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Sanjuan-Badillo A, P. Martínez-Castilla L, García-Sandoval R, Ballester P, Ferrándiz C, Sanchez MDLP, García-Ponce B, Garay-Arroyo A, R. Álvarez-Buylla E. HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2024; 19:2353536. [PMID: 38771929 PMCID: PMC11110687 DOI: 10.1080/15592324.2024.2353536] [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: 02/27/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of Arabidopsis thaliana HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the Arabidopsis thaliana deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated in vitro and in vivo HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
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Affiliation(s)
- Andrea Sanjuan-Badillo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Programa de Doctorado en Ciencias Biomédicas, de la Universidad Nacional Autónoma de México, Ciudad de México, México
| | - León P. Martínez-Castilla
- Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | | | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Cui X, Dard A, Reichheld JP, Zhou DX. Multifaceted functions of histone deacetylases in stress response. TRENDS IN PLANT SCIENCE 2023; 28:1245-1256. [PMID: 37394308 DOI: 10.1016/j.tplants.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023]
Abstract
Histone deacetylases (HDACs) are important chromatin regulators essential for plant tolerance to adverse environments. In addition to histone deacetylation and epigenetic regulation, HDACs deacetylate non-histone proteins and thereby regulate multiple pathways. Like other post-translational modifications (PTMs), acetylation/deacetylation is a reversible switch regulating different cellular processes in plants. Here, by focusing on results obtained in arabidopsis (Arabidopsis thaliana) and rice plants, we analyze the different aspects of HDAC functions and the underlying regulatory mechanisms in modulating plant responses to stress. We hypothesize that, in addition to epigenetic regulation of gene expression, HDACs can also control plant tolerance to stress by regulating transcription, translation, and metabolic activities and possibly assembly-disassembly of stress granules (SGs) through lysine deacetylation of non-histone proteins.
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Affiliation(s)
- Xiaoyun Cui
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Saclay, 91405 Orsay, France
| | - Avilien Dard
- Laboratoire Génome et Développement des Plantes, CNRS, Université Perpignan Via Domitia, 66860 Perpignan, France; VIB-UGent Center for Plant Systems Biology, Ghent University, Technologiepark-Zwijnaarde 71, - 9052 Ghent, Belgium
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, CNRS, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Saclay, 91405 Orsay, France; National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China.
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3
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Chen Y, Hung FY, Sugimoto K. Epigenomic reprogramming in plant regeneration: Locate before you modify. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102415. [PMID: 37437389 DOI: 10.1016/j.pbi.2023.102415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Plants possess remarkable abilities for regeneration, and this developmental capability is strongly influenced by environmental conditions. Previous research has highlighted the positive effects of wound signaling and warm temperature on plant regeneration, and recent studies suggest that light and nutrient signals also influence the regenerative efficiencies. Several epigenetic factors, such as histone acetyl-transferases (HATs), POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), and H2A variants, play crucial roles in regulating the expression of genes implicated in plant regeneration. However, how these epigenetic factors recognize specific genomic regions to regulate regeneration genes is still unclear. In this article, we describe the latest studies of epigenetic regulation and discuss the functional coordination between transcription factors and epigenetic modifiers in plant regeneration.
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Affiliation(s)
- Yu Chen
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Fu-Yu Hung
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan.
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan.
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4
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Tilak P, Kotnik F, Née G, Seidel J, Sindlinger J, Heinkow P, Eirich J, Schwarzer D, Finkemeier I. Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36961081 DOI: 10.1111/tpj.16206] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins play important roles in the acclimation of plants to environmental stress. Lysine acetylation is a dynamic and reversible PTM, which can be removed by histone deacetylases. Here we investigated the role of lysine acetylation in the response of Arabidopsis leaves to 1 week of salt stress. A quantitative mass spectrometry analysis revealed an increase in lysine acetylation of several proteins from cytosol and plastids, which was accompanied by altered histone deacetylase activities in the salt-treated leaves. While activities of HDA14 and HDA15 were decreased upon salt stress, HDA5 showed a mild and HDA19 a strong increase in activity. Since HDA5 is a cytosolic-nuclear enzyme from the class II histone deacetylase family with yet unknown protein substrates, we performed a lysine acetylome analysis on hda5 mutants and characterized its substrate proteins. Next to histone H2B, the salt stress-responsive transcription factor GT2L and the dehydration-related protein ERD7 were identified as HDA5 substrates. In addition, in protein-protein interaction studies, HDA18 was discovered, among other interacting proteins, to work in a complex together with HDA5. Altogether, this study revealed the substrate proteins of HDA5 and identified new lysine acetylation sites which are hyperacetylated upon salt stress. The identification of specific histone deacetylase substrate proteins, apart from histones, will be important to unravel the acclimation response of Arabidopsis to salt stress and their role in plant physiology.
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Affiliation(s)
- Priyadarshini Tilak
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Florian Kotnik
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Guillaume Née
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Julian Seidel
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Paulina Heinkow
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
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Fan L, Shi G, Yang J, Liu G, Niu Z, Ye W, Wu S, Wang L, Guan Q. A Protective Role of Phenylalanine Ammonia-Lyase from Astragalus membranaceus against Saline-Alkali Stress. Int J Mol Sci 2022; 23:ijms232415686. [PMID: 36555329 PMCID: PMC9779599 DOI: 10.3390/ijms232415686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Phenylalanine ammonia-lyase (PAL, E.C.4.3.1.5) catalyzes the benzene propane metabolism and is the most extensively studied enzyme of the phenylpropanoid pathway. However, the role of PAL genes in Astragalus membranaceus, a non-model plant showing high capability toward abiotic stress, is less studied. Here, we cloned AmPAL and found that it encodes a protein that resides in the cytoplasmic membrane. The mRNA of AmPAL was strongly induced by NaCl or NaHCO3 treatment, especially in the root. Overexpressing AmPAL in Nicotiana tabacum resulted in higher PAL enzyme activities, lower levels of malondialdehyde (MDA), and better root elongation in the seedlings under stress treatment compared to the control plants. The protective role of AmPAL under saline-alkali stress was also observed in 30-day soil-grown plants, which showed higher levels of superoxide dismutase (SOD), proline, and chlorophyll compared to wild-type N. Tabacum. Collectively, we provide evidence that AmPAL is responsive to multiple abiotic stresses and that manipulating the expression of AmPAL can be used to increase the tolerance to adverse environmental factors in plants.
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Affiliation(s)
- Lijuan Fan
- The College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Gongfa Shi
- The College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Juan Yang
- The College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Guiling Liu
- The College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Zhaoqian Niu
- The College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Wangbin Ye
- The College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Songquan Wu
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University, Yanji 133002, China
| | - Ling Wang
- The College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
- Correspondence: or (L.W.); (Q.G.)
| | - Qingjie Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
- Correspondence: or (L.W.); (Q.G.)
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Xiong L, Zhou W, Mas P. Illuminating the Arabidopsis circadian epigenome: Dynamics of histone acetylation and deacetylation. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102268. [PMID: 35921796 DOI: 10.1016/j.pbi.2022.102268] [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: 02/08/2022] [Revised: 06/21/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock generates rhythms in biological processes including plant development and metabolism. Light synchronizes the circadian clock with the day and night cycle and also triggers developmental transitions such as germination, or flowering. The circadian and light signaling pathways are closely interconnected and understanding their mechanisms of action and regulation requires the integration of both pathways in their complexity. Here, we provide a glimpse into how chromatin remodeling lies at the interface of the circadian and light signaling regulation. We focus on histone acetylation/deacetylation and the generation of permissive or repressive states for transcription. Several chromatin remodelers intervene in both pathways, suggesting that interaction with specific transcription factors might specify the proper timing or light-dependent responses. Deciphering the repertoire of chromatin remodelers and their interacting transcription factors will provide a view on the circadian and light-dependent epigenetic landscape amenable for mechanistic studies and timely regulation of transcription in plants.
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Affiliation(s)
- Lu Xiong
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Wenguan Zhou
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), 08028, Barcelona, Spain.
