Characterization and subcellular localization of histone deacetylases and their roles in response to abiotic stresses in soybean

Abstract

BackgroundHistone 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.ResultsIn 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.ConclusionWe 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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1454-7) contains supplementary material, which is available to authorized users.

Epigenetic regulation in plant abiotic stress responses

“…On the one hand, HSFA1s are partly controlled by phosphorylation/dephosphorylation, SUMOylation and protein–protein interactions; on the other hand, HSFA1s are predicted to directly regulate the expression of heat‐induced TFs such as DEHYDRATION‐RESPONSIVE ELEMENT BINDING PROTEIN 2A (DREB2A), HSFA2, HSF7s, HSFBs, and MULTIPROTEIN BRIDGING FACTOR 1C (MBF1C) which are responsible for the activation of downstream heat responsive genes (Ohama et al 2017). Several studies have revealed that histone dynamics and the RdDM pathway are involved in the heat stress response (Popova et al 2013; Lamke et al 2016; Yang et al 2018a). Heat shock proteins (HSPs) play a key role in conferring heat tolerance.…”

Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments

“…Based on sequence homology with yeast HDACs, plant HDACs are classified into three different groups, including Reduced Potassium Dependency-3/Histone Deacetylase 1 (RPD3/HDA1), which requires a zinc ion cofactor for deacetylase activity ( Yang & Seto, 2007 ), Silent Information Regulator 2 (SIR2), which depends on nicotinamide adenine dinucleotide (NAD + ), and Histone Deacetylase 2 (HD2), which is unique in plants ( Hirschey, 2011 ; Pandey et al., 2002 ). Researchers have identified and characterized some HDAC genes in a wide range of plant species, such as maize ( Zea mays ) ( Forestan et al, 2018 ), A. thaliana ( Hollender & Liu, 2008 ), rice ( Oryza sativa ) ( Fu, Wu & Duan, 2007 ), barley ( Hordeum vulgare ) ( Demetriou et al, 2009 ), potato ( Solanum chacoense ) ( Lagacé et al, 2003 ), grape ( Vitis vinifera ) ( Busconi et al, 2009 ), tobacco ( Nicotiana tabacum ) ( Bourque et al, 2011 ), black cottonwood ( Populus trichocarpa ) ( Alinsug, Yu & Wu, 2009 ), banana ( Musa acuminata ) ( Fu et al, 2018 ), soybean ( Glycine max ) ( Yang et al, 2018 ), litchi ( Litchi chinensis ) ( Peng et al, 2017 ), common bean ( Phaseolus vulgaris ) ( Hayford et al, 2017 ), common liverwort ( Marchantia polymorpha ) ( Chu & Chen, 2018 ) and tomato ( Solanum lycopersicum ) ( Zhao et al, 2015 ), and have studied the functions of certain HDAC genes. For example, HDAC genes are involved in plant responses to stress-related hormones such as salicylic acid (SA), abscisic acid (ABA) or jasmonic acid (JA) and stress stimuli such as drought, cold, salt, and pathogens ( Ma et al, 2013 ).…”

Genome-wide Identification and Characterization of FCS-Like Zinc Finger (FLZ) Family Genes in Maize (Zea mays) and Functional Analysis of ZmFLZ25 in Plant Abscisic Acid Response

“…Search of FLZ proteins in maize was done as described previously [36]. Briefly, the protein sequences of FLZ domain from AtFLZs were used as queries to run the BLAST program against the B73 reference genome (RefGen_v4) (https://www.maizegdb.org/; accessed on 1 September 2019) [37].…”