Histone acetyltransferases in rice (Oryza sativa L.): phylogenetic analysis, subcellular localization and expression

Unveiling the role of epigenetics in leaf senescence: a comparative study to identify different epigenetic regulations of senescence types in barley leaves

BACKGROUND

Developmental leaf senescence (DLS) is an irreversible process followed by cell death. Dark-induced leaf senescence (DILS) is a reversible process that allows adaptations to changing environmental conditions. As a result of exposure to adverse environmental changes, plants have developed mechanisms that enable them to survive. One of these is the redirection of metabolism into the senescence pathway. The plant seeks to optimise resource allocation. Our research aims to demonstrate how epigenetic machinery regulates leaf senescence, including its irreversibility.

RESULTS

In silico analyses allowed the complex identification and characterisation of 117 genes involved in epigenetic processes in barley. These genes include those responsible for DNA methylation, post-translational histone modifications, and ATP-dependent chromatin remodelling complexes. We then performed RNAseq analysis after DILS and DLS to evaluate their expression in senescence-dependent leaf metabolism. Principal component analysis revealed that evaluated gene expression in developmental senescence was similar to controls, while induced senescence displayed a distinct profile. Western blot experiments revealed that senescence engages senescence-specific histone modification. During DILS and DLS, the methylation of histone proteins H3K4me3 and H3K9me2 increased. H3K9ac acetylation levels significantly decreased during DILS and remained unchanged during DLS.

CONCLUSIONS

The study identified different epigenetic regulations of senescence types in barley leaves. These findings are valuable for exploring epigenetic regulation of senescence-related molecular mechanisms, particularly in response to premature, induced leaf senescence. Based on the results, we suggest the presence of an epigenetically regulated molecular switch between cell survival and cell death in DILS, highlighting an epigenetically driven cell survival metabolic response.

Advances in understanding the roles of plant HAT and HDAC in non-histone protein acetylation and deacetylation

MAIN CONCLUSION

This review focuses on HATs and HDACs that modify non-histone proteins, summarizes functional mechanisms of non-histone acetylation as well as the roles of HATs and HDACs in rice and Arabidopsis. The growth and development of plants, as well as their responses to biotic and abiotic stresses, are governed by intricate gene and protein regulatory networks, in which epigenetic modifying enzymes play a crucial role. Histone lysine acetylation levels, modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), are well-studied in the realm of transcriptional regulation. However, the advent of advanced proteomics has unveiled that non-histone proteins also undergo acetylation, with its underlying mechanisms now being clarified. Indeed, non-histone acetylation influences protein functionality through diverse pathways, such as modulating protein stability, adjusting enzymatic activity, steering subcellular localization, influencing interactions with other post-translational modifications, and managing protein-protein and protein-DNA interactions. This review delves into the recent insights into the functional mechanisms of non-histone acetylation in plants. We also provide a summary of the roles of HATs and HDACs in rice and Arabidopsis, and explore their potential involvement in the regulation of non-histone proteins.

Systematic Analysis of the BrHAT Gene Family and Physiological Characteristics of Brassica rapa L. Treated with Histone Acetylase and Deacetylase Inhibitors under Low Temperature

Brassica rapa L. is an important overwintering oilseed crop in Northwest China. Histone acetyltransferases (HATs) play an important role in epigenetic regulation, as well as the regulation of plant growth, development, and responses to abiotic stresses. To clarify the role of histone acetylation in the low-temperature response of B. rapa L., we identified 29 HAT genes in B. rapa L. using bioinformatics tools. We also conducted a comprehensive analysis of the physicochemical properties, gene structure, chromosomal localization, conserved structural domains and motifs, cis-acting regulatory elements, and evolutionary relationships of these genes. Using transcriptome data, we analyzed the expression patterns of BrHAT family members and predicted interactions between proteins; the results indicated that BrHATs play an important role in the low-temperature response of B. rapa L. HAT inhibitor (curcumin; CUR) and histone deacetylase inhibitor (Trichostatin A; TSA) were applied to four B. rapa L. varieties varying in cold resistance under the same low-temperature conditions, and changes in the physiological indexes of these four varieties were analyzed. The inhibitor treatment attenuated the effect of low temperature on seed germination, and curcumin treatment was most effective, indicating that the germination period was primarily regulated by histone acetylase. Both inhibitor treatments increased the activity of protective enzymes and the content of osmoregulatory substances in plants, suggesting that histone acetylation and deacetylation play a significant role in the response of B. rapa L. to low-temperature stress. The qRT-PCR analyses showed that the expression patterns of BrHATs were altered under different inhibitor treatments and low-temperature stress; meanwhile, we found three significantly differentially expressed genes. In sum, the process of histone acetylation is involved in the cold response and the BrHATs gene plays a role in the cold stress response.

