Histone Deacetylases in Rice Development and Stress Responses

2022 ◽  
Author(s):  
Hyeryung Yoon ◽  
Gayeong Seong ◽  
Sang-Ji Lee ◽  
Chaemyeong Lim ◽  
Nam-Chon Paek
Keyword(s):  
Stress Responses ◽  
Histone Deacetylases

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

The Protective Mechanism of SIRT1 in the Regulation of Mitochondrial Biogenesis and Mitochondrial Autophagy in Alzheimer’s Disease

2021 ◽  
pp. 1-9
Author(s):  
Fan Ye ◽  
Anshi Wu
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Mitochondrial Biogenesis ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Neuronal Morphology ◽  
Protective Mechanism ◽  
Peroxisome Proliferator ◽  
Class Iii ◽  
Peroxisome Proliferator Activated Receptor

Silent information-regulated transcription factor 1 (SIRT1) is the most prominent and widely studied member of the sirtuins (a family of mammalian class III histone deacetylases). It is a nuclear protein, and the deacetylation of the peroxisome proliferator-activated receptor coactivator-1 has been extensively implicated in metabolic control and mitochondrial biogenesis and is the basis for studies into its involvement in caloric restriction and its effects on lifespan. The present study discusses the potentially protective mechanism of SIRT1 in the regulation of the mitochondrial biogenesis and autophagy involved in the modulation of Alzheimer’s disease, which may be correlated with the role of SIRT1 in affecting neuronal morphology, learning, and memory during development; regulating metabolism; counteracting stress responses; and maintaining genomic stability. Drugs that activate SIRT1 may offer a promising approach to treating Alzheimer’s disease

scholarly journals Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferases and Histone Deacetylases Involved in the Response to Drought in Wheat

2020 ◽  
Author(s):  
Hua Li ◽  
Huajie Liu ◽  
Xinxin Pei ◽  
Hongyu Chen ◽  
Xiao Li ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Gene Expression Analysis ◽  
Regulatory Elements ◽  
Wheat Genome ◽  
Histone Acetyltransferases ◽  
Promoter Regions ◽  
Conserved Domain ◽  
Genome Wide

Abstract Background: Histone acetyltransferases (HATs) and histone deacetylases (HDACs) contribute to plant growth, development, and stress responses. A number of HAT and HDAC genes have been identified in several plants. However, wheat HATs and HDACs have not been comprehensively characterized. In this study, we identified TaHATs and TaHDACs in the wheat genome using bioinformatics tools. Result: In total, 30 TaHAT genes and 53 TaHDAC genes were detected in the wheat genome. As described in other plants, TaHATs were classified into four subfamilies (i.e., GNAT, p300/CBP, MYST, and TAFII250) and TaHDACs were divided into three subfamilies (i.e., RPD3/HDA1, HD2, and SIR2). Phylogenetic and conserved domain analyses showed that TaHATs and TaHDACs are highly similar to those in Arabidopsis and rice; however, divergence and expansion from Arabidopsis and rice were also observed. We detected many stress-related cis-regulatory elements in the promoter regions of these genes (i.e., ABRE, STRE, MYB et al.). Further, based on a comparative expression analyses of three varieties with different degrees of drought resistance under drought stress, we found that TaHAG2, TaHAG3, TaHAC2, TaHDA18, TaHDT1, and TaHDT2 are likely regulate drought stress in wheat. Conclusions: In this study, TaHATs and TaHDACs from the wheat genome were identified. Three TaHATs and three TaHDACs were very likely to regulate drought stress based on a promoter analysis and gene expression analysis. These results provide a foundation for further research on the regulation of acetylation in wheat and its role in the response to drought stress.

scholarly journals Cauliflower mosaic virus P6 Dysfunctions Histone Deacetylase HD2C to Promote Virus Infection

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2278
Author(s):  
Shun Li ◽  
Shanwu Lyu ◽  
Yujuan Liu ◽  
Ming Luo ◽  
Suhua Shi ◽  
...  
Keyword(s):  
Histone Acetylation ◽  
Mosaic Virus ◽  
Histone Deacetylase ◽  
Plant Development ◽  
Stress Responses ◽  
Biotic Stress ◽  
Histone Deacetylases ◽  
Cauliflower Mosaic Virus ◽  
Physical Interaction ◽  
Epigenetic Modifiers

