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Seni S, Singh RK, Prasad M. Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194966. [PMID: 37532097 DOI: 10.1016/j.bbagrm.2023.194966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.
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Affiliation(s)
- Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India.
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Hu L, Zhou K, Liu Y, Yang S, Zhang J, Gong X, Ma F. Overexpression of MdMIPS1 enhances salt tolerance by improving osmosis, ion balance, and antioxidant activity in transgenic apple. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110654. [PMID: 33218625 DOI: 10.1016/j.plantsci.2020.110654] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/15/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
Myo-inositol and its derivatives play vital roles in plant stress tolerance. Myo-inositol-1-phosphate synthase (MIPS) is the rate-limiting enzyme of myo-inositol biosynthesis. However, the role of apple MIPS-mediated myo-inositol biosynthesis in stress tolerance remains elusive. In this study, we found that ectopic expression of MdMIPS1 from apple increased myo-inositol content and enhanced tolerance to salt and osmotic stresses in transgenic Arabidopsis lines. In transgenic apple lines over-expressing MdMIPS1, the increased myo-inositol levels could promote accumulation of other osmoprotectants such as glucose, sucrose, galactose, and fructose, to alleviate salinity-induced osmotic stress. Also, it was shown that overexpression of MdMIPS1 enhanced salinity tolerance by improving the antioxidant system to scavenge ROS, as well as Na+ and K+ homeostasis. Taken together, our results revealed a protective role of MdMIPS1-mediated myo-inositol biosynthesis in salt tolerance by improving osmotic balance, antioxidant defense system, and ion homeostasis in apple.
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Affiliation(s)
- Lingyu Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit, Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Kun Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shulin Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jingyun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Serre NBC, Sarthou M, Gigarel O, Figuet S, Corso M, Choulet J, Rofidal V, Alban C, Santoni V, Bourguignon J, Verbruggen N, Ravanel S. Protein lysine methylation contributes to modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress. PLANT, CELL & ENVIRONMENT 2020; 43:760-774. [PMID: 31759334 DOI: 10.1111/pce.13692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/04/2019] [Accepted: 11/19/2019] [Indexed: 05/10/2023]
Abstract
The mechanisms underlying the response and adaptation of plants to excess of trace elements are not fully described. Here, we analysed the importance of protein lysine methylation for plants to cope with cadmium. We analysed the effect of cadmium on lysine-methylated proteins and protein lysine methyltransferases (KMTs) in two cadmium-sensitive species, Arabidopsis thaliana and A. lyrata, and in three populations of A. halleri with contrasting cadmium accumulation and tolerance traits. We showed that some proteins are differentially methylated at lysine residues in response to Cd and that a few genes coding KMTs are regulated by cadmium. Also, we showed that 9 out of 23 A. thaliana mutants disrupted in KMT genes have a tolerance to cadmium that is significantly different from that of wild-type seedlings. We further characterized two of these mutants, one was knocked out in the calmodulin lysine methyltransferase gene and displayed increased tolerance to cadmium, and the other was interrupted in a KMT gene of unknown function and showed a decreased capacity to cope with cadmium. Together, our results showed that lysine methylation of non-histone proteins is impacted by cadmium and that several methylation events are important for modulating the response of Arabidopsis plants to cadmium stress.
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Affiliation(s)
- Nelson B C Serre
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Manon Sarthou
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Océane Gigarel
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Sylvie Figuet
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Massimiliano Corso
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Justine Choulet
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Valérie Rofidal
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier, Cedex 2, France
| | - Claude Alban
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Véronique Santoni
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier, Cedex 2, France
| | | | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Stéphane Ravanel
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
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Serre NBC, Alban C, Bourguignon J, Ravanel S. An outlook on lysine methylation of non-histone proteins in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4569-4581. [PMID: 29931361 DOI: 10.1093/jxb/ery231] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein methylation is a very diverse, widespread, and important post-translational modification affecting all aspects of cellular biology in eukaryotes. Methylation on the side-chain of lysine residues in histones has received considerable attention due to its major role in determining chromatin structure and the epigenetic regulation of gene expression. Over the last 20 years, lysine methylation of non-histone proteins has been recognized as a very common modification that contributes to the fine-tuned regulation of protein function. In plants, our knowledge in this field is much more fragmentary than in yeast and animal cells. In this review, we describe the plant enzymes involved in the methylation of non-histone substrates, and we consider historical and recent advances in the identification of non-histone lysine-methylated proteins in photosynthetic organisms. Finally, we discuss our current knowledge about the role of protein lysine methylation in regulating molecular and cellular functions in plants, and consider challenges for future research.
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Affiliation(s)
- Nelson B C Serre
- Univ. Grenoble Alpes, INRA, CEA, CNRS, BIG, PCV, Grenoble, France
| | - Claude Alban
- Univ. Grenoble Alpes, INRA, CEA, CNRS, BIG, PCV, Grenoble, France
| | | | - Stéphane Ravanel
- Univ. Grenoble Alpes, INRA, CEA, CNRS, BIG, PCV, Grenoble, France
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Hamey JJ, Wilkins MR. Methylation of Elongation Factor 1A: Where, Who, and Why? Trends Biochem Sci 2018; 43:211-223. [PMID: 29398204 DOI: 10.1016/j.tibs.2018.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 11/17/2022]
Abstract
Eukaryotic elongation factor 1A (eEF1A) is an essential and highly conserved protein involved in diverse cellular processes, including translation, cytoskeleton organisation, nuclear export, and proteasomal degradation. Recently, nine novel and site-specific methyltransferases were discovered that target eEF1A, five in yeast and four in human, making it the eukaryotic protein with the highest number of independent methyltransferases. Some of these methyltransferases show striking evolutionary conservation. Yet, they come from diverse methyltransferase families, indicating they confer competitive advantage through independent origins. As might be expected, the first functional studies of specific methylation sites found them to have distinct effects, notably on eEF1A-related processes of translation and tRNA aminoacylation. Further functional studies of sites will likely reveal other unique roles for this interesting modification.