Research Progress on the Mechanism and Function of Histone Acetylation Regulating the Interaction between Pathogenic Fungi and Plant Hosts

Histone acetylation is a crucial epigenetic modification, one that holds the key to regulating gene expression by meticulously modulating the conformation of chromatin. Most histone acetylation enzymes (HATs) and deacetylation enzymes (HDACs) in fungi were originally discovered in yeast. The functions and mechanisms of HATs and HDACs in yeast that have been documented offer us an excellent entry point for gaining insights into these two types of enzymes. In the interaction between plants and pathogenic fungi, histone acetylation assumes a critical role, governing fungal pathogenicity and plant immunity. This review paper delves deep into the recent advancements in understanding how histone acetylation shapes the interaction between plants and fungi. It explores how this epigenetic modification influences the intricate balance of power between these two kingdoms of life, highlighting the intricate network of interactions and the subtle shifts in these interactions that can lead to either mutual coexistence or hostile confrontation.

Identification of the histone acetyltransferase gene family in the Artemisia annua genome

As the most effective therapeutic drug for malaria, artemisinin can only be extracted from Artemisia annua L., which is sensitive to the surrounding growing habitat. Histone acetyltransferases (HATs) contain acetyl groups, which modulate mRNA transcription and thereby regulate plant environmental adaptation. Comprehensive analyses of HATs have been performed in many plants, but systematic identification of HATs in medicinal plants is lacking. In the present study, we identified 11 AaHATs and characterized these genes into four classes according to their conserved protein structures. According to the phylogenetic analysis results, potential functions of HAT genes from Arabidopsis thaliana, Oryza sativa, and A. annua were found. According to our results, AaHAT has a highly conserved evolutionary history and is rich in highly variable regions; thus, AaHAT has become a comparatively ideal object of medical plant identification and systematic study. Moreover, motifs commonly present in histone acetyltransferases in the A. annua genome may be associated with functional AaHATs. AaHATs appear to be related to gene-specific functions. AaHATs are regulated by cis-elements, and these genes may affect phytohormone responsiveness, adaptability to stress, and developmental growth. We performed expression analyses to determine the potential roles of AaHATs in response to three environmental stresses. Our results revealed a cluster of AaHATs that potentially plays a role in the response of plants to dynamic environments.

Plant responses to abiotic stress regulated by histone acetylation

In eukaryotes, histone acetylation and deacetylation play an important role in the regulation of gene expression. Histone acetylation levels are reversibly regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Increasing evidence highlights histone acetylation plays essential roles in the regulation of gene expression in plant response to environmental stress. In this review, we discussed the recent advance of histone acetylation in the regulation of abiotic stress responses including temperature, light, salt and drought stress. This information will contribute to our understanding of how plants adapt to environmental changes. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in improvement of agricultural productivity.

Effects of copper, and aluminium in ionic, and nanoparticulate form on growth rate and gene expression of Setaria italica seedlings