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7
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Patitaki E, Schivre G, Zioutopoulou A, Perrella G, Bourbousse C, Barneche F, Kaiserli E. Light, chromatin, action: nuclear events regulating light signaling in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:333-349. [PMID: 35949052 PMCID: PMC9826491 DOI: 10.1111/nph.18424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/26/2022] [Indexed: 05/31/2023]
Abstract
The plant nucleus provides a major hub for environmental signal integration at the chromatin level. Multiple light signaling pathways operate and exchange information by regulating a large repertoire of gene targets that shape plant responses to a changing environment. In addition to the established role of transcription factors in triggering photoregulated changes in gene expression, there are eminent reports on the significance of chromatin regulators and nuclear scaffold dynamics in promoting light-induced plant responses. Here, we report and discuss recent advances in chromatin-regulatory mechanisms modulating plant architecture and development in response to light, including the molecular and physiological roles of key modifications such as DNA, RNA and histone methylation, and/or acetylation. The significance of the formation of biomolecular condensates of key light signaling components is discussed and potential applications to agricultural practices overviewed.
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Affiliation(s)
- Eirini Patitaki
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Geoffrey Schivre
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
- Université Paris‐SaclayOrsay91400France
| | - Anna Zioutopoulou
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Giorgio Perrella
- Department of BiosciencesUniversity of MilanVia Giovanni Celoria, 2620133MilanItaly
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
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Huang D, Lan W, Ma W, Huang R, Lin W, Li M, Chen CY, Wu K, Miao Y. WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1411-1429. [PMID: 35510566 DOI: 10.1111/jipb.13272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Leaf senescence is controlled by a complex regulatory network in which robustness is ensured by the activity of transcription factors and epigenetic regulators. However, how these coordinate the process of leaf senescence remains poorly understood. We found that WHIRLY1 interacts with Histone Deacetylase (HDA)15, a Reduced Potassium Dependence3 (RPD3)/HDA1-type HDA, by using green fluorescent protein-nanotrap-mass spectrum assays. The development-dependent interaction between WHIRLY1 and HDA15 was further confirmed by bimolecular fluorescence complementation assays and co-immunoprecipitation assays in Arabidopsis. Multi-omics genome-wide transcriptome and H3K9 acetylome enrichment analysis showed that HDA15 delays leaf senescence and flowering by repressing the expression of the positive regulators of leaf senescence and flowering, such as LOX2 and LARP1C, and reducing H3K9ac levels at these loci; WHIRLY1 and HDA15 co-target to the region near the transcription start site of a subset of nutrient recycling-related genes (e.g., Glutathione S-transferases 10, non-coding RNA, and photosystem II protein D1 synthesizer attenuator PDIL1-2), as well as WRKY53 and ELF4, and co-repress their expression by removing H3K9 acetylation. Our study revealed a key transcription regulatory node of nutrient recycling and senescence-associated genes involved in leaf senescence and flowering via the recruitment of HDA15 by the single-stranded DNA/RNA-binding protein WHIRLY1.
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Affiliation(s)
- Dongmei Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Lan
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Weibo Ma
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rulin Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenfang Lin
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengsi Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chia-Yang Chen
- Institute of Botany, College of Life Sciences, Taiwan University, Taibei, 106, China
| | - Keqiang Wu
- Institute of Botany, College of Life Sciences, Taiwan University, Taibei, 106, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Sai CB, Chidambaranathan P, Samantaray S. Role of histone deacetylase inhibitors in androgenic callus induction of Oryza sativa sub indica, in sight into evolution and mode of action of histone deacetylase genes. Mol Biol Rep 2022; 49:2169-2183. [PMID: 34985645 DOI: 10.1007/s11033-021-07036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The potential of paddy breeding has reached its pinnacle, and hybrids have been the principal research outcome. Hence, our hypothesis was based on improvising the callus induction efficiency of recalcitrant Oryza sativa sub. indica hybrids by intervening into their cellular functions like cell division and histone regulation for the production of doubled haploids, a better output compared to hybrids. METHODOLOGY AND RESULTS Insight into the mechanism of cell division is the foremost concern in altering the same and hence studies on evolution, expression and action of histone deacetylase and its 12 genes (9 HDA and 3 HD-tunin genes) were chosen in the hypothesis. Expression of HDA genes at three stages (anther dehiscence, 1st callusing and second callusing stages) with inhibitor (trichostatin-A) interventions indicated 1st callusing stage as the most important in influencing callus induction and also the genes HDA19, 6, 15 and 5 were the most important. TSA alone had a significant impact on the regulation of the genes HDT 702, HDA19, HDA9, and HDA6. Higher expression of HDA19 and HDA6 was involved in maximizing callus induction; HDA15 had an antagonistic expression compared to HDA19/6 and might be involved in chlorophyll regulation during regeneration. Results of evolutionary analysis on histone deacetylases indicated a long and single lineage of origin denoting its importance in the basic cellular functions. The tubulin deacetylation gene HDA5, which was exclusively found in dicotyledons, had a recent evolutionary history only from terrestrial plants, and also had significant conservation in its motifs and NLS region. CONCLUSION By combating the recalcitrant nature of Indica cultivars, molecular editing on a combination of HDA genes will enhance the callus induction and regeneration efficiency of the next generation of doubled haploids, therby improving the total yield.
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Affiliation(s)
- Cayalvizhi B Sai
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India.
| | - Parameswaran Chidambaranathan
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India
| | - Sangamitra Samantaray
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India
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Du Q, Fang Y, Jiang J, Chen M, Fu X, Yang Z, Luo L, Wu Q, Yang Q, Wang L, Qu Z, Li X, Xie X. Characterization of histone deacetylases and their roles in response to abiotic and PAMPs stresses in Sorghum bicolor. BMC Genomics 2022; 23:28. [PMID: 34991465 PMCID: PMC8739980 DOI: 10.1186/s12864-021-08229-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Histone deacetylases (HDACs) play an important role in the regulation of gene expression, which is indispensable in plant growth, development, and responses to environmental stresses. In Arabidopsis and rice, the molecular functions of HDACs have been well-described. However, systematic analysis of the HDAC gene family and gene expression in response to biotic and abiotic stresses has not been reported for sorghum. RESULTS We conducted a systematic analysis of the sorghum HDAC gene family and identified 19 SbHDACs mainly distributed on eight chromosomes. Phylogenetic tree analysis of SbHDACs showed that the gene family was divided into three subfamilies: RPD3/HDA1, SIR2, and HD2. Tissue-specific expression results showed that SbHDACs displayed different expression patterns in different tissues, indicating that these genes may perform different functions in growth and development. The expression pattern of SbHDACs under different stresses (high and low temperature, drought, osmotic and salt) and pathogen-associated molecular model (PAMPs) elf18, chitin, and flg22) indicated that SbHDAC genes may participate in adversity responses and biological stress defenses. Overexpression of SbHDA1, SbHDA3, SbHDT2 and SbSRT2 in Escherichia coli promoted the growth of recombinant cells under abiotic stress. Interestingly, we also showed that the sorghum acetylation level was enhanced when plants were under cold, heat, drought, osmotic and salt stresses. The findings will help us to understand the HDAC gene family in sorghum, and illuminate the molecular mechanism of the responses to abiotic and biotic stresses. CONCLUSION We have identified and classified 19 HDAC genes in sorghum. Our data provides insights into the evolution of the HDAC gene family and further support the hypothesis that these genes are important for the plant responses to abiotic and biotic stresses.
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Affiliation(s)
- Qiaoli Du
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, PR China
| | - Meiqing Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Xiaodong Fu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Zaifu Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Liting Luo
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Qijiao Wu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Qian Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Lujie Wang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Zhiguang Qu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, PR China
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, 550025, PR China.
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11
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Yruela I, Moreno-Yruela C, Olsen CA. Zn 2+-Dependent Histone Deacetylases in Plants: Structure and Evolution. TRENDS IN PLANT SCIENCE 2021; 26:741-757. [PMID: 33461867 DOI: 10.1016/j.tplants.2020.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Zn2+-dependent histone deacetylases are widely distributed in archaea, bacteria, and eukaryotes. Through deacetylation of histones and other biomolecules, these enzymes regulate mammalian gene expression, microtubule stability, and polyamine metabolism. In plants, they play essential roles in development and stress response, but little is known about their biochemistry. We provide here a holistic revision of plant histone deacetylase (HDA) phylogeny and translate recent lessons from other organisms. HDA evolution correlates with a gain of structural ductility/disorder, as observed for other proteins. We also highlight two recently identified Brassicaceae-specific HDAs, as well as unprecedented key mutations that would affect the catalytic activity of individual HDAs. This revised phylogeny will contextualize future studies and illuminate research on plant development and adaptation.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Montañana 1005, 50059 Zaragoza, Spain; Group of Biochemistry, Biophysics, and Computational Biology (GBsC), Institute for Biocomputation and Physics of Complex Systems (BIFI) and Universidad de Zaragoza (UNIZAR) Joint Unit to CSIC, Zaragoza, Spain.