Histone deacetylases (HDACs) are vital epigenetic modifiers not only in regulating plant development but also in abiotic- and biotic-stress responses. Though to date, the functions of HD2C—an HD2-type HDAC—In plant development and abiotic stress have been intensively explored, its function in biotic stress remains unknown. In this study, we have identified HD2C as an interaction partner of the Cauliflower mosaic virus (CaMV) P6 protein. It functions as a positive regulator in defending against CaMV infection. The hd2c mutants show enhanced susceptibility to CaMV infection. In support, the accumulation of viral DNA, viral transcripts, and the deposition of histone acetylation on the viral minichromosomes are increased in hd2c mutants. P6 interferes with the interaction between HD2C and HDA6, and P6 overexpression lines have similar phenotypes with hd2c mutants. In further investigations, P6 overexpression lines, together with CaMV infection plants, are more sensitive to ABA and NaCl with a concomitant increasing expression of ABA/NaCl-regulated genes. Moreover, the global levels of histone acetylation are increased in P6 overexpression lines and CaMV infection plants. Collectively, our results suggest that P6 dysfunctions histone deacetylase HD2C by physical interaction to promote CaMV infection.

scholarly journals HD2-type histone deacetylases: Unique regulators of plant development and stress responses

2021 ◽  
Author(s):  
Muhammad Sufyan Tahir ◽  
Lining Tian
Keyword(s):  
Stress Responses ◽  
Histone Deacetylases ◽  
Growth And Development ◽  
Regulatory Networks ◽  
Research Progress ◽  
Plant Responses ◽  
Biotic And Abiotic Stresses ◽  
Lysine Residues ◽  
Gene Regulatory ◽  
Stable Growth

Abstract Plants have developed sophisticated and complex epigenetic regulation-based mechanisms to maintain stable growth and development under diverse environmental conditions. Histone deacetylases (HDACs) are important epigenetic regulators in eukaryotes that are involved in the deacetylation of lysine residues of histone H3 and H4 proteins. Plants have developed a unique HDAC family, HD2, in addition to the RPD3 and Sir2 families, which are also present in other eukaryotes. HD2s are well conserved plant-specific HDACs, which were first identified as nucleolar phosphoproteins in maize. The HD2 family plays important roles not only in fundamental developmental processes, including seed germination, root and leaf development, floral transition, and seed development, but also in regulating plant responses to biotic and abiotic stresses. Some of the HD2 members coordinate each other to function. The HD2 family proteins also show functional association with RPD3-type HDACs and other transcription factors as a part of repression complexes in gene regulatory networks involved in environmental stress responses. This review aims to analyse and summarise recent research progress in the HD2 family, and to describe their role in plant growth and development and in response to different environmental stresses.

scholarly journals Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10932
Author(s):  
Hanzeng Wang ◽  
Xue Leng ◽  
Jia Yang ◽  
Mengqiu Zhang ◽  
Minzhen Zeng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Growth And Development ◽  
Populus Trichocarpa ◽  
Purifying Selection ◽  
Specific Expression ◽  
Real Time Quantitative Pcr ◽  
Specific Expression Pattern ◽  
Gene Functional Analysis

The AT-hook motif nuclear-localized (AHL) family is a plant transcription factor family, which plays an important role in growth and development and stress responses. We identified and analyzed 37 AHL genes in poplar (Populus trichocarpa). Phylogenetic analysis classified the PtrAHL members into three subfamilies based on their conserved domain. All PtrAHL paralogous pairs evolved under purifying selection. The promoter analysis revealed the presence of stress-related and phytohormone-related cis-elements of the PtrAHL genes. Our analysis of the tissue-specific expression pattern of PtrAHL genes indicated their significance in tissue and organ development. Network-based prediction suggested that PtrAHL genes may interact with histone deacetylases (HDAC) and participate in the development of organs, such as roots. Drought negatively impacts plant growth and development. ABA is produced under osmotic stress condition, and it takes an important part in the stress response and tolerance of plants. Real-time quantitative PCR (qRT-PCR) showed that PtrAHL genes were induced by drought stress and ABA treatment. These insights into the expression of PtrAHL genes under stress provide a basis for PtrAHL gene functional analysis. Our study will help develop new breeding strategies to improve drought tolerance in poplar.

scholarly journals The role of sirtuins in cardiac disease

2015 ◽  
Vol 309 (9) ◽  
pp. H1375-H1389 ◽  
Author(s):  
Shouji Matsushima ◽  
Junichi Sadoshima
Keyword(s):  
Cardiac Hypertrophy ◽  
Mating Type ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Class Iii ◽  
Beneficial Effects ◽  
Damage Repair ◽  
Wide Range ◽  
Apoptosis And Inflammation

