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Bano N, Fakhrah S, Lone RA, Mohanty CS, Bag SK. Genome-wide identification and expression analysis of the HD2 protein family and its response to drought and salt stress in Gossypium species. FRONTIERS IN PLANT SCIENCE 2023; 14:1109031. [PMID: 36860898 PMCID: PMC9968887 DOI: 10.3389/fpls.2023.1109031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Histone deacetylase 2 (HD2) proteins play an important role in the regulation of gene expression. This helps with the growth and development of plants and also plays a crucial role in responses to biotic and abiotic stress es. HD2s comprise a C2H2-type Zn2+ finger at their C-terminal and an HD2 label, deacetylation and phosphorylation sites, and NLS motifs at their N-terminal. In this study, a total of 27 HD2 members were identified, using Hidden Markov model profiles, in two diploid cotton genomes (Gossypium raimondii and Gossypium arboretum) and two tetraploid cotton genomes (Gossypium hirsutum and Gossypium barbadense). These cotton HD2 members were classified into 10 major phylogenetic groups (I-X), of which group III was found to be the largest with 13 cotton HD2 members. An evolutionary investigation showed that the expansion of HD2 members primarily occurred as a result of segmental duplication in paralogous gene pairs. Further qRT-PCR validation of nine putative genes using RNA-Seq data suggested that GhHDT3D.2 exhibits significantly higher levels of expression at 12h, 24h, 48h, and 72h of exposure to both drought and salt stress conditions compared to a control measure at 0h. Furthermore, gene ontology, pathways, and co-expression network study of GhHDT3D.2 gene affirmed their significance in drought and salt stress responses.
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Affiliation(s)
- Nasreen Bano
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shafquat Fakhrah
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Rayees Ahmad Lone
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandra Sekhar Mohanty
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sumit Kumar Bag
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Bobde RC, Kumar A, Vasudevan D. Plant-specific HDT family histone deacetylases are nucleoplasmins. THE PLANT CELL 2022; 34:4760-4777. [PMID: 36069647 PMCID: PMC9709999 DOI: 10.1093/plcell/koac275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-mediated histone acetylation and deacetylation regulate nucleosome dynamics and gene expression. HDACs are classified into different families, with HD-tuins or HDTs being specific to plants. HDTs show some sequence similarity to nucleoplasmins, the histone chaperones that aid in binding, storing, and loading H2A/H2B dimers to assemble nucleosomes. Here, we solved the crystal structure of the N-terminal domain (NTD) of all four HDTs (HDT1, HDT2, HDT3, and HDT4) from Arabidopsis (Arabidopsis thaliana). The NTDs form a nucleoplasmin fold, exist as pentamers in solution, and are resistant to protease treatment, high temperature, salt, and urea conditions. Structurally, HDTs do not form a decamer, unlike certain classical nucleoplasmins. The HDT-NTD requires an additional A2 acidic tract C-terminal to the nucleoplasmin domain for interaction with histone H3/H4 and H2A/H2B oligomers. We also report the in-solution structures of HDT2 pentamers in complex with histone oligomers. Our study provides a detailed structural and in vitro functional characterization of HDTs, revealing them to be nucleoplasmin family histone chaperones. The experimental confirmation that HDTs are nucleoplasmins may spark new interest in this enigmatic family of proteins.
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Affiliation(s)
- Ruchir C Bobde
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Ashish Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
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Gong D, He F, Liu J, Zhang C, Wang Y, Tian S, Sun C, Zhang X. Understanding of Hormonal Regulation in Rice Seed Germination. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071021. [PMID: 35888110 PMCID: PMC9324290 DOI: 10.3390/life12071021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 01/06/2023]
Abstract
Seed germination is a critical stage during the life cycle of plants. It is well known that germination is regulated by a series of internal and external factors, especially plant hormones. In Arabidopsis, many germination-related factors have been identified, while in rice, the important crop and monocot model species and the further molecular mechanisms and regulatory networks controlling germination still need to be elucidated. Hormonal signals, especially those of abscisic acid (ABA) and gibberellin (GA), play a dominant role in determining whether a seed germinates or not. The balance between the content and sensitivity of these two hormones is the key to the regulation of germination. In this review, we present the foundational knowledge of ABA and GA pathways obtained from germination research in Arabidopsis. Then, we highlight the current advances in the identification of the regulatory genes involved in ABA- or GA-mediated germination in rice. Furthermore, other plant hormones regulate seed germination, most likely by participating in the ABA or GA pathways. Finally, the results from some regulatory layers, including transcription factors, post-transcriptional regulations, and reactive oxygen species, are also discussed. This review aims to summarize our current understanding of the complex molecular networks involving the key roles of plant hormones in regulating the seed germination of rice.