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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12
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Zhang M, Teixeira da Silva JA, Yu Z, Wang H, Si C, Zhao C, He C, Duan J. Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments. PeerJ 2020; 8:e10482. [PMID: 33362966 PMCID: PMC7747690 DOI: 10.7717/peerj.10482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/12/2020] [Indexed: 11/20/2022] Open
Abstract
The deacetylation of core histones controlled by the action of histone deacetylases (HDACs) plays an important role in the epigenetic regulation of plant gene transcription. However, no systematic analysis of HDAC genes in Dendrobium officinale, a medicinal orchid, has been performed. In the current study, a total of 14 histone deacetylases in D. officinale were identified and characterized using bioinformatics-based methods. These genes were classified into RPD3/HDA1, SIR2, and HD2 subfamilies. Most DoHDAC genes in the same subfamily shared similar structures, and their encoded proteins contained similar motifs, suggesting that the HDAC family members are highly conserved and might have similar functions. Different cis-acting elements in promoters were related to abiotic stresses and exogenous plant hormones. A transient expression assay in onion epidermal cells by Agrobacterium-mediated transformation indicated that all of the detected histone deacetylases such as DoHDA7, DoHDA9, DoHDA10, DoHDT3, DoHDT4, DoSRT1 and DoSRT2, were localized in the nucleus. A tissue-specific analysis based on RNA-seq suggested that DoHDAC genes play a role in growth and development in D. officinale. The expression profiles of selected DoHDAC genes under abiotic stresses and plant hormone treatments were analyzed by qRT-PCR. DoHDA3, DoHDA8, DoHDA10 and DoHDT4 were modulated by multiple abiotic stresses and phytohormones, indicating that these genes were involved in abiotic stress response and phytohormone signaling pathways. These results provide valuable information for molecular studies to further elucidate the function of DoHDAC genes.
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Affiliation(s)
- Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Haobin Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Conghui Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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13
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Alinsug MV, Radziejwoski A, Deocaris CC. AtHDA15 binds directly to COP1 positively regulating photomorphogenesis. Biochem Biophys Res Commun 2020; 533:806-812. [PMID: 32993965 DOI: 10.1016/j.bbrc.2020.09.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 11/18/2022]
Abstract
Reversible histone acetylation and deacetylation play crucial roles in modulating light-regulated gene expression during seedling development. However, it remains largely unknown how histone-modifying enzymes interpose within the molecular framework of light signaling network. In this study, we show that AtHDA15 positively regulates photomorphogenesis by directly binding to COP1, a master regulator in the repression of photomorphogenesis. hda15 T-DNA knock-out and RNAi lines exhibited light hyposensitivity with reduced HY5 and PIF3 protein levels leading to long hypocotyl phenotypes in the dark while its overexpression leads to increased HY5 concentrations and short hypocotyl phenotypes. In vivo and in vitro binding assays show that HDA15 directly interacts with COP1 inside the nucleus modulating COP1's repressive activities. As COP1 is established to act within the nucleus to regulate specific transcription factors associated with growth and development in skotomorphogenesis, the direct binding by HDA15 is predicted to abrogate activities of COP1 in the presence of light and modulate its repressive activities in the dark. Our results append the mounting evidence for the role of HDACs in post-translational regulation in addition to their well-known histone modifying functions.
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Affiliation(s)
- Malona V Alinsug
- Institute of Plant Biology, College of Life Sciences, National Taiwan University, Taipei, Taiwan; Center for Food & Bio Convergence, College of Agriculture & Life Sciences, Seoul National University, South Korea; Science Department, College of Natural Sciences & Mathematics, Mindanao State University-General Santos City, Philippines.
| | - Amandine Radziejwoski
- Institute of Plant Biology, College of Life Sciences, National Taiwan University, Taipei, Taiwan; Department of Life Sciences, College of Science, Pohang University of Science & Technology, Pohang, South Korea
| | - Custer C Deocaris
- Biomedical Research Section, Philippine Nuclear Research Institute, Department of Science and Technology, Commonwealth Avenue, Diliman, Quezon City, Philippines; Technological Institute of the Philippines, Cubao, Quezon City, Philippines
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14
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Wang X, Ajab Z, Liu C, Hu S, Liu J, Guan Q. Overexpression of transcription factor SlWRKY28 improved the tolerance of Populus davidiana × P. bolleana to alkaline salt stress. BMC Genet 2020; 21:103. [PMID: 32928116 PMCID: PMC7488863 DOI: 10.1186/s12863-020-00904-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/20/2020] [Indexed: 11/24/2022] Open
Abstract
Background WRKY transcription factors (TFs) have been suggested to play crucial roles in the response to biotic and abiotic stresses. This study is the first to report the alkaline salt regulation of the WRKY gene. Results In this study, we cloned a WRKY gene (SlWRKY28) from the Salix linearistipularis and then transferred to the Populus davidiana × P. bolleana for expression. Sequence analysis on the transcriptome of Salix linearistipular showed the significant up-regulation of WRKY gene expression in response to salt-alkali stress in seedlings. Our data showed that SlWRKY28 localized to the nucleus. Furthermore, the expression of the SlWRKY28 from female plants increased with saline-alkali stress according to the northern blot analysis results. The results of 3,3′-Diaminobenzidine (DAB) staining showed that hydrogen peroxide (H2O2) concentration was lower under stress, but ascorbate peroxidase (APX) enzyme activity was significantly higher in the overexpressed plants than that in non-transgenic (NT) plants. Conclusions We found out the SlWRKY28 induced regulation of the enzyme gene in the reactive oxygen species (ROS) scavenging pathway is a potential mechanism for transgenic lines to improve their resistance to alkaline salt. This study shows theoretical and practical significance in determining SlWRKY28 transcription factors involved in the regulation of alkaline salt tolerance.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Zainab Ajab
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Chenxi Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Songmiao Hu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Jiali Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Qingjie Guan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China.
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15
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Jiang J, Ding AB, Liu F, Zhong X. Linking signaling pathways to histone acetylation dynamics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5179-5190. [PMID: 32333777 PMCID: PMC7475247 DOI: 10.1093/jxb/eraa202] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants face versatile environmental challenges and require proper responses at multiple levels for survival. Epigenetic modification of DNA and histones is a conserved gene-regulatory mechanism and plays critical roles in diverse aspects of biological processes, ranging from genome defense and imprinting to development and physiology. In recent years, emerging studies have revealed the interplay between signaling transduction pathways, epigenetic modifications, and chromatin cascades. Specifically, histone acetylation and deacetylation dictate plant responses to environmental cues by modulating chromatin dynamics to regulate downstream gene expression as signaling outputs. In this review, we summarize current understandings of the link between plant signaling pathways and epigenetic modifications with a focus on histone acetylation and deacetylation.
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Affiliation(s)
- Jianjun Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Correspondence: or
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Correspondence: or
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16
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Gipson AB, Giloteaux L, Hanson MR, Bentolila S. Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PLANTS 2020; 9:plants9030307. [PMID: 32121603 PMCID: PMC7154859 DOI: 10.3390/plants9030307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
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17
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Lacroix B, Citovsky V. Biolistic Approach for Transient Gene Expression Studies in Plants. Methods Mol Biol 2020; 2124:125-139. [PMID: 32277451 DOI: 10.1007/978-1-0716-0356-7_6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since its inception in the late 1980s, the delivery of exogenous nucleic acids into living cells via high-velocity microprojectiles (biolistic, or microparticle bombardment) has been an invaluable tool for both agricultural and fundamental plant research. Here, we review the technical aspects and the major applications of the biolistic method for studies involving transient gene expression in plant cells. These studies cover multiple areas of plant research, including gene expression, protein subcellular localization and cell-to-cell movement, plant virology, silencing, and the more recently developed targeted genome editing via transient expression of customized endonucleases.
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Affiliation(s)
- Benoît Lacroix
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, USA.