This study aims to determine the effects of copper, copper oxide nanoparticles, aluminium, and aluminium oxide nanoparticles on the growth rate and expression of ACT-1, CDPK, LIP, NFC, P5CR, P5CS, GR, and SiZIP1 genes in five days old seedling of Setaria italica ssp. maxima, cultivated in hydroponic culture. Depending on their concentration (ranging from 0.1 to 1.8 mg L-1), all tested substances had both stimulating and inhibiting effects on the growth rate of the seedlings. Copper and copper oxide-NPs had generally a stimulating effect whereas aluminium and aluminium oxide-NPs at first had a positive effect but in higher concentrations they inhibited the growth. Treating the seedlings with 0.4 mg L-1 of each tested toxicant was mostly stimulating to the expression of the genes and reduced the differences between the transcript levels of the coleoptiles and roots. Increasing concentrations of the tested substances had both stimulating and inhibiting effects on the expression levels of the genes. The highest expression levels were usually noted at concentrations between 0.4 and 1.0 mg/L of each metal and metal nanoparticle, except for SiZIP1, which had the highest transcript amount at 1.6 mg L-1 of Cu2+ and at 0.1-0.8 mg L-1 of CuO-NPs, and LIP and GR from the seedling treated with Al2O3-NPs at concentrations of 0.1 and 1.6 mg L-1, respectively.

Genome-wide identification and expression analysis of histone deacetylase and histone acetyltransferase genes in response to drought in poplars

BACKGROUND

Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are involved in plant growth and development as well as in response to environmental changes, by dynamically regulating gene acetylation levels. Although there have been numerous reports on the identification and function of HDAC and HAT in herbaceous plants, there are fewer report related genes in woody plants under drought stress.

RESULTS

In this study, we performed a genome-wide analysis of the HDAC and HAT families in Populus trichocarpa, including phylogenetic analysis, gene structure, conserved domains, and expression analysis. A total of 16 PtrHDACs and 12 PtrHATs were identified in P. trichocarpa genome. Analysis of cis-elements in the promoters of PtrHDACs and PtrHATs revealed that both gene families could respond to a variety of environmental signals, including hormones and drought. Furthermore, real time quantitative PCR indicated that PtrHDA906 and PtrHAG3 were significantly responsive to drought. PtrHDA906, PtrHAC1, PtrHAC3, PtrHAG2, PtrHAG6 and PtrHAF1 consistently responded to abscisic acid, methyl jasmonate and salicylic acid under drought conditions.

CONCLUSIONS

Our study demonstrates that PtrHDACs and PtrHATs may respond to drought through hormone signaling pathways, which helps to reveal the hub of acetylation modification in hormone regulation of abiotic stress.

Recent advancements in the role of histone acetylation dynamics to improve stress responses in plants

In eukaryotes, transcriptional regulation is determined by the DNA sequence and is facilitated through sophisticated and complex chromatin alterations and histone remodelling. Recent research has shown that the histone acetylation dynamic, an intermittent and reversible substitution, constitutes a prerequisite for chromatin modification. These changes in chromatin structure modulate genome-wide and specific changes in response to external and internal cues like cell differentiation, development, growth, light temperature, and biotic stresses. Histone acetylation dynamics also control the cell cycle. HATs and HDACs play a critical role in gene expression modulation during plant growth and response to environmental circumstances. It has been well established that HATs and HDACs interact with various distinct transcription factors and chromatin-remodelling proteins (CRPs) involved in the transcriptional regulation of several developmental processes. This review explores recent research on histone acyltransferases and histone deacetylases, mainly focusing on their involvement in plant biotic stress responses. Moreover, we also emphasized the research gaps that must be filled to fully understand the complete function of histone acetylation dynamics during biotic stress responses in plants. A thorough understanding of histone acetylation will make it possible to enhance tolerance against various kinds of stress and decrease yield losses in many crops.

Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress

MAIN CONCLUSION

This study identified seven histone acetyltransferase-encoding genes (HATs) from Beta vulgaris L. (sugar beet) genome through bioinformatics tools and analyzed their expression profiles under salt stress. Sugar beet HATs are phylogenetically divided into four families: GNAT, MYST, CBP, and TAFII250. The BvHAT genes were differentially transcribed in leaves, stems, and roots of B. vulgaris salt-resistant (Casino) and -sensitive (Bravo) cultivars under salt stress. Histone acetylation is regulated by histone acetyltransferases (HATs), which catalyze ɛ-amino bond formation between lysine residues and acetyl groups with a cofactor, acetyl-CoA. Even though the HATs are known to participate in stress response and development in model plants, little is known about the functions of HATs in crops. In sugar beet (Beta vulgaris L.), they have not yet been identified and characterized. Here, an in silico analysis of the HAT gene family in sugar beet was performed, and their expression patterns in leaves, stems, and roots of B. vulgaris were analyzed under salt stress. Salt-resistant (Casino) and -sensitive (Bravo) beet cultivars were used for gene expression assays. Seven HATs were identified from sugar beet genome, and named BvHAG1, BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2, and BvHAF1. The HAT proteins were divided into 4 groups including MYST, GNAT (GCN5, HAT1, ELP3), CBP and TAFII250. Analysis of cis-acting elements indicated that the BvHAT genes might be involved in hormonal regulation, light response, plant development, and abiotic stress response. The BvHAT genes were differentially expressed in leaves, stems, and roots under control and 300 mM NaCl. In roots of B. vulgaris cv. Bravo, the BvHAG1, BvHAG2, BvHAG4, BvHAF1, and BvHAC1 genes were dramatically expressed after 7 and 14 days of salt stress. Interestingly, the BvHAC2 gene was not expressed under both control and stress conditions. However, the expression of BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2 genes showed a significant increase in response to salt stress in the roots of cv. Casino. This study provides new insights into the potential roles of histone acetyltransferases in sugar beet.

Regulation of Disease-Resistance Genes against CWMV Infection by NbHAG1-Mediated H3K36ac

Post-translational modification of proteins plays a critical role in plant-pathogen interactions. Here, we demonstrate in Nicotiana benthamiana that knockout of NbHAG1 promotes Chinese wheat mosaic virus (CWMV) infection, whereas NbHAG1 overexpression inhibits infection. Transcriptome sequencing indicated that a series of disease resistance-related genes were up-regulated after overexpression of NbHAG1. In addition, cleavage under targets and tagmentation (Cut&Tag)-qPCR results demonstrated that NbHAG1 may activate the transcription of its downstream disease-resistance genes by facilitating the acetylation level of H3K36ac. Therefore, we suggest that NbHAG1 is an important positive regulator of resistance to CWMV infestation.

Rice responds to Spodoptera frugiperda infestation via epigenetic regulation of H3K9ac in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways

KEY MESSAGE

This study provided important insights into the complex epigenetic regulatory of H3K9ac-modified genes involved in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways of rice in response to Spodoptera frugiperda infestation. Physiological and molecular mechanisms underlying plant responses to insect herbivores have been well studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of hidden genes remain largely unknown. Histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plants that can activate gene transcription. In this study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using CUT&Tag-seq and RNA-seq. There were 3269 and 4609 up-regulated genes identified in plants infested by FAW larvae for 3 h and 12 h, respectively, which were mainly enriched in alpha-linolenic acid and phenylpropanoid pathways according to transcriptomic analysis. In addition, CUT&Tag-seq analysis revealed increased H3K9ac in FAW-infested plants, and there were 422 and 543 up-regulated genes enriched with H3K9ac observed at 3 h and 12 h after FAW feeding, respectively. Genes with increased H3K9ac were mainly enriched in the transcription start site (TSS), suggesting that H3K9ac is related to gene transcription. Integrative analysis of both RNA-seq and CUT&Tag-seq data showed that up-expressed genes with H3K9ac enrichment were mainly involved in the jasmonic acid (JA) and phenylpropanoid pathways. Particularly, two spermidine hydroxycinnamoyl transferase genes SHT1 and SHT2 involved in phenolamide biosynthesis were highly modified by H3K9ac in FAW-infested plants. Furthermore, the Ossht1 and Ossht2 transgenic lines exhibited decreased resistance against FAW larvae. Our findings suggest that rice responds to insect herbivory via H3K9ac epigenetic regulation in the JA signaling and phenolamide biosynthesis pathways.