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Affiliation(s)
- Diankai Gong
- Liaoning Rice Research Institute, Shenyang 110115, China; (D.G.); (C.Z.); (Y.W.); (S.T.); (C.S.)
| | - Fei He
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China; (F.H.); (J.L.)
| | - Jingyan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China; (F.H.); (J.L.)
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang 110115, China; (D.G.); (C.Z.); (Y.W.); (S.T.); (C.S.)
| | - Yanrong Wang
- Liaoning Rice Research Institute, Shenyang 110115, China; (D.G.); (C.Z.); (Y.W.); (S.T.); (C.S.)
| | - Shujun Tian
- Liaoning Rice Research Institute, Shenyang 110115, China; (D.G.); (C.Z.); (Y.W.); (S.T.); (C.S.)
| | - Chi Sun
- Liaoning Rice Research Institute, Shenyang 110115, China; (D.G.); (C.Z.); (Y.W.); (S.T.); (C.S.)
| | - Xue Zhang
- Liaoning Rice Research Institute, Shenyang 110115, China; (D.G.); (C.Z.); (Y.W.); (S.T.); (C.S.)
- Correspondence: ; Tel.: +86-150-4020-6835
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Tahir MS, Tian L. HD2-type histone deacetylases: unique regulators of plant development and stress responses. PLANT CELL REPORTS 2021; 40:1603-1615. [PMID: 34041586 DOI: 10.1007/s00299-021-02688-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Plants have developed sophisticated and complex epigenetic regulation-based mechanisms to maintain stable growth and development under diverse environmental conditions. Histone deacetylases (HDACs) are important epigenetic regulators in eukaryotes that are involved in the deacetylation of lysine residues of histone H3 and H4 proteins. Plants have developed a unique HDAC family, HD2, in addition to the RPD3 and Sir2 families, which are also present in other eukaryotes. HD2s are well conserved plant-specific HDACs, which were first identified as nucleolar phosphoproteins in maize. The HD2 family plays important roles not only in fundamental developmental processes, including seed germination, root and leaf development, floral transition, and seed development but also in regulating plant responses to biotic and abiotic stresses. Some of the HD2 members coordinate with each other to function. The HD2 family proteins also show functional association with RPD3-type HDACs and other transcription factors as a part of repression complexes in gene regulatory networks involved in environmental stress responses. This review aims to analyse and summarise recent research progress in the HD2 family, and to describe their role in plant growth and development and in response to different environmental stresses.
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Affiliation(s)
- Muhammad Sufyan Tahir
- Department of Biology, University of Western Ontario, London, ON, Canada.
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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5
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Tognacca RS, Botto JF. Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions. PLANT COMMUNICATIONS 2021; 2:100169. [PMID: 34327318 PMCID: PMC8299061 DOI: 10.1016/j.xplc.2021.100169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 05/06/2023]
Abstract
Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.
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Affiliation(s)
- Rocío Soledad Tognacca
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CP1428 Buenos Aires, Argentina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| | - Javier Francisco Botto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
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Li H, Schilderink S, Cao Q, Kulikova O, Bisseling T. Plant-specific histone deacetylases are essential for early and late stages of Medicago nodule development. PLANT PHYSIOLOGY 2021; 186:1591-1605. [PMID: 33744928 PMCID: PMC8260124 DOI: 10.1093/plphys/kiab140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/18/2021] [Indexed: 05/22/2023]
Abstract
Legume and rhizobium species can establish a nitrogen-fixing nodule symbiosis. Previous studies have shown that several transcription factors that play a role in (lateral) root development are also involved in nodule development. Chromatin remodeling factors, like transcription factors, are key players in regulating gene expression. However, studies have not investigated whether chromatin remodeling genes that are essential for root development are also involved in nodule development. Here, we studied the role of Medicago (Medicago truncatula) histone deacetylases (MtHDTs) in nodule development. Arabidopsis (Arabidopsis thaliana) orthologs of HDTs have been shown to play a role in root development. MtHDT expression is induced in nodule primordia and is maintained in the nodule meristem and infection zone. Conditional, nodule-specific knockdown of MtHDT expression by RNAi blocks nodule primordium development. A few nodules may still form, but their nodule meristems are smaller, and rhizobial colonization of the cells derived from the meristem is markedly reduced. Although the HDTs are expressed during nodule and root development, transcriptome analyses indicate that HDTs control the development of each organ in a different manner. During nodule development, the MtHDTs positively regulate 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 (MtHMGR1). Decreased expression of MtHMGR1 is sufficient to explain the inhibition of primordium formation.
