeline Teyssier
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d’Ornon, France
| | - Graham B. Seymour
- School of Biosciences, University of Nottingham Sutton Bonington, UK
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16
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Liu DD, Dong QL, Fang MJ, Chen KQ, Hao YJ. Ectopic expression of an apple apomixis-related gene MhFIE induces co-suppression and results in abnormal vegetative and reproductive development in tomato. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:1866-73. [PMID: 23000466 DOI: 10.1016/j.jplph.2012.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 05/10/2023]
Abstract
It has been well documented that FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) plays important regulatory roles in diverse developmental processes in model plant Arabidopsis thaliana. However, it is largely unknown how FIE genes function in economically important crops. In this study, MhFIE gene, which was previously isolated from apomictic tea crabapple (Malus hupehensis Redh. var. pingyiensis), was introduced into tomato. The hemizygous transgenic tomato lines produced curly leaves and decreased in seed germination. In addition, the co-suppression of the transgenic MhFIE and endogenous (SlFIE) genes occurred in homozygous transgenic tomatoes. As a result, FIE silencing brought about abnormal phenotypes during reproductive development in tomato, such as increased sepal and petal numbers in flower, a fused ovule and pistil and parthenocarpic fruit formation. A yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC) demonstrated that MhFIE interacted with a tomato protein, EZ2 (SlEZ2). Its ectopic expression and SlFIE co-suppression notably influenced the expression of genes associated with leaf, flower, and fruit development. Therefore, together with other PcG proteins, FIE was involved in the regulation of vegetative and reproductive development by modulating the expression of related genes in plants.
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Affiliation(s)
- Dan-Dan Liu
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
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17
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Almada R, Cabrera N, Casaretto JA, Peña-Cortés H, Ruiz-Lara S, González Villanueva E. Epigenetic repressor-like genes are differentially regulated during grapevine (Vitis vinifera L.) development. PLANT CELL REPORTS 2011; 30:1959-1968. [PMID: 21681473 DOI: 10.1007/s00299-011-1104-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/18/2011] [Accepted: 06/02/2011] [Indexed: 05/28/2023]
Abstract
Grapevine sexual reproduction involves a seasonal separation between inflorescence primordia (flowering induction) and flower development. We hypothesized that a repression mechanism implicating epigenetic changes could play a role in the seasonal separation of these two developmental processes in grapevine. Therefore, the expression of five grapevine genes with homology to the Arabidopsis epigenetic repressor genes FERTILIZATION INDEPENDENT ENDOSPERM (FIE), EMBRYONIC FLOWER 2 (EMF2), CURLY LEAF (CLF), MULTICOPY SUPPRESSOR OF IRA 1 (MSI1) and SWINGER (SWN) was analyzed during the development of buds and vegetative and reproductive organs. During bud development, the putative grapevine epigenetic repressor genes VvCLF, VvEMF2, VvMSI1, VvSWN and VvFIE are mainly expressed in latent buds at the flowering induction period, but also detected during bud burst and inflorescence/flower development. The overlapping expression patterns of grapevine PcG-like genes in buds suggest that chromatin remodeling mechanisms could be operating during grapevine bud development for controlling processes such as seasonal flowering, dormancy and bud burst. Furthermore, the expression of grapevine PcG-like genes was also detected in fruits and vegetative organs, suggesting that epigenetic changes could be at the basis of the regulation of various proliferation-differentiation cell transitions that occur during grapevine development.
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Affiliation(s)
- Rubén Almada
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, Talca, Chile.
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18
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Butenko Y, Ohad N. Polycomb-group mediated epigenetic mechanisms through plant evolution. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:395-406. [PMID: 21664995 DOI: 10.1016/j.bbagrm.2011.05.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/23/2011] [Accepted: 05/26/2011] [Indexed: 12/01/2022]
Abstract
Polycomb Group (PcG) proteins form an epigenetic "memory system", conserved in both plants and animals, controlling global gene expression during development via histone modifications. The role of PcG proteins in plants was primarily explored in Arabidopsis thaliana, where PcG regulation of developmental processes was demonstrated throughout the plant life cycle. Our knowledge about the PcG machinery in terrestrial plants other than Arabidopsis began to accumulate only in recent years. In this review we summarize recent emerging data on the evolution and diversification of PcG mechanisms in various phyla, from early-diverging plants, including members of the Chlorophyte algae, through bryophytes and flowering plants. We describe the compositions of the PcG gene families, their so-far studied expression profiles, and finally summarize commonalities vs. differences among PcG functions across the various species. This article is part of a Special Issue entitled: Epigenetic control of cellular and developmental processes in plants.
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Affiliation(s)
- Yana Butenko
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Israel
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Thorstensen T, Grini PE, Aalen RB. SET domain proteins in plant development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:407-20. [PMID: 21664308 DOI: 10.1016/j.bbagrm.2011.05.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/08/2011] [Accepted: 05/10/2011] [Indexed: 10/18/2022]
Abstract
Post-translational methylation of lysine residues on histone tails is an epigenetic modification crucial for regulation of chromatin structure and gene expression in eukaryotes. The majority of the histone lysine methyltransferases (HKMTases) conferring such modifications are proteins with a conserved SET domain responsible for the enzymatic activity. The SET domain proteins in the model plant Arabidopsis thaliana can be assigned to evolutionarily conserved classes with different specificities allowing for different outcomes on chromatin structure. Here we review the present knowledge of the biochemical and biological functions of plant SET domain proteins in developmental processes. This article is part of a Special Issue entitled: Epigenetic control of cellular and developmental processes in plants.
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Affiliation(s)
- Tage Thorstensen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
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