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, USA
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18
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Chen X, Ding AB, Zhong X. Functions and mechanisms of plant histone deacetylases. SCIENCE CHINA-LIFE SCIENCES 2019; 63:206-216. [PMID: 31879846 DOI: 10.1007/s11427-019-1587-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
Lysine acetylation, one of the major types of post-translational modifications, plays critical roles in regulating gene expression and protein function. Histone deacetylases (HDACs) are responsible for removing acetyl groups from lysines of both histone and non-histone proteins. While tremendous progress has been made in understanding the function and mechanism of HDACs in animals in the past two decades, nearly half of the HDAC studies in plants were reported within the past five years. In this review, we summarize the major findings on plant HDACs, with a focus on the model plant Arabidopsis thaliana, and highlight the components, regulatory mechanisms, and biological functions of HDAC complexes.
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Affiliation(s)
- Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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19
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Ueda M, Matsui A, Watanabe S, Kobayashi M, Saito K, Tanaka M, Ishida J, Kusano M, Seo M, Seki M. Transcriptome Analysis of the Hierarchical Response of Histone Deacetylase Proteins That Respond in an Antagonistic Manner to Salinity Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:1323. [PMID: 31681394 PMCID: PMC6813852 DOI: 10.3389/fpls.2019.01323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/23/2019] [Indexed: 05/29/2023]
Abstract
Acetylation in histone and non-histone proteins is balanced by histone acetyltransferase and histone deacetylase (HDAC) enzymatic activity, an essential aspect of fine-tuning plant response to environmental stresses. HDACs in Arabidopsis are composed of three families (RPD3-like, SIRT, and HD-tuins). A previous study indicated that class I (HDA19) and class II (HDA5/14/15/18) RPD3-like family HDACs control positive and negative responses to salinity stress, respectively. Furthermore, quintuple hda5/14/15/18/19 mutants (quint) exhibit salinity stress tolerance, suggesting that hda19 suppresses the sensitivity to salinity stress present in quadruple hda5/14/15/18 mutants (quad). In the present study, transcriptome analysis of the quint mutant was conducted to elucidate the hierarchical control of salinity stress response operated by RPD3-like family HDACs (HDA5/14/15/18/19). The analysis identified 4,832 salt-responsive genes in wild-type (Col-0), hda19-3, quad, and quint plants and revealed that 56.7% of the salt-responsive genes exhibited a similar expression pattern in both the hda19-3 and quint plants. These results indicate that deficiency in HDA19 has a bigger impact on salinity stress response than in class II HDACs. Furthermore, the expression pattern of genes encoding enzymes that metabolize phytohormones raises the possibility that a drastic change in the homeostasis of phytohormones, such as abscisic acid, brassinosteroid, and gibberellin, may contribute to increasing stress tolerance in hda19-3 and quint plants. Among these phytohormones, abscisic acid accumulation actually increased in hda19-3 and quint plants, and decreased in quad, compared with wild-type plants. Importantly, 7.8% of the salt-responsive genes in quint plants exhibited a similar expression pattern in quad plants, suggesting that some gene sets are regulated in an HDA5/14/15/18-dependent manner. The transcriptome analysis conducted in the present study revealed the hierarchical and independent regulation of salt stress response that is mediated through HDA19 and class II HDACs.
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Affiliation(s)
- Minoru Ueda
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Shunsuke Watanabe
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Makoto Kobayashi
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Junko Ishida
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Miyako Kusano
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mitsunori Seo
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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20
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Molecular cloning and subcellular localization of six HDACs and their roles in response to salt and drought stress in kenaf (Hibiscus cannabinus L.). Biol Res 2019; 52:20. [PMID: 30954076 PMCID: PMC6451785 DOI: 10.1186/s40659-019-0227-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 03/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone acetylation is an important epigenetic modification that regulates gene activity in response to stress. Histone acetylation levels are reversibly regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). The imperative roles of HDACs in gene transcription, transcriptional regulation, growth and responses to stressful environment have been widely investigated in Arabidopsis. However, data regarding HDACs in kenaf crop has not been disclosed yet. RESULTS In this study, six HDACs genes (HcHDA2, HcHDA6, HcHDA8, HcHDA9, HcHDA19, and HcSRT2) were isolated and characterized. Phylogenetic tree revealed that these HcHDACs shared high degree of sequence homology with those of Gossypium arboreum. Subcellular localization analysis showed that GFP-tagged HcHDA2 and HcHDA8 were predominantly localized in the nucleus, HcHDA6 and HcHDA19 in nucleus and cytosol. The HcHDA9 was found in both nucleus and plasma membranes. Real-time quantitative PCR showed that the six HcHDACs genes were expressed with distinct expression patterns across plant tissues. Furthermore, we determined differential accumulation of HcHDACs transcripts under salt and drought treatments, indicating that these enzymes may participate in the biological process under stress in kenaf. Finally, we showed that the levels of histone H3 and H4 acetylation were modulated by salt and drought stress in kenaf. CONCLUSIONS We have isolated and characterized six HDACs genes from kenaf. These data showed that HDACs are imperative players for growth and development as well abiotic stress responses in kenaf.
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21
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Shi C, Zhao L, Zhang X, Lv G, Pan Y, Chen F. Gene regulatory network and abundant genetic variation play critical roles in heading stage of polyploidy wheat. BMC PLANT BIOLOGY 2019; 19:6. [PMID: 30606101 PMCID: PMC6318890 DOI: 10.1186/s12870-018-1591-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/05/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND The extensive adaptability of polyploidy wheat is attributed to its complex genome, and accurately controlling heading stage is a prime target in wheat breeding process. Wheat heading stage is an essential growth and development processes since it starts at a crucial point in the transition from vegetative phase to reproductive phase. MAIN BODY Heading stage is mainly decided by vernalization, photoperiod, hormone (like gibberellic acid, GA), and earliness per se (Eps). As a polyploidy species, common wheat possesses the abundant genetic variation, such as allelic variation, copy number variation etc., which have a strong effect on regulation of wheat growth and development. Therefore, understanding genetic manipulation of heading stage is pivotal for controlling the heading stage in wheat. In this review, we summarized the recent advances in the genetic regulatory mechanisms and abundant variation in genetic diversity controlling heading stage in wheat, as well as the interaction mechanism of different signals and the contribution of different genetic variation. We first summarized the genes involved in vernalization, photoperoid and other signals cross-talk with each other to control wheat heading stage, then the abundant genetic variation related to signal components associated with wheat heading stage was also elaborated in detail. CONCLUSION Our knowledge of the regulatory network of wheat heading can be used to adjust the duration of the growth phase for the purpose of acclimatizing to different geographical environments.
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Affiliation(s)
- Chaonan Shi
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Xiangfen Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Guoguo Lv
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Yubo Pan
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
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22
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Bourbousse C, Barneche F, Laloi C. Plant Chromatin Catches the Sun. FRONTIERS IN PLANT SCIENCE 2019; 10:1728. [PMID: 32038692 PMCID: PMC6992579 DOI: 10.3389/fpls.2019.01728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/09/2019] [Indexed: 05/08/2023]
Abstract
Plants use solar radiation as energy source for photosynthesis. They also take advantage of the information provided by the varying properties of sunlight, such as wavelength, orientation, and periodicity, to trigger physiological and developmental adaptations to a changing environment. After more than a century of research efforts in plant photobiology, multiple light signaling pathways converging onto chromatin-based mechanisms have now been identified, which in some instances play critical roles in plant phenotypic plasticity. In addition to locus-specific changes linked to transcription regulation, light signals impact higher-order chromatin organization. Here, we summarize current knowledge on how light can affect the global composition and the spatial distribution of chromatin domains. We introduce emerging questions on the functional links between light signaling and the epigenome, and further discuss how different chromatin regulatory layers may interconnect during plant adaptive responses to light.