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Affiliation(s)
- Huchen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Stefan Schilderink
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Present address: St. Bonifatius College, Burgemeester Fockema Andreaelaan 7–9, 3582 KA Utrecht, The Netherlands
| | - Qingqin Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Olga Kulikova
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Author for communication:
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7
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Pagano A, L'Andolina C, Sabatini ME, de Sousa Araújo S, Balestrazzi A, Macovei A. Sodium butyrate induces genotoxic stress in function of photoperiod variations and differentially modulates the expression of genes involved in chromatin modification and DNA repair in Petunia hybrida seedlings. PLANTA 2020; 251:102. [PMID: 32350684 DOI: 10.1007/s00425-020-03392-4] [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: 05/17/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Sodium butyrate applied to Petunia hybrida seeds under a long-day photoperiod has a negative impact (reduced seedling length, decreased production of photosynthetic pigments, and accumulation of DNA damage) on early seedling development, whereas its administration under dark/light conditions (complete dark conditions for 5 days followed by exposure to long-day photoperiod for 5 days) bypasses some of the adverse effects. Genotoxic stress impairs plant development. To circumvent DNA damage, plants activate DNA repair pathways in concert with chromatin dynamics. These are essential during seed germination and seedling establishment, and may be influenced by photoperiod variations. To assess this interplay, an experimental design was developed in Petunia hybrida, a relevant horticultural crop and model species. Seeds were treated with different doses of sodium butyrate (NaB, 1 mM and 5 mM) as a stress agent applied under different light/dark conditions throughout a time period of 10 days. Phenotypic (germination percentage and speed, seedling length, and photosynthetic pigments) and molecular (DNA damage and gene expression profiles) analyses were performed to monitor the response to the imposed conditions. Seed germination was not affected by the treatments. Seedling development was hampered by increasing NaB concentrations applied under a long-day photoperiod (L) as reflected by the decreased seedling length accompanied by increased DNA damage. When seedlings were grown under dark conditions for 5 days and then exposed to long-day photoperiod for the remaining 5 days (D/L), the damaging effects of NaB were circumvented. NaB exposure under L conditions resulted in enhanced expression of HAT/HDAC (HISTONE ACETYLTRANSFERASES/HISTONE DEACTEYLASES) genes along with repression of genes involved in DNA repair. Differently, under D/L conditions, the expression of DNA repair genes was increased by NaB treatment and this was associated with lower levels of DNA damage. The observed DNA damage and gene expression profiles suggest the involvement of chromatin modification- and DNA repair-associated pathways in response to NaB and dark/light exposure during seedling development.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Corrado L'Andolina
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Maria Elisa Sabatini
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
- Viral Control of Cellular Pathways and Biology of Tumorigenesis Unit, European Institute of Oncology (IFOM-IEO), via Adamello 16, 20139, Milano, Italy
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química E Biológica António Xavier (ITQB-NOVA), Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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Zheng W. Review: The plant sirtuins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110434. [PMID: 32081272 DOI: 10.1016/j.plantsci.2020.110434] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/05/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
The sirtuin family of intracellular enzymes are able to catalyze a unique β-nicotinamide adenine dinucleotide (β-NAD+)-dependent Nε-acyl-lysine deacylation reaction on histone and non-histone protein substrates. Since 2000, the sirtuin family members have been identified in both prokaryotes and eukaryotes; tremendous accomplishments have also been achieved on the mechanistic and functional (pharmacological) understanding of the sirtuin-catalyzed deacylation reaction. Among the eukaryotic organisms, past research has been focused more on the yeast and mammalian sirtuins than on the plant sirtuins, however, the very presence of sirtuins in various plant species and the functional studies on plant sirtuins published thus far attest to the importance of this particular subfamily of eukaryotic sirtuins in regulating the growth and development of plants and their responses to biotic and abiotic stresses. In this review, an integrated and updated account will be presented on the biochemical, cellular, and functional profiles of all the plant sirtuins identified thus far. It is hoped that this article will also set a stage for expanded efforts in the identification, characterization, and functional interrogation of plant sirtuins; and the development and exploration of their chemical modulators (activators and inhibitors) in plant research and agriculture.