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Affiliation(s)
- Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia.
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Avramova Z. Transcriptional 'memory' of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:149-59. [PMID: 25788029 DOI: 10.1111/tpj.12832] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 05/17/2023]
Abstract
Drought, salinity, extreme temperature variations, pathogen and herbivory attacks are recurring environmental stresses experienced by plants throughout their life. To survive repeated stresses, plants provide responses that may be different from their response during the first encounter with the stress. A different response to a similar stress represents the concept of 'stress memory'. A coordinated reaction at the organismal, cellular and gene/genome levels is thought to increase survival chances by improving the plant's tolerance/avoidance abilities. Ultimately, stress memory may provide a mechanism for acclimation and adaptation. At the molecular level, the concept of stress memory indicates that the mechanisms responsible for memory-type transcription during repeated stresses are not based on repetitive activation of the same response pathways activated by the first stress. Some recent advances in the search for transcription 'memory factors' are discussed with an emphasis on super-induced dehydration stress memory response genes in Arabidopsis.
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Affiliation(s)
- Zoya Avramova
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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Fromm M, Avramova Z. ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes? CURRENT OPINION IN PLANT BIOLOGY 2014; 21:75-82. [PMID: 25047977 DOI: 10.1016/j.pbi.2014.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/26/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or 'registers', activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity about the role of H3K4me3 as an activating mark is due to the unknown duality of the ATX1/AtCOMPASS to facilitate PIC assembly and to generate H3K4me3, which is essential for activating transcriptional elongation.
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Affiliation(s)
- Michael Fromm
- Department of Agronomy and Plant Science Innovation, UNL, Lincoln, NE 68588-6008, USA
| | - Zoya Avramova
- School of Biological Science, UNL, Lincoln, NE 68588-6008, USA.
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Coordinating metabolite changes with our perception of plant abiotic stress responses: emerging views revealed by integrative-omic analyses. Metabolites 2013; 3:761-86. [PMID: 24958149 PMCID: PMC3901284 DOI: 10.3390/metabo3030761] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/21/2013] [Accepted: 08/28/2013] [Indexed: 11/17/2022] Open
Abstract
Metabolic configuration and adaptation under a range of abiotic stresses, including drought, heat, salinity, cold, and nutrient deprivation, are subjected to an intricate span of molecular pathways that work in parallel in order to enhance plant fitness and increase stress tolerance. In recent years, unprecedented advances have been made in identifying and linking different abiotic stresses, and the current challenge in plant molecular biology is deciphering how the signaling responses are integrated and transduced throughout metabolism. Metabolomics have often played a fundamental role in elucidating the distinct and overlapping biochemical changes that occur in plants. However, a far greater understanding and appreciation of the complexity in plant metabolism under specific stress conditions have become apparent when combining metabolomics with other—omic platforms. This review focuses on recent advances made in understanding the global changes occurring in plant metabolism under abiotic stress conditions using metabolite profiling as an integrated discovery platform.
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Valluru R, Van den Ende W. Myo-inositol and beyond--emerging networks under stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:387-400. [PMID: 21889044 DOI: 10.1016/j.plantsci.2011.07.009] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 05/18/2023]
Abstract
Myo-inositol is a versatile compound that generates diversified derivatives upon phosphorylation by lipid-dependent and -independent pathways. Phosphatidylinositols form one such group of myo-inositol derivatives that act both as membrane structural lipid molecules and as signals. The significance of these compounds lies in their dual functions as signals as well as key metabolites under stress. Several stress- and non-stress related pathways regulated by phosphatidylinositol isoforms and associated enzymes, kinases and phosphatases, appear to function in parallel to coordinatively adapt growth and stress responses in plants. Recent evidence also postulates their crucial roles in nuclear functions as they interact with the key players of chromatin structure, yet other nuclear functions remain largely unknown. Phosphatidylinositol monophosphate 5-kinase interacts with and represses a cytosolic neutral invertase, a key enzyme of sugar metabolism suggesting a crosstalk between lipid and sugar signaling. Besides phosphatidylinositol, myo-inositol derived galactinol and associated raffinose-family oligosaccharides are emerging as antioxidants and putative signaling compounds too. Importantly, myo-inositol polyphosphate 5-phosphatase (5PTase) acts, depending on sugar status, as a positive or negative regulator of a global energy sensor, SnRK1. This implies that both myo-inositol- and sugar-derived (e.g. trehalose 6-phosphate) molecules form part of a broad regulatory network with SnRK1 as the central regulator. Recently, it was shown that the transcription factor bZIP11 also takes part in this network. Moreover, a functional coordination between neutral invertase and hexokinase is emerging as a sweet network that contributes to oxidative stress homeostasis in plants. In this review, we focus on myo-inositol, its direct and more downstream derivatives (galactinol, raffinose), and the contribution of their associated networks to plant stress tolerance.
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Affiliation(s)
- Ravi Valluru
- Ecophysiology of Plants Under Environmental Stress, INRA-SUPAGRO, Institute of Integrative Plant Biology, 2 Place Viala, Montpellier, France
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