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Affiliation(s)
- Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Christophe Laloi
- Aix Marseille Univ, CEA, CNRS, BIAM, Luminy Génétique et Biophysique des Plantes, Marseille, France
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23
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Yang C, Shen W, Chen H, Chu L, Xu Y, Zhou X, Liu C, Chen C, Zeng J, Liu J, Li Q, Gao C, Charron JB, Luo M. Characterization and subcellular localization of histone deacetylases and their roles in response to abiotic stresses in soybean. BMC PLANT BIOLOGY 2018; 18:226. [PMID: 30305032 PMCID: PMC6180487 DOI: 10.1186/s12870-018-1454-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 10/01/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Histone deacetylases (HDACs) function as key epigenetic factors in repressing the expression of genes in multiple aspects of plant growth, development and plant response to abiotic or biotic stresses. To date, the molecular function of HDACs is well described in Arabidopsis thaliana, but no systematic analysis of this gene family in soybean (Glycine max) has been reported. RESULTS In this study, 28 HDAC genes from soybean genome were identified, which were asymmetrically distributed on 12 chromosomes. Phylogenetic analysis demonstrated that GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2. Subcellular localization analysis revealed that YFP-tagged GmSRT4, GmHDT2 and GmHDT4 were predominantly localized in the nucleus, whereas GmHDA6, GmHDA13, GmHDA14 and GmHDA16 were found in both the cytoplasm and nucleus. Real-time quantitative PCR showed that GmHDA6, GmHDA13, GmHDA14, GmHDA16 and GmHDT4 were broadly expressed across plant tissues, while GmHDA8, GmSRT2, GmSRT4 and GmHDT2 showed differential expression across various tissues. Interestingly, we measured differential changes in GmHDACs transcripts accumulation in response to several abiotic cues, indicating that these epigenetic modifiers could potentially be part of a dynamic transcriptional response to stress in soybean. Finally, we show that the levels of histone marks previously reported to be associated with plant HDACs are modulated by cold and heat in this legume. CONCLUSION We have identified and classified 28 HDAC genes in soybean. Our data provides insights into the evolution of the HDAC gene family and further support the hypothesis that these genes are important for the plant responses to environmental stress.
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Affiliation(s)
- Chao Yang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Hongfeng Chen
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Liutian Chu
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yingchao Xu
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaochen Zhou
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chuanliang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Chunmiao Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Jiahui Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Jin Liu
- Institute for Food and Bioresource Engineering, Department of Energy and Resources Engineering and BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
| | - Qianfeng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009 China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Jean-Benoit Charron
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
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Zhao ML, Wang W, Nie H, Cao SS, Du LF. In silico structure prediction and inhibition mechanism studies of AtHDA14 as revealed by homology modeling, docking, molecular dynamics simulation. Comput Biol Chem 2018; 75:120-130. [PMID: 29775968 DOI: 10.1016/j.compbiolchem.2018.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/03/2018] [Accepted: 05/06/2018] [Indexed: 12/14/2022]
Abstract
Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots. We also performed virtual screening of AtHDA14 by docking with small molecule drugs and predicted their ADMET properties to select representative inhibitors. MD simulation for representative AtHDA14-ligand complexes was carried out to further research and reveal their stability and inhibition mechanism. Meanwhile, MM/PBSA method was utilized to obtain more valuable information about the residues energy contribution. Moreover, compared with four candidate inhibitors, we also found that compound 645533 and 6918837 might be a more potent AtHDA14 inhibitor than TSA (444732) and SAHA (5311). Therefore, compound 6445533 and 6918837 was anticipated to be a promising drug candidate for inhibition of AtHDA14.
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Affiliation(s)
- Ming-Lang Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Wang Wang
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Hu Nie
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Sha-Sha Cao
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Lin-Fang Du
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
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Ueda M, Matsui A, Tanaka M, Nakamura T, Abe T, Sako K, Sasaki T, Kim JM, Ito A, Nishino N, Shimada H, Yoshida M, Seki M. The Distinct Roles of Class I and II RPD3-Like Histone Deacetylases in Salinity Stress Response. PLANT PHYSIOLOGY 2017; 175:1760-1773. [PMID: 29018096 PMCID: PMC5717743 DOI: 10.1104/pp.17.01332] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/06/2017] [Indexed: 05/06/2023]
Abstract
Histone acetylation is an essential process in the epigenetic regulation of diverse biological processes, including environmental stress responses in plants. Previously, our research group identified a histone deacetylase (HDAC) inhibitor (HDI) that confers salt tolerance in Arabidopsis (Arabidopsis thaliana). In this study, we demonstrate that class I HDAC (HDA19) and class II HDACs (HDA5/14/15/18) control responses to salt stress through different pathways. The screening of 12 different selective HDIs indicated that seven newly reported HDIs enhance salt tolerance. Genetic analysis, based on a pharmacological study, identified which HDACs function in salinity stress tolerance. In the wild-type Columbia-0 background, hda19 plants exhibit tolerance to high-salinity stress, while hda5/14/15/18 plants exhibit hypersensitivity to salt stress. Transcriptome analysis revealed that the effect of HDA19 deficiency on the response to salinity stress is distinct from that of HDA5/14/15/18 deficiencies. In hda19 plants, the expression levels of stress tolerance-related genes, late embryogenesis abundant proteins that prevent protein aggregation and positive regulators such as ABI5 and NAC019 in abscisic acid signaling, were induced strongly relative to the wild type. Neither of these elements was up-regulated in the hda5/14/15/18 plants. The mutagenesis of HDA19 by genome editing in the hda5/14/15/18 plants enhanced salt tolerance, suggesting that suppression of HDA19 masks the phenotype caused by the suppression of class II HDACs in the salinity stress response. Collectively, our results demonstrate that HDIs that inhibit class I HDACs allow the rescue of plants from salinity stress regardless of their selectivity, and they provide insight into the hierarchal regulation of environmental stress responses through HDAC isoforms.
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Affiliation(s)
- Minoru Ueda
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Tomoe Nakamura
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika-ku, Tokyo 125-8585, Japan
| | - Takahiro Abe
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa 244-0813, Japan
| | - Kaori Sako
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Taku Sasaki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Norikazu Nishino
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika-ku, Tokyo 125-8585, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa 244-0813, Japan
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Guan Q, Liao X, He M, Li X, Wang Z, Ma H, Yu S, Liu S. Tolerance analysis of chloroplast OsCu/Zn-SOD overexpressing rice under NaCl and NaHCO3 stress. PLoS One 2017; 12:e0186052. [PMID: 29020034 PMCID: PMC5636109 DOI: 10.1371/journal.pone.0186052] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/25/2017] [Indexed: 12/16/2022] Open
Abstract
The 636-bp-long cDNA sequence of OsCu/Zn-SOD (AK059841) was cloned from Oryza sativa var. Longjing11 via reverse transcription polymerase chain reaction (RT-PCR). The encoded protein comprised of 211 amino acids is highly homologous to Cu/Zn-SOD proteins from tuscacera rice and millet. Quantitative RT-PCR revealed that in rice, the level of OsCu/Zn-SOD gene expression was lowest in roots and was highest in petals and during the S5 leaf stage. Moreover, the expression level of OsCu/Zn-SOD gene expression decreased during the L5 leaf stage to maturity. The level of OsCu/Zn-SOD gene expression, however, was increased under saline–sodic stress and NaHCO3 stress. Germination tests under 125, 150, and 175 mM NaCl revealed that OsCu/Zn-SOD-overexpressing lines performed better than the non-transgenic (NT) Longjing11 lines in terms of germination rate and height. Subjecting seedlings to NaHCO3 and water stress revealed that OsCu/Zn-SOD-overexpressing lines performed better than NT in terms of SOD activity, fresh weight, root length, and height. Under simulated NaHCO3 stress, OsCu/Zn-SOD-overexpressing lines performed better than NT in terms of survival rate (25.19% > 6.67%) and yield traits (average grain weight 20.6 > 18.15 g). This study showed that OsCu/Zn-SOD gene overexpression increases the detoxification capacity of reactive oxygen species in O. sativa and reduces salt-induced oxidative damage. We also revealed the regulatory mechanism of OsCu/Zn-SOD enzyme in saline–sodic stress resistance in O. sativa. Moreover, we provided an experimental foundation for studying the mechanism of OsCu/Zn-SOD enzymes in the chloroplast.