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Affiliation(s)
- Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China.
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Ma X, Liang X, Lv S, Guan T, Jiang T, Cheng Y. Histone deacetylase gene PtHDT902 modifies adventitious root formation and negatively regulates salt stress tolerance in poplar. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110301. [PMID: 31779889 DOI: 10.1016/j.plantsci.2019.110301] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 05/24/2023]
Abstract
Histone deacetylases (HDACs) regulate gene transcription, and play a critical role in plant growth, development and stress responses. HD2 proteins are plant specific histone deacetylases. In woody plants, functions of HD2s are not known. In this study, we cloned an HD2 gene PtHDT902 from Populus trichocarpa and investigated its sequence, expression, subcellular localization, and functions in root development and salt stress responses. Our findings indicated that PtHDT902 was a nuclear protein and its expression was regulated by abiotic stresses. The over-expression of PtHDT902 in both Arabidopsis and poplar increased the expression levels of gibberellin (GA) biosynthetic genes. The expression of PtHDT902 in Arabidopsis enhanced primary root growth, and its over-expression in poplar inhibited adventitious root formation. These phenotypes resulted from over-expression of PtHDT902 were consistent with the GA-overproduction phenotypes. In addition, the poplar plants over-expressing PtHDT902 exhibited lower tolerance to salt than non-transgenic plants. These findings indicated that PtHDT902 worked as an important regulator in adventitious root formation and salt stress tolerance in poplar.
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Affiliation(s)
- Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Xueying Liang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Shibo Lv
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Tao Guan
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China.
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Bürger M, Chory J. Structural and chemical biology of deacetylases for carbohydrates, proteins, small molecules and histones. Commun Biol 2018; 1:217. [PMID: 30534609 PMCID: PMC6281622 DOI: 10.1038/s42003-018-0214-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/31/2018] [Indexed: 01/02/2023] Open
Abstract
Deacetylation is the removal of an acetyl group and occurs on a plethora of targets and for a wide range of biological reasons. Several pathogens deacetylate their surface carbohydrates to evade immune response or to support biofilm formation. Furthermore, dynamic acetylation/deacetylation cycles govern processes from chromatin remodeling to posttranslational modifications that compete with phosphorylation. Acetylation usually occurs on nitrogen and oxygen atoms and are referred to as N- and O-acetylation, respectively. This review discusses the structural prerequisites that enzymes must have to catalyze the deacetylation reaction, and how they adapted by formation of specific substrate and metal binding sites. Marco Bürger and Joanne Chory discuss the structural requirements for enzymes carrying out deacetylation reactions for various functions across phyla. They explore how these enzymes have adapted to and achieved specificity on a large number of target molecules.
