Functional analyses of plant-specific histone deacetylases : Their role in root development, stress responses and symbiotic interactions

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.

Download Full-text

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

Journal of Alzheimer s Disease ◽

10.3233/jad-210132 ◽

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

Download Full-text

Transcriptomic Evidence of Adaptive Evolution of the Epiphytic Fern Asplenium nidus

International Journal of Genomics ◽

10.1155/2019/1429316 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9

Author(s):

Jiao Zhang ◽

Li Liu ◽

Jiang-Ping Shu ◽

Dong-Mei Jin ◽

Hui Shen ◽

...

Keyword(s):

Root Development ◽

Stress Responses ◽

Tropical Rainforest ◽

Extreme Environments ◽

Mads Box ◽

Rna Seq ◽

Lateral Root Development ◽

Underlying Basis ◽

Asplenium Nidus ◽

Epiphytic Fern

Epiphytic ferns have been found to flourish after angiosperms dominated forest communities, and they play important roles in rainforest canopies. How do epiphytic ferns adapt to tropical rainforest canopy habitats? At present, we know little about the molecular mechanism underlying this adaptation. Asplenium nidus is a well-known epiphytic fern that is closely related to the terrestrial species Asplenium komarovii. Here, RNA-seq and comparative transcriptomic analyses were performed to explore the underlying basis of the adaptation of A. nidus to extreme environments. A total of 44.04 and 44.57 Mb clean reads were obtained from A. nidus and A. komarovii, respectively, and they were assembled into 89,741 and 77,912 unigenes. Functional annotation showed that 52,305 (58.28% of the total genes for A. nidus) and 45,938 (58.96% of the total genes for A. komarovii) unigenes were annotated in public databases. Genes involved in stress responses and photosynthesis were found to have undergone positive selection in A. nidus. Compared to A. komarovii, transcription factors related to stress response, leaf development, and root development were found to be considerably expanded in A. nidus, especially in the ANR1 subclade of MADS-box family genes which played roles in lateral root development. This study improves our understanding of the adaptation of A. nidus to epiphytic habitats by forming unique strategies.

Download Full-text

Identification of Genes Associated with Nitrogen Stress Responses in Apple Leaves

Plants ◽

10.3390/plants10122649 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2649

Author(s):

Youngsuk Lee ◽

Van Giap Do ◽

Seonae Kim ◽

Hunjoong Kweon

Keyword(s):

Stress Responses ◽

Interaction Network ◽

Stress Conditions ◽

Future Research ◽

Protein Protein Interaction ◽

Physiological Processes ◽

Apple Leaves ◽

Survival And Development ◽

Molecular Signals ◽

Functional Analyses

Nitrogen (N) is an essential macronutrient that regulates diverse physiological processes for plant survival and development. In apple orchards, inappropriate N conditions can cause imbalanced growth and subsequent physiological disorders in trees. In order to investigate the molecular basis underlying the physiological signals for N stress responses, we examined the metabolic signals responsive to contrasting N stress conditions (deficient/excessive) in apple leaves using transcriptome approaches. The clustering of differentially expressed genes (DEGs) showed the expression dynamics of genes associated with each N stress group. Functional analyses of gene ontology and pathway enrichments revealed the potential candidates of metabolic signals responsible for N-deficient/excessive stress responses. The functional interactions of DEGs in each cluster were further explored by protein–protein interaction network analysis. Our results provided a comprehensive insight into molecular signals responsive to N stress conditions, and will be useful in future research to enhance the nutrition tolerance of tree crops.

Download Full-text

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

10.21203/rs.3.rs-123885/v1 ◽

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.

Download Full-text

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

Cells ◽

10.3390/cells10092278 ◽

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.