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Affiliation(s)
- Qingjie Guan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Xu Liao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Mingliang He
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Xiufeng Li
- Lab of Soybean Molecular Biology and Molecular Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin City, Heilongjiang, China
| | - Zhenyu Wang
- Lab of Soybean Molecular Biology and Molecular Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin City, Heilongjiang, China
| | - Haiyan Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Song Yu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Shenkui Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
- * E-mail:
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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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Remarkable Evolutionary Conservation of Antiobesity ADIPOSE/WDTC1 Homologs in Animals and Plants. Genetics 2017; 207:153-162. [PMID: 28663238 DOI: 10.1534/genetics.116.198382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 06/25/2017] [Indexed: 11/18/2022] Open
Abstract
ASG2 (Altered Seed Germination 2) is a prenylated protein in Arabidopsis thaliana that participates to abscisic acid signaling and is proposed to act as a substrate adaptor for the DDB1 (DNA damage-binding protein 1)-CUL4 (Cullin 4) E3 ubiquitin ligase complex. ASG2 harbors WD40 and TetratricoPeptide Repeat (TPR) domains, and resembles the well-conserved animal gene called ADP (antiobesity factor ADIPOSE) in fly and WDTC1 (WD40 and TPR 1) in humans. Loss of function of WDTC1 results in an increase in adipocytes, fat accumulation, and obesity. Antiadipogenic functions of WDTC1 involve regulation of fat-related gene transcription, notably through its binding to histone deacetylases (HDACs). Our sequence and phylogenetic analysis reveals that ASG2 belongs to the ADP/WDTC1 cluster. ASG2 and WDTC1 share a highly conserved organization that encompasses structural and functional motifs: seven WD40 domains and WD40 hotspot-related residues, three TPR protein-protein interaction domains, DDB1-binding elements [H-box and DWD (DDB1-binding WD40 protein)-box], and a prenylatable C-terminus. Furthermore, ASG2 involvement in fat metabolism was confirmed by reverse genetic approaches using asg2 knockout Arabidopsis plants. Under limited irradiance, asg2 mutants produce "obese" seeds characterized by increased weight, oil body density, and higher fatty acid contents. In addition, considering some ASG2- and WDTC1-peculiar properties, we show that the WDTC1 C-terminus is prenylated in vitro and HDAC-binding capability is conserved in ASG2, suggesting that the regulation mechanism and targets of ADP/WDTC1-like proteins may be conserved features. Our findings reveal the remarkable evolutionary conservation of the structure and the physiological role of ADIPOSE homologs in animals and plants.
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Tang Y, Liu X, Liu X, Li Y, Wu K, Hou X. Arabidopsis NF-YCs Mediate the Light-Controlled Hypocotyl Elongation via Modulating Histone Acetylation. MOLECULAR PLANT 2017; 10:260-273. [PMID: 27876642 DOI: 10.1016/j.molp.2016.11.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 05/20/2023]
Abstract
Light is a crucial environmental signal that promotes photomorphogenesis, the developmental process with a series of light-dependent alterations for plants to adapt various external challenges. Chromatin modification has been proposed to be involved in such light-mediated growth, but the underlying mechanism is still elusive. In this study, we identified four Arabidopsis thaliana Nuclear Factor-YC homologs, NF-YC1, NF-YC3, NF-YC4, and NF-YC9 (NF-YCs), which function redundantly as repressors of light-controlled hypocotyl elongation via histone deacetylation. Obvious etiolation phenotypes are observed in NF-YCs loss-of-function mutant seedlings grown under light conditions, including significant elongated hypocotyls and fewer opened cotyledons. We found that NF-YCs interact with histone deacetylase HDA15 in the light, co-target the promoters of a set of hypocotyl elongation-related genes, and modulate the levels of histone H4 acetylation on the associated chromatins, thus repressing gene expression. In contrast, NF-YC-HDA15 complex is dismissed from the target genes in the dark, resulting in increased level of H4 acetylation and consequent etiolated growth. Further analyses revealed that transcriptional repression activity of NF-YCs on the light-controlled hypocotyl elongation partially depends on the deacetylation activity of HDA15, and loss of HDA15 function could rescue the short-hypocotyl phenotype of NF-YCs overexpression plants. Taken together, our results indicate that NF-YC1, NF-YC3, NF-YC4, and NF-YC9 function as transcriptional co-repressors by interacting with HDA15 to inhibit hypocotyl elongation in photomorphogenesis during the early seedling stage. Our findings highlight that NF-YCs can modulate plant development in response to environmental cues via epigenetic regulation.
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Affiliation(s)
- Yang Tang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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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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Guan QJ, Ma HY, Wang ZJ, Wang ZY, Bu QY, Liu SK. A rice LSD1-like-type ZFP gene OsLOL5 enhances saline-alkaline tolerance in transgenic Arabidopsis thaliana, yeast and rice. BMC Genomics 2016; 17:142. [PMID: 26920613 PMCID: PMC4769587 DOI: 10.1186/s12864-016-2460-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/10/2016] [Indexed: 11/26/2022] Open
Abstract
Background Zinc finger proteins (ZFPs) play an important role in regulating plant responses to abiotic stress. However, little is known about the function of LSD1-like-type ZFP in saline-alkaline (SA) stress resistance of rice. In this study, OsLOL5 (GenBank No. AJ620677), containing two LSD1-like-type C2C2 domains, was isolated and analyzed its protection roles in transgenic plants and yeast. OsLOL5 was located in the nucleus as evidenced by the bombardment of onion epidermal cells. Results OsLOL5 expression significantly increased in rice leaves and roots under 150 mmol L-1 NaCl, 30 mM NaHCO3, and 10 mmol L-1 H2O2 treatment, respectively. Overexpression of OsLOL5 in yeast resulted in SA tolerance at significant level. Transgenic Arabidopsis plants overexpressing OsLOL5 grew well in the presence ofboth NaCl and NaHCO3 treatments, whereas wild-type plants exhibited chlorosis, stunted growth phenotype, and even death. SA stress caused significant changes in the malondialdehyde (MDA) contents in non-transgenic plants compared with those in transgenic lines. Transgenic rice overexpressing OsLOL5 exhibited stronger resistance than NT under NaHCO3 treatment, as demonstrated by its greater shoot length, and fresh weight. The genes associated with oxidative stress, such as OsAPX2, OsCAT, OsCu/Zn-SOD, and OsRGRC2, were significantly upregulated in OsLOL5-overexpressing rice. The results suggested that OsLOL5 improved SA tolerance in plants, and regulated oxidative and salinity stress retardation via the active oxygen detoxification pathway. Conclusions The yeast INVScI bacterium grew significantly better than the control strain under NaCl, NaHCO3, and H2O2 treatments. These findings illustrated that OsLOL5 overexpression enhanced yeast resistance for SA stress through active oxygen species. The present study showed that the OsLOL5 genes involved in the ROS signaling pathways may combine with the model plant Arabidopsis and rice in LDS1-type ZFP by ROS signaling pathways that regulate cell necrosis. We speculated that the OsLOL5 active oxygen scavenging system may have coordinating roles. The present study further revealed that OsLOL5 ZFP could regulate oxidative stress function, but could also provide a basis for salt-resistant rice strains. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2460-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Q J Guan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
| | - H Y Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
| | - Z J Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
| | - Z Y Wang
- Lab of Soybean Molecular Biology and Molecular Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No.138 Haping Road, Nangang District, Harbin City, Heilongjiang, 150081, China.
| | - Q Y Bu
- Lab of Soybean Molecular Biology and Molecular Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No.138 Haping Road, Nangang District, Harbin City, Heilongjiang, 150081, China.
| | - S K Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
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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: 189] [Impact Index Per Article: 21.0] [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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Expression pattern and subcellular localization of the ovate protein family in rice. PLoS One 2015; 10:e0118966. [PMID: 25760462 PMCID: PMC4356581 DOI: 10.1371/journal.pone.0118966] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 01/08/2015] [Indexed: 02/05/2023] Open
Abstract
The Arabidopsis ovate family proteins (AtOFPs) have been shown to function as transcriptional repressors and regulate multiple aspects of plant growth and development. There are 31 genes that encode the full-length OVATE-domain containing proteins in the rice genome. In this study, the gene structure analysis revealed that OsOFPs are intron poor. Phylogenetic analysis suggested that OVATE proteins from rice, Arabidopsis and tomato can be divided into 4 groups (I–IV). Real-time quantitative polymerase chain reaction (RT-qPCR) analysis identified OsOFPs with different tissue-specific expression patterns at all stages of development in the rice plant. Interestingly, nearly half of the total number of OsOFP family was more highly expressed during the seed developmental stage. In addition, seed developmental cis-elements were found in the promoter region of the OsOFPs. Subcellular localization analysis revealed that YFP-OsOFP fusion proteins predominantly localized in the nucleus. Our results suggest that OsOFPs may act as regulatory proteins and play pivotal roles in the growth and development of rice.