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Affiliation(s)
- Marco Bürger
- 1Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA
| | - Joanne Chory
- 1Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA.,2Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA
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Tong B, Xia D, Lv S, Ma X. Cloning and expression analysis of PtHDT903, a HD2-type histone deacetylase gene in Populus trichocarpa. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1478749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Dean Xia
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Shibo Lv
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
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12
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Nicolas-Francès V, Grandperret V, Liegard B, Jeandroz S, Vasselon D, Aimé S, Klinguer A, Lamotte O, Julio E, de Borne FD, Wendehenne D, Bourque S. Evolutionary diversification of type-2 HDAC structure, function and regulation in Nicotiana tabacum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:66-74. [PMID: 29606218 DOI: 10.1016/j.plantsci.2018.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 06/08/2023]
Abstract
Type-2 HDACs (HD2s) are plant-specific histone deacetylases that play diverse roles during development and in responses to biotic and abiotic stresses. In this study we characterized the six tobacco genes encoding HD2s that mainly differ by the presence or the absence of a typical zinc finger in their C-terminal part. Of particular interest, these HD2 genes exhibit a highly conserved intron/exon structure. We then further investigated the phylogenetic relationships among the HD2 gene family, and proposed a model of the genetic events that led to the organization of the HD2 family in Solanaceae. Absolute quantification of HD2 mRNAs in N. tabacum and in its precursors, N. tomentosiformis and N. sylvestris, did not reveal any pseudogenization of any of the HD2 genes, but rather specific regulation of HD2 expression in these three species. Functional complementation approaches in Arabidopsis thaliana demonstrated that the four zinc finger-containing HD2 proteins exhibit the same biological function in response to salt stress, whereas the two HD2 proteins without zinc finger have different biological function.
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Affiliation(s)
- Valérie Nicolas-Francès
- Université de Bourgogne-Franche Comté, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Vincent Grandperret
- Université de Bourgogne-Franche Comté, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Benjamin Liegard
- Université de Bourgogne-Franche Comté, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Sylvain Jeandroz
- Université de Bourgogne-Franche Comté, UMR 1347 Agroécologie, AgroSup Dijon, BP 86510, F-21000, Dijon, France.
| | - Damien Vasselon
- Université de Bourgogne-Franche Comté, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Sébastien Aimé
- INRA, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Agnès Klinguer
- INRA, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Olivier Lamotte
- ERL CNRS 6300, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Emilie Julio
- Institut du Tabac, Domaine de la Tour, LBCM, 24100, Bergerac, France.
| | | | - David Wendehenne
- Université de Bourgogne-Franche Comté, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
| | - Stéphane Bourque
- Université de Bourgogne-Franche Comté, UMR 1347 Agroécologie, BP 86510, F-21000, Dijon, France.
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Uhrig RG, Schläpfer P, Mehta D, Hirsch-Hoffmann M, Gruissem W. Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes. BMC Genomics 2017; 18:514. [PMID: 28679357 PMCID: PMC5499015 DOI: 10.1186/s12864-017-3894-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/21/2017] [Indexed: 12/30/2022] Open
Abstract
Background Reversible protein acetylation occurring on Lys-Ne has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) that catalyze the addition and removal of acetyl groups from target proteins. Estimates indicate that protein acetylation is second to protein phosphorylation in abundance, with thousands of acetylated sites now identified in different subcellular compartments. Considering the important regulatory role of protein phosphorylation, elucidating the diversity of KATs and KDACs across photosynthetic eukaryotes is essential in furthering our understanding of the impact of reversible protein acetylation on plant cell processes. Results We report a genome-scale analysis of lysine acetyltransferase (KAT)- and lysine deacetylase (KDAC)-families from 53 photosynthetic eukaryotes. KAT and KDAC orthologs were identified in sequenced genomes ranging from glaucophytes and algae to land plants and then analyzed for evolutionary relationships. Based on consensus molecular phylogenetic and subcellular localization data we found new sub-classes of enzymes in established KAT- and KDAC-families. Specifically, we identified a non-photosynthetic origin of the HD-tuin family KDACs, a new monocot-specific Class I HDA-family sub-class, and a phylogenetically distinct Class II algal/heterokont sub-class which maintains an ankyrin domain not conserved in land plant Class II KDACs. Protein structure analysis showed that HDA- and SRT-KDACs exist as bare catalytic subunits with highly conserved median protein length, while all KATs maintained auxiliary domains, with CBP- and TAFII250-KATs displaying protein domain gain and loss over the course of photosynthetic eukaryote evolution in addition to variable protein length. Lastly, promoter element enrichment analyses across species revealed conserved cis-regulatory sequences that support KAT and KDAC involvement in the regulation of plant development, cold/drought stress response, as well as cellular processes such as the circadian clock. Conclusions Our results reveal new evolutionary, structural, and biological insights into the KAT- and KDAC-families of photosynthetic eukaryotes, including evolutionary parallels to protein kinases and protein phosphatases. Further, we provide a comprehensive annotation framework through our extensive phylogenetic analysis, from which future research investigating aspects of protein acetylation in plants can use to position new findings in a broader context. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3894-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R Glen Uhrig
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.