Download Full-text

Histone Deacetylases in Rice Development and Stress Responses

Journal of Plant Biology ◽

10.1007/s12374-021-09346-x ◽

2022 ◽

Author(s):

Hyeryung Yoon ◽

Gayeong Seong ◽

Sang-Ji Lee ◽

Chaemyeong Lim ◽

Nam-Chon Paek

Keyword(s):

Stress Responses ◽

Histone Deacetylases

Download Full-text

Functional analyses of cotton (Gossypium hirsutum L.) immature fiber (im) mutant infer that fiber cell wall development is associated with stress responses

BMC Genomics ◽

10.1186/1471-2164-14-889 ◽

2013 ◽

Vol 14 (1) ◽

pp. 889 ◽

Cited By ~ 28

Author(s):

Hee Kim ◽

Yuhong Tang ◽

Hong S Moon ◽

Christopher D Delhom ◽

David D Fang

Keyword(s):

Cell Wall ◽

Gossypium Hirsutum ◽

Stress Responses ◽

Fiber Cell ◽

Gossypium Hirsutum L ◽

Cell Wall Development ◽

Fiber Cell Wall ◽

Functional Analyses

Download Full-text

Transcription Factor GmWRKY46 Enhanced Phosphate Starvation Tolerance and Root Development in Transgenic Plants

Frontiers in Plant Science ◽

10.3389/fpls.2021.700651 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cheng Li ◽

Kangning Li ◽

Xinyi Liu ◽

Hui Ruan ◽

Mingming Zheng ◽

...

Keyword(s):

Transcription Factor ◽

Root Development ◽

Stress Responses ◽

Molecular Genetic ◽

Wrky Transcription Factor ◽

Lateral Root Development ◽

Group Iii ◽

Pi Starvation

Phosphorus (P) is one of the essential macronutrients, whose deficiency limits the growth and development of plants. In this study, we investigated the possible role of GmWRKY46 in the phosphate (Pi) starvation stress tolerance of soybean. GmWRKY46 belonged to the group III subfamily of the WRKY transcription factor family, which was localized in the nucleus and had transcriptional activator activity. GmWRKY46 could be strongly induced by Pi starvation, especially in soybean roots. Overexpression of GmWRKY46 significantly enhanced tolerance to Pi starvation and lateral root development in transgenic Arabidopsis. RNA-seq analysis showed that overexpression of GmWRKY46 led to change in many genes related to energy metabolisms, stress responses, and plant hormone signal transduction in transgenic Arabidopsis. Among these differential expression genes, we found that overexpression of AtAED1 alone could enhance the tolerance of transgenic Arabidopsis to Pi starvation. Y1H and ChIP-qPCR analyses showed that GmWRKY46 could directly bind to the W-box motif of the AtAED1 promoter in vitro and in vivo. Furthermore, results from intact soybean composite plants with GmWRKY46 overexpression showed that GmWRKY46 was involved in hairy roots development and subsequently affected plant growth and Pi uptake. These results provide a basis for the molecular genetic breeding of soybean tolerant to Pi starvation.

Download Full-text

Plant-specific histone deacetylases are essential for early as well as late stages of Medicago nodule development

10.1101/2020.11.09.374819 ◽

2020 ◽

Author(s):

Huchen Li ◽

Stefan Schilderink ◽

Qingqin Cao ◽

Olga Kulikova ◽

Ton Bisseling

Keyword(s):

Transcription Factors ◽

Root Development ◽

Histone Deacetylases ◽

Coenzyme A ◽

Chromatin Remodelling ◽

Nodule Development ◽

Lateral Root Development ◽

Late Stages ◽

Nodule Symbiosis

ABSTRACTLegume and rhizobium can establish a nitrogen-fixing nodule symbiosis. Previous studies have shown that several transcription factors that play a role in (lateral) root development are also involved in nodule development. Chromatin remodelling factors, like transcription factors, are key players in regulating gene expression. However, it has not been studied whether chromatin remodelling genes that are essential for root development get involved in nodule development. Here we studied the role of Medicago histone deacetylases (MtHDTs) in nodule development. Their Arabidopsis orthologs have been shown to play a role in root development. The expression of MtHDTs is induced in nodule primordia and is maintained in nodule meristem and infection zone. Conditional knock-down of their expression in a nodule-specific way by RNAi blocks nodule primordium development. A few nodules still can be formed but their nodule meristems are smaller and rhizobial colonization of the cells derived from the meristem is markedly reduced. Although the HDTs are expressed during nodule and root development, transcriptome analyses indicate that HDTs control the development of these organs in a different manner. During nodule development the MtHDTs positively regulate 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 (MtHMGR1). The decreased expression of MtHMGR1 is sufficient to explain the block of primordium formation.ONE SENTENCE SUMMARYPlant-specific histone deacetylases regulate the expression of 3-hydroxy-3-methylglutaryl-coenzyme A reductases to control root nodule development.

Download Full-text