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Guan Q, Wang Z, Wang X, Takano T, Liu S. A peroxisomal APX from Puccinellia tenuiflora improves the abiotic stress tolerance of transgenic Arabidopsis thaliana through decreasing of H2O2 accumulation. JOURNAL OF PLANT PHYSIOLOGY 2015; 175:183-91. [PMID: 25644292 DOI: 10.1016/j.jplph.2014.10.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 05/21/2023]
Abstract
Ascorbate peroxidase (APX, EC 1.11.1.11) is one of the major members of the ROS scavenging system that plays an important role in improving saline-alkali tolerance. Puccinellia tenuiflora, as a perennial wild grass, is able to grow in extreme saline-alkali soil environments. In this study, we investigated the relationship between the P. tenuiflora ascorbate peroxidase (PutAPX) gene and saline-alkali tolerance. A phylogenetic analysis indicated that PutAPX is closely related to AtAPX3 and OsAPX4 and that these genes are on the same branch. The PutAPX-GFP fusion protein is located in the peroxisome in onion epidermal cells. The transcriptional expression of PutAPX increased with prolonged exposure to NaCl, NaHCO3, PEG6000 and H2O2 stresses in P. tenuiflora. The overexpression of PutAPX in Arabidopsis thaliana significantly increased the tolerance of plants treated with 150 and 175mM NaCl and decreased the extent of lipid peroxidation. The transgenic seedlings presented higher chlorophyll content than wild type (WT) seedlings treated with 1, 3, and 5mM NaHCO3 and 3mM H2O2. The DAB staining results revealed that the H2O2 content in transgenic seedlings was significantly lower than that in WT plants under both normal conditions and 200mM NaCl stress. Moreover, the expression of APX proteins and enzyme activity in the transgenic seedlings increased to level that were greater than twofold higher than those found in WT plants exposed to 200mM NaCl. The saline-alkali tolerance conferred by the PutAPX gene may provide a reliable basis for the use of molecular breeding techniques to improve plant tolerance and obtain a better understanding of the physiological mechanism of anti-oxidative and ROS stresses.
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Affiliation(s)
- Qingjie Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No. 26 Hexing Road, Nangang District, Harbin 150040, China; Laboratory of Soybean Molecular Biology and Molecular Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No. 138 Haping Road, Nangang District, Harbin 150081, China
| | - Zhenjuan Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No. 26 Hexing Road, Nangang District, Harbin 150040, China
| | - Xuhui Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No. 26 Hexing Road, Nangang District, Harbin 150040, China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center, The University of Tokyo, Nishitokyo, Tokyo 188-0002, Japan
| | - Shenkui Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No. 26 Hexing Road, Nangang District, Harbin 150040, China.
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Rao RSP, Thelen JJ, Miernyk JA. Is Lys-Nɛ-acetylation the next big thing in post-translational modifications? TRENDS IN PLANT SCIENCE 2014; 19:550-3. [PMID: 24866592 DOI: 10.1016/j.tplants.2014.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/18/2014] [Accepted: 05/01/2014] [Indexed: 05/22/2023]
Abstract
Lys-N(ɛ)-acetylation (PKA) has recently ascended from a post-translational modification (PTM) of limited distribution to one approaching the abundance of O-phosphorylation. Thousands of KAC proteins have been identified in Archaea, bacteria, and Eukarya, and the KAC system of acetyltransferases, deacetylases, and binding proteins is superficially comparable with the kinases, phosphatases, and phospho- (P-)protein binding-proteins of O-phosphorylation. Herein, we describe recent results and compare several aspects of these two major systems of PTM in plants.
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Affiliation(s)
- R Shyama Prasad Rao
- Division of Biochemistry, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA
| | - Jay J Thelen
- Division of Biochemistry, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA
| | - Ján A Miernyk
- Division of Biochemistry, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA; Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA.
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Guan QJ, Wang LF, Bu QY, Wang ZY. The rice gene OsZFP6 functions in multiple stress tolerance responses in yeast and Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 82:1-8. [PMID: 24862452 DOI: 10.1016/j.plaphy.2014.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 04/26/2014] [Indexed: 06/03/2023]
Abstract
The role of zinc finger proteins in organismal stress conditions has been widely reported. However, little is known concerning the function of CCHC-type zinc finger proteins in rice. In this study, OsZFP6, a rice CCHC-type zinc finger protein 6 gene, was cloned from rice using RT-PCR. The OsZFP6 protein contains 305 amino acids and a conserved zinc finger domain and is localised to the nucleus. Southern blot analysis revealed that a single copy was encoded in the rice genome. OsZFP6 expression was increased by abiotic stress, including salt (NaCl), alkali (NaHCO3) and H2O2 treatment. When OsZFP6 was transformed into yeast, the transgenic yeast showed significantly increased resistance to NaHCO3 compared to the control. Moreover, Arabidopsis transgenic plants overexpressing OsZFP6 were more tolerant to both NaHCO3 and H2O2 treatments. Overall, we uncovered a role for OsZFP6 in abiotic stress responses and identified OsZFP6 as a putatively useful gene for developing crops with increased alkali and H2O2 tolerance.
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Affiliation(s)
- Qing-jie Guan
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, Heilongjiang 150081, China; Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Li-feng Wang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, State Key Laboratory Incubation Base for Cultivation and Physiology of Tropical Crops, Rubber Research Institute, CATAS, Danzhou, Hainan 571737, China
| | - Qing-yun Bu
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, Heilongjiang 150081, China
| | - Zhen-yu Wang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, Heilongjiang 150081, China.
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Grandperret V, Nicolas-Francès V, Wendehenne D, Bourque S. Type-II histone deacetylases: elusive plant nuclear signal transducers. PLANT, CELL & ENVIRONMENT 2014; 37:1259-69. [PMID: 24236403 DOI: 10.1111/pce.12236] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/04/2013] [Accepted: 11/10/2013] [Indexed: 05/20/2023]
Abstract
Since the beginning of the 21st century, numerous studies have concluded that the plant cell nucleus is one of the cellular compartments that define the specificity of the cellular response to an external stimulus or to a specific developmental stage. To that purpose, the nucleus contains all the enzymatic machinery required to carry out a wide variety of nuclear protein post-translational modifications (PTMs), which play an important role in signal transduction pathways leading to the modulation of specific sets of genes. PTMs include protein (de)acetylation which is controlled by the antagonistic activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Regarding protein deacetylation, plants are of particular interest: in addition to the RPD3-HDA1 and Sir2 HDAC families that they share with other eukaryotic organisms, plants have developed a specific family called type-II HDACs (HD2s). Interestingly, these HD2s are well conserved in plants and control fundamental biological processes such as seed germination, flowering or the response to pathogens. The aim of this review was to summarize current knowledge regarding this fascinating, but still poorly understood nuclear protein family.
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Affiliation(s)
- Vincent Grandperret
- Pôle Mécanisme et Gestion des Interactions Plantes-microorganismes - ERL CNRS 6300, Université de Bourgogne, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, Dijon cedex, 21065, France
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Barneche F, Malapeira J, Mas P. The impact of chromatin dynamics on plant light responses and circadian clock function. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2895-913. [PMID: 24520020 DOI: 10.1093/jxb/eru011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Research on the functional properties of nucleosome structure and composition dynamics has revealed that chromatin-level regulation is an essential component of light signalling and clock function in plants, two processes that rely extensively on transcriptional controls. In particular, several types of histone post-translational modifications and chromatin-bound factors act sequentially or in combination to establish transcriptional patterns and to fine-tune the transcript abundance of a large repertoire of light-responsive genes and clock components. Cytogenetic approaches have also identified light-induced higher-order chromatin changes that dynamically organize the condensation of chromosomal domains into sub-nuclear foci containing silenced repeat elements. In this review, we report recently identified molecular actors that establish chromatin state dynamics in response to light signals such as photoperiod, intensity, and spectral quality. We also highlight the chromatin-dependent mechanisms that contribute to the 24-h circadian gene expression and its impact on plant physiology and development. The commonalities and contrasts of light- and clock-associated chromatin-based mechanisms are discussed, with particular emphasis on their impact on the selective regulation and rapid modulation of responsive genes.