| | - Pascal Schläpfer
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.,Plant Biology Department, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Devang Mehta
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Matthias Hirsch-Hoffmann
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
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14
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Farhi J, Tian G, Fang H, Maxwell D, Xing T, Tian L. Histone deacetylase HD2D is involved in regulating plant development and flowering time in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1300742. [PMID: 28737472 PMCID: PMC5586354 DOI: 10.1080/15592324.2017.1300742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
HD2D is one of the 4 plant specific HD2 family histone deacetylases (HDAC) identified in Arabidopsis and it is distantly related to the other HD2 members. At this time, little is known about the function of HD2D in plants. Here we provide evidence that HD2D is involved in the control of flowering time. Flowering was delayed in transgenic plants overexpressing HD2D and hd2d mutant plants flowered earlier compared with wild-type in both long day and short day conditions. Expression of several floral identity genes was altered in these plants. Taken together, our findings suggest that HD2D is a negative regulator of flowering that modulates the transition of vegetative to reproductive growth in a photoperiod independent manner.
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Affiliation(s)
- Joshua Farhi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Gang Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Hui Fang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Denis Maxwell
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Tim Xing
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Lining Tian
- Department of Biology, University of Western Ontario, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- CONTACT Lining Tian London Research and Development Center, Agriculture and Agri-Food Canada, 1391 Sanford Street, London, Ontario, Canada, N5V 4T3
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15
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Pagano A, Araújo SDS, Macovei A, Leonetti P, Balestrazzi A. The Seed Repair Response during Germination: Disclosing Correlations between DNA Repair, Antioxidant Response, and Chromatin Remodeling in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2017; 8:1972. [PMID: 29184569 PMCID: PMC5694548 DOI: 10.3389/fpls.2017.01972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/01/2017] [Indexed: 05/05/2023]
Abstract
This work provides novel insights into the effects caused by the histone deacetylase inhibitor trichostatin A (TSA) during Medicago truncatula seed germination, with emphasis on the seed repair response. Seeds treated with H2O and TSA (10 and 20 μM) were collected during imbibition (8 h) and at the radicle protrusion phase. Biometric data showed delayed germination and impaired seedling growth in TSA-treated samples. Comet assay, performed on radicles at the protrusion phase and 4-days old M. truncatula seedlings, revealed accumulation of DNA strand breaks upon exposure to TSA. Activation of DNA repair toward TSA-mediated genotoxic damage was evidenced by the up-regulation of MtOGG1(8-OXOGUANINE GLYCOSYLASE/LYASE) gene involved in the removal of oxidative DNA lesions, MtLIGIV(LIGASE IV) gene, a key determinant of seed quality, required for the rejoining of DNA double strand breaks and TDP(TYROSYL-DNA PHOSPHODIESTERASE) genes encoding the multipurpose DNA repair enzymes tyrosyl-DNA phosphodiesterases. Since radical scavenging can prevent DNA damage, the specific antioxidant activity (SAA) was measured by DPPH (1,1-diphenyl-2-picrylhydrazyl) and Folin-Ciocalteu reagent assays. Fluctuations of SAA were observed in TSA-treated seeds/seedlings concomitant with the up-regulation of antioxidant genes MtSOD(SUPEROXIDE DISMUTASE, MtAPX(ASCORBATE PEROXIDASE) and MtMT2(TYPE 2 METALLOTHIONEIN). Chromatin remodeling, required to facilitate the access of DNA repair enzymes at the damaged sites, is also part of the multifaceted seed repair response. To address this aspect, still poorly explored in plants, the MtTRRAP(TRANSFORMATION/TRANSACTIVATION DOMAIN-ASSOCIATED PROTEIN) gene was analyzed. TRRAP is a transcriptional adaptor, so far characterized only in human cells where it is needed for the recruitment of histone acetyltransferase complexes to chromatin during DNA repair. The MtTRRAP gene and the predicted interacting partners MtHAM2 (HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY) and MtADA2A (TRANSCRIPTIONAL ADAPTOR) showed tissue- and dose-dependent fluctuations in transcript levels. PCA (Principal Component Analysis) and correlation analyses suggest for a new putative link between DNA repair and chromatin remodeling that involves MtOGG1 and MtTRRAP genes, in the context of seed germination. Interesting correlations also connect DNA repair and chromatin remodeling with antioxidant players and proliferation markers.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Susana de Sousa Araújo
- Plant Cell Biotechnology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Oeiras, Portugal
| | - Anca Macovei
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Paola Leonetti
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
- *Correspondence: Alma Balestrazzi
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16
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Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V. The Evolution of HD2 Proteins in Green Plants. TRENDS IN PLANT SCIENCE 2016; 21:1008-1016. [PMID: 27789157 DOI: 10.1016/j.tplants.2016.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/28/2016] [Accepted: 10/04/2016] [Indexed: 05/18/2023]
Abstract
In eukaryotes, protein deacetylation is carried out by two well-conserved histone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.