Modification of histones is one of the important mechanisms of epigenetics, in which genetic control is determined by factors other than an individual's DNA sequence. Sirtuin family proteins, which are class III histone deacetylases, were originally identified as gene silencers that affect the mating type of yeast, leading to the name “silent mating-type information regulation 2” (SIR2). They are characterized by their requirement of nicotinamide adenine dinucleotide for their enzyme activity, unlike other classes of histone deacetylases. Sirtuins have been traditionally linked to longevity and the beneficial effects of calorie restriction and DNA damage repair. Recently, sirtuins have been shown to be involved in a wide range of physiological and pathological processes, including aging, energy responses to low calorie availability, and stress resistance, as well as apoptosis and inflammation. Sirtuins can also regulate mitochondrial biogenesis and circadian clocks. Seven sirtuin family proteins (Sirt1-7) have been identified as mammalian SIR2 orthologs, localized in different subcellular compartments, namely, the cytoplasm (Sirt1, 2), the mitochondria (Sirt3, 4, 5), and the nucleus (Sirt1, 2, 6, 7). Sirt1 is evolutionarily close to yeast SIR2 and has been the most intensively investigated in the cardiovascular system. Endogenous Sirt1 plays a pivotal role in mediating the cell death/survival process and has been implicated in the pathogenesis of cardiovascular disease. Downregulation of Sirt2 is protective against ischemic-reperfusion injury. Increased Sirt3 expression has been shown to correlate with longevity in humans. In addition, Sirt3 protects cardiomyocytes from aging and oxidative stress and suppresses cardiac hypertrophy. Sirt6 has also recently been demonstrated to attenuate cardiac hypertrophy, and Sirt7 is known to regulate apoptosis and stress responses in the heart. On the other hand, the roles of Sirt4 and Sirt5 in the heart remain largely uncharacterized.

scholarly journals Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses

PLoS Biology ◽  
2020 ◽  
Vol 18 (11) ◽  
pp. e3000981
Author(s):  
Ryan Houston ◽  
Shiori Sekine ◽  
Michael J. Calderon ◽  
Fayaz Seifuddin ◽  
Guanghui Wang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Histone Deacetylases ◽  
Culture Media ◽  
Lipid Synthesis ◽  
Essential Element ◽  
Cell System ◽  
Acetyl Coa ◽  
Atp Production ◽  
Wide Range ◽  
A Cell

The metabolite acetyl-coenzyme A (acetyl-CoA) serves as an essential element for a wide range of cellular functions including adenosine triphosphate (ATP) production, lipid synthesis, and protein acetylation. Intracellular acetyl-CoA concentrations are associated with nutrient availability, but the mechanisms by which a cell responds to fluctuations in acetyl-CoA levels remain elusive. Here, we generate a cell system to selectively manipulate the nucleo-cytoplasmic levels of acetyl-CoA using clustered regularly interspaced short palindromic repeat (CRISPR)-mediated gene editing and acetate supplementation of the culture media. Using this system and quantitative omics analyses, we demonstrate that acetyl-CoA depletion alters the integrity of the nucleolus, impairing ribosomal RNA synthesis and evoking the ribosomal protein-dependent activation of p53. This nucleolar remodeling appears to be mediated through the class IIa histone deacetylases (HDACs). Our findings highlight acetylation-mediated control of the nucleolus as an important hub linking acetyl-CoA fluctuations to cellular stress responses.

Histone acetylation/deacetylation in Candida albicans and their potential as antifungal targets

2020 ◽  
Vol 15 (11) ◽  
pp. 1075-1090
Author(s):  
Shan Su ◽  
Xiuyun Li ◽  
Xinmei Yang ◽  
Yiman Li ◽  
Xueqi Chen ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Candida Albicans ◽  
Histone Acetylation ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Fungal Pathogen ◽  
Antifungal Agents ◽  
Fungal Infections ◽  
Histone Acetyltransferases ◽  
Opportunistic Fungal Pathogen

Recently, the incidence of invasive fungal infections has significantly increased. Candida albicans (C. albicans) is the most common opportunistic fungal pathogen that infects humans. The limited number of available antifungal agents and the emergence of drug resistance pose difficulties to treatment, thus new antifungals are urgently needed. Through their functions in DNA replication, DNA repair and transcription, histone acetyltransferases (HATs) and histone deacetylases (HDACs) perform essential functions relating to growth, virulence, drug resistance and stress responses of C. albicans. Here, we summarize the physiological and pathological functions of HATs/HDACs, potential antifungal targets and underlying antifungal compounds that impact histone acetylation and deacetylation. We anticipate this review will stimulate the identification of new HAT/HDAC-related antifungal targets and antifungal agents.

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