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Affiliation(s)
- Fredy Barneche
- Environmental and Evolutionary Genomics Section, Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France Inserm, U1024, Paris, F-75005 France CNRS, UMR 8197, Paris, F-75005 France
| | - Jordi Malapeira
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
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Ma X, Lv S, Zhang C, Yang C. Histone deacetylases and their functions in plants. PLANT CELL REPORTS 2013; 32:465-78. [PMID: 23408190 DOI: 10.1007/s00299-013-1393-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 01/12/2013] [Accepted: 01/24/2013] [Indexed: 05/07/2023]
Abstract
Histone deacetylases (HDACs) mediate histone deacetylation and act in concert with histone acetyltransferases to regulate dynamic and reversible histone acetylation which modifies chromatin structure and function, affects gene transcription, thus, controlling multiple cellular processes. HDACs are widely distributed in almost all eukaryotes, and there have been many researches focusing on plant HDACs recently. An increasing number of HDAC genes have been identified and characterized in a variety of plant species and the functions of certain HDACs have been studied. The present studies indicate that HDACs play a key role in regulating plant growth, development and stress responses. This paper reviews recent findings on HDACs and their functions in plants, especially their roles in development and stress responses.
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Affiliation(s)
- Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040, China
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Liu X, Chen CY, Wang KC, Luo M, Tai R, Yuan L, Zhao M, Yang S, Tian G, Cui Y, Hsieh HL, Wu K. PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings. THE PLANT CELL 2013; 25:1258-73. [PMID: 23548744 PMCID: PMC3663266 DOI: 10.1105/tpc.113.109710] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/22/2013] [Accepted: 03/15/2013] [Indexed: 05/18/2023]
Abstract
PHYTOCHROME INTERACTING FACTOR3 (PIF3) is a key basic helix-loop-helix transcription factor of Arabidopsis thaliana that negatively regulates light responses, repressing chlorophyll biosynthesis, photosynthesis, and photomorphogenesis in the dark. However, the mechanism for the PIF3-mediated transcription regulation remains largely unknown. In this study, we found that the REDUCED POTASSIUM DEPENDENCY3/HISTONE DEACETYLASE1-type histone deacetylase HDA15 directly interacted with PIF3 in vivo and in vitro. Genome-wide transcriptome analysis revealed that HDA15 acts mainly as a transcriptional repressor and negatively regulates chlorophyll biosynthesis and photosynthesis gene expression in etiolated seedlings. HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression by decreasing the acetylation levels and RNA Polymerase II-associated transcription. The binding of HDA15 to the target genes depends on the presence of PIF3. In addition, PIF3 and HDA15 are dissociated from the target genes upon exposure to red light. Taken together, our results indicate that PIF3 associates with HDA15 to repress chlorophyll biosynthetic and photosynthetic genes in etiolated seedlings.
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Affiliation(s)
- Xuncheng Liu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chia-Yang Chen
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ko-Ching Wang
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ming Luo
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ready Tai
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Lianyu Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Minglei Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Songguang Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Gang Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario N5V 4T3, Canada
| | - Yuhai Cui
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario N5V 4T3, Canada
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Address correspondence to
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Hartl M, Finkemeier I. Plant mitochondrial retrograde signaling: post-translational modifications enter the stage. FRONTIERS IN PLANT SCIENCE 2012; 3:253. [PMID: 23162565 PMCID: PMC3495340 DOI: 10.3389/fpls.2012.00253] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 10/22/2012] [Indexed: 05/23/2023]
Abstract
Beside their central function in respiration plant mitochondria play important roles in diverse processes such as redox homeostasis, provision of precursor molecules for essential biosynthetic pathways, and programmed cell death. These different functions require the organelle to communicate with the rest of the cell by perceiving, transducing, and emitting signals. As the vast majority of mitochondrial proteins are encoded in the nuclear genome, changes in mitochondrial status must be fed back to the nucleus to coordinate gene expression accordingly, a process termed retrograde signaling. However, the nature of these signaling pathways in plants and their underlying signaling molecules - or indirect metabolite or redox signals - are not completely resolved. We explore the potential of different post-translational modifications (PTMs) to contribute to mitochondrial retrograde signaling. Remarkably, the substrates used for modifying proteins in many major PTMs are either central metabolites or redox-active compounds, as for example ATP, acetyl-CoA, NAD(+), and glutathione. This suggests that the metabolic status of organelles and of the cell in general could be indirectly gaged by the enzymes catalyzing the various PTMs. We examine the evidence supporting this hypothesis with regard to three major PTMs, namely phosphorylation, lysine acetylation, and glutathionylation and assess their potential to regulate not only organellar processes by modifying metabolic enzymes but also to influence nuclear gene expression.
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Affiliation(s)
| | - Iris Finkemeier
- *Correspondence: Iris Finkemeier, Department Biology I, Ludwig Maximilians University Munich, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany. e-mail:
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Liu X, Luo M, Zhang W, Zhao J, Zhang J, Wu K, Tian L, Duan J. Histone acetyltransferases in rice (Oryza sativa L.): phylogenetic analysis, subcellular localization and expression. BMC PLANT BIOLOGY 2012; 12:145. [PMID: 22894565 PMCID: PMC3502346 DOI: 10.1186/1471-2229-12-145] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 08/10/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND Histone acetyltransferases (HATs) play an important role in eukaryotic transcription. Eight HATs identified in rice (OsHATs) can be organized into four families, namely the CBP (OsHAC701, OsHAC703, and OsHAC704), TAFII250 (OsHAF701), GNAT (OsHAG702, OsHAG703, and OsHAG704), and MYST (OsHAM701) families. The biological functions of HATs in rice remain unknown, so a comprehensive protein sequence analysis of the HAT families was conducted to investigate their potential functions. In addition, the subcellular localization and expression patterns of the eight OsHATs were analyzed. RESULTS On the basis of a phylogenetic and domain analysis, monocotyledonous CBP family proteins can be subdivided into two groups, namely Group I and Group II. Similarly, dicotyledonous CBP family proteins can be divided into two groups, namely Group A and Group B. High similarities of protein sequences, conserved domains and three-dimensional models were identified among OsHATs and their homologs in Arabidopsis thaliana and maize. Subcellular localization predictions indicated that all OsHATs might localize in both the nucleus and cytosol. Transient expression in Arabidopsis protoplasts confirmed the nuclear and cytosolic localization of OsHAC701, OsHAG702, and OsHAG704. Real-time quantitative polymerase chain reaction analysis demonstrated that the eight OsHATs were expressed in all tissues examined with significant differences in transcript abundance, and their expression was modulated by abscisic acid and salicylic acid as well as abiotic factors such as salt, cold, and heat stresses. CONCLUSIONS Both monocotyledonous and dicotyledonous CBP family proteins can be divided into two distinct groups, which suggest the possibility of functional diversification. The high similarities of protein sequences, conserved domains and three-dimensional models among OsHATs and their homologs in Arabidopsis and maize suggested that OsHATs have multiple functions. OsHAC701, OsHAG702, and OsHAG704 were localized in both the nucleus and cytosol in transient expression analyses with Arabidopsis protoplasts. OsHATs were expressed constitutively in rice, and their expression was regulated by exogenous hormones and abiotic stresses, which suggested that OsHATs may play important roles in plant defense responses.
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Affiliation(s)
- Xia Liu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Ming Luo
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Wei Zhang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jinhui Zhao
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jianxia Zhang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Lining Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Jun Duan
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Luo M, Wang YY, Liu X, Yang S, Wu K. HD2 proteins interact with RPD3-type histone deacetylases. PLANT SIGNALING & BEHAVIOR 2012; 7:608-10. [PMID: 22580696 PMCID: PMC3442851 DOI: 10.4161/psb.20044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
HD2 proteins were previously identified as plant specific histone deacetylases (HDACs). The molecular mechanism of the function of HD2 proteins is still unclear. Using Bimolecular fluorescence complementation assay, we demonstrated that Arabidopsis HD2 proteins, HD2A, HD2C and HD2D, can interact with RPD3-type HDACs, HDA6 and HDA19, suggesting that that these proteins may act in the same protein complex. Our study indicates that HD2 proteins may functionally associate with RPD3-type HDACs to regulate gene expression in plants.
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Affiliation(s)
- Ming Luo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou, China
- Institute of Plant Biology; National Taiwan University; Taipei, Taiwan
| | - Yu-Yuan Wang
- Institute of Plant Biology; National Taiwan University; Taipei, Taiwan
| | - Xuncheng Liu
- Institute of Plant Biology; National Taiwan University; Taipei, Taiwan
| | - Songguang Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou, China
| | - Keqiang Wu
- Institute of Plant Biology; National Taiwan University; Taipei, Taiwan
- * Correspondence to: Keqiang Wu;
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