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Affiliation(s)
- S Bourque
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France.
| | - S Jeandroz
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - V Grandperret
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - N Lehotai
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - S Aimé
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - D E Soltis
- Department of Biology, Florida Museum of Natural History, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - N W Miles
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76201, USA
| | - M Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | - M K Deyholos
- Department of Biology, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - J H Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - M W Chase
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK; Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Western Australia
| | - C J Rothfels
- University Herbarium and Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - D W Stevenson
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - S W Graham
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - X Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, CAS, 1-104 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - S Wu
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, CAS, 1-104 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - J C Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - P P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Z Yan
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Y Xie
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - E J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - G K S Wong
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - D Wendehenne
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - V Nicolas-Francès
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
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17
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Bègue H, Jeandroz S, Blanchard C, Wendehenne D, Rosnoblet C. Structure and functions of the chaperone-like p97/CDC48 in plants. Biochim Biophys Acta Gen Subj 2016; 1861:3053-3060. [PMID: 27717811 DOI: 10.1016/j.bbagen.2016.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The chaperone-like p97 is a member of the AAA+ ATPase enzyme family that contributes to numerous cellular activities. P97 has been broadly studied in mammals (VCP/p97) and yeasts (CDC48: Cell Division Cycle 48/p97) and numerous investigations highlighted that this protein is post-translationally regulated, is structured in homohexamer and interacts with partners and cofactors that direct it to distinct cellular signalization pathway including protein quality control and degradation, cell cycle regulation, genome stability, vesicular trafficking, autophagy and immunity. SCOPE OF REVIEW p97 is also conserved in plants (CDC48) but its functions are less understood. In the present review we intended to present the state of the art of the structure, regulation and functions of CDC48 in plants. MAJOR CONCLUSIONS Evidence accumulated underline that CDC48 plays a crucial role in development, cell cycle regulation and protein turnover in plants. Furthermore, its involvement in plant immunity has recently emerged and first interacting partners have been identified, shedding light on its putative cellular activities. GENERAL SIGNIFICANCE Identification of emerging functions of CDC48 in plants opens new roads of research in immunity and provides new insights into the mechanisms of protein quality control.
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Affiliation(s)
- Hervé Bègue
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sylvain Jeandroz
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Cécile Blanchard
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - David Wendehenne
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Claire Rosnoblet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France.
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18
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Shen Y, Issakidis-Bourguet E, Zhou DX. Perspectives on the interactions between metabolism, redox, and epigenetics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5291-5300. [PMID: 27531885 DOI: 10.1093/jxb/erw310] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Epigenetic modifications of chromatin usually involve consumption of key metabolites and redox-active molecules. Primary metabolic flux and cellular redox states control the activity of enzymes involved in chromatin modifications, such as DNA methylation, histone acetylation, and histone methylation, which in turn regulate gene expression and/or enzymatic activity of specific metabolic and redox pathways. Thus, coordination of metabolism and epigenetic regulation of gene expression is critical to control growth and development in response to the cellular environment. Much has been learned from animal and yeast cells with regard to the interplay between metabolism and epigenetic regulation, and now the metabolic control of epigenetic pathways in plants is an increasing area of study. Epigenetic mechanisms are largely similar between plant and mammalian cells, but plants display very important differences in both metabolism and metabolic/redox signaling pathways. In this review, we summarize recent developments in the field and discuss perspectives of studying interactions between plant epigenetic and metabolism/redox systems, which are essential for plant adaptation to environmental conditions.
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Affiliation(s)
- Yuan Shen
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-sud 11, 91400 Orsay, France
| | | | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-sud 11, 91400 Orsay, France
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19
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Han Z, Yu H, Zhao Z, Hunter D, Luo X, Duan J, Tian L. AtHD2D Gene Plays a Role in Plant Growth, Development, and Response to Abiotic Stresses in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:310. [PMID: 27066015 PMCID: PMC4815178 DOI: 10.3389/fpls.2016.00310] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 02/29/2016] [Indexed: 05/20/2023]
Abstract
The histone deacetylases play important roles in the regulation of gene expression and the subsequent control of a number of important biological processes, including those involved in the response to environmental stress. A specific group of histone deacetylase genes, HD2, is present in plants. In Arabidopsis, HD2s include HD2A, HD2B, HD2C, and HD2D. Previous research showed that HD2A, HD2B, and HD2C are more related in terms of expression and function, but not HD2D. In this report, we studied different aspects of AtHD2D in Arabidopsis with respect to plant response to drought and other abiotic stresses. Bioinformatics analysis indicates that HD2D is distantly related to other HD2 genes. Transient expression in Nicotiana benthamiana and stable expression in Arabidopsis of AtHD2D fused with gfp showed that AtHD2D was expressed in the nucleus. Overexpression of AtHD2D resulted in developmental changes including fewer main roots, more lateral roots, and a higher root:shoot ratio. Seed germination and plant flowering time were delayed in transgenic plants expressing AtHD2D, but these plants exhibited higher degrees of tolerance to abiotic stresses, including drought, salt, and cold stresses. Physiological studies indicated that the malondialdehyde (MDA) content was high in wild-type plants but in plants overexpressing HD2D the MDA level increased slowly in response to stress conditions of drought, cold, and salt stress. Furthermore, electrolyte leakage in leaf cells of wild type plants increased but remained stable in transgenic plants. Our results indicate that AtHD2D is unique among HD2 genes and it plays a role in plant growth and development regulation and these changes can modulate plant stress responses.
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Affiliation(s)
- Zhaofen Han
- College of Life Science, Northwest A & F UniversityYangling, China
| | - Huimin Yu
- Department of E-A Information Engineering, Liaoning Institute of Science and TechnologyBenxi, China
| | - Zhong Zhao
- College of Forestry, Northwest A & F UniversityYangling, China
- *Correspondence: Zhong Zhao
| | - David Hunter
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-food CanadaLondon, ON, Canada
| | - Xinjuan Luo
- College of Life Science, Northwest A & F UniversityYangling, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Lining Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-food CanadaLondon, ON, Canada
- Lining Tian
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20
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Shen Y, Wei W, Zhou DX. Histone Acetylation Enzymes Coordinate Metabolism and Gene Expression. TRENDS IN PLANT SCIENCE 2015; 20:614-621. [PMID: 26440431 DOI: 10.1016/j.tplants.2015.07.005] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 07/23/2015] [Indexed: 05/18/2023]
Abstract
Histone lysine acetylation is well known for being important in the epigenetic regulation of gene expression in eukaryotic cells. Recent studies have uncovered a plethora of acetylated proteins involved in important metabolic pathways, such as photosynthesis and respiration in plants. Enzymes involved in histone acetylation and deacetylation are being identified as regulators of acetylation of metabolic enzymes. Importantly, key metabolites, such as acetyl-CoA and NAD(+), are involved in protein acetylation and deacetylation processes, and their cellular levels may regulate the activity of histone acetyltransferases (HAT) and deacetylases (HDAC). Further research is required to determine whether and how HATs and HDACs sense cellular metabolite signals to control gene expression and metabolic enzyme activity through lysine acetylation and deacetylation.
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Affiliation(s)
- Yuan Shen
- Institute of Plant Sciences Paris-Saclay (IPS2), University Paris-sud 11, 91405 Orsay, France
| | - Wei Wei
- Institute of interdisciplinary Scientific Research, Jianghan University, 430056, Wuhan, China
| | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), University Paris-sud 11, 91405 Orsay, France.
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