ACL and HAT1 form a nuclear module to acetylate histone H4K5 and promote cell proliferation

Acetyl-CoA utilized by histone acetyltransferases (HAT) for chromatin modification is mainly generated by ATP-citrate lyase (ACL) from glucose sources. How ACL locally establishes acetyl-CoA production for histone acetylation remains unclear. Here we show that ACL subunit A2 (ACLA2) is present in nuclear condensates, is required for nuclear acetyl-CoA accumulation and acetylation of specific histone lysine residues, and interacts with Histone AcetylTransferase1 (HAT1) in rice. The rice HAT1 acetylates histone H4K5 and H4K16 and its activity on H4K5 requires ACLA2. Mutations of rice ACLA2 and HAT1 (HAG704) genes impair cell division in developing endosperm, result in decreases of H4K5 acetylation at largely the same genomic regions, affect the expression of similar sets of genes, and lead to cell cycle S phase stagnation in the endosperm dividing nuclei. These results indicate that the HAT1-ACLA2 module selectively promotes histone lysine acetylation in specific genomic regions and unravel a mechanism of local acetyl-CoA production which couples energy metabolism with cell division.

Identification of histone acetyltransferase genes responsible for cannabinoid synthesis in hemp

BACKGROUND

Histone acetyltransferases (HATs) play an important role in plant growth and development, stress response, and regulation of secondary metabolite biosynthesis. Hemp (Cannabis sativa L.) is famous for its high industrial, nutritional, and medicinal value. It contains non-psychoactive cannabinoid cannabidiol (CBD) and cannabinol (CBG), which play important roles as anti-inflammatory and anti-anxiety. At present, the involvement of HATs in the regulation of cannabinoid CBD and CBG synthesis has not been clarified.

METHODS

The members of HAT genes family in hemp were systematically analyzed by bioinformatics analysis. In addition, the expression level of HATs and the level of histone acetylation modification were analyzed based on transcriptome data and protein modification data. Real-time quantitative PCR was used to verify the changes in gene expression levels after inhibitor treatment. The changes of CBD and CBG contents after inhibitor treatment were verified by HPLC-MS analysis.

RESULTS

Here, 11 HAT genes were identified in the hemp genome. Phylogenetic analysis showed that hemp HAT family genes can be divided into six groups. Cannabinoid synthesis genes exhibited spatiotemporal specificity, and histones were acetylated in different inflorescence developmental stages. The expression of cannabinoid synthesis genes was inhibited and the content of CBD and CBG declined by 10% to 55% in the samples treated by HAT inhibitor (PU139). Results indicated that CsHAT genes may regulate cannabinoid synthesis through altering histone acetylation.

CONCLUSIONS

Our study provides genetic information of HATs responsible for cannabinoid synthesis, and offers a new approach for increasing the content of cannabinoid in hemp.

Histone acetyltransferase HAM1 interacts with molecular chaperone DNAJA2 and confers immune responses through salicylic acid biosynthetic genes in cassava

Cassava bacterial blight (CBB) is one of the most serious diseases in cassava production, so it is essential to explore the underlying mechanism of immune responses. Histone acetylation is an important epigenetic modification, however, its relationship with cassava disease resistance remains unclear. Here, we identified 10 histone acetyltransferases in cassava and found that the transcript of MeHAM1 showed the highest induction to CBB. Functional analysis showed that MeHAM1 positively regulated disease resistance to CBB through modulation of salicylic acid (SA) accumulation. Further investigation revealed that MeHAM1 directly activated SA biosynthetic genes' expression via promoting lysine 9 of histone 3 (H3K9) acetylation and lysine 5 of histone 4 (H4K5) acetylation of these genes. In addition, molecular chaperone MeDNAJA2 physically interacted with MeHAM1, and MeDNAJA2 also regulated plant immune responses and SA biosynthetic genes. In conclusion, this study illustrates that MeHAM1 and MeDNAJA2 confer immune responses through transcriptional programming of SA biosynthetic genes via histone acetylation. The MeHAM1 & MeDNAJA2-SA biosynthesis module not only constructs the direct relationship between histone acetylation and cassava disease resistance, but also provides gene network with potential value for genetic improvement of cassava disease resistance.

Comprehensive Analyses of the Histone Deacetylases Tuin (HDT) Gene Family in Brassicaceae Reveals Their Roles in Stress Response

Histone deacetylases tuin (HDT) is a plant-specific protein subfamily of histone deacetylation enzymes (HDAC) which has a variety of functions in plant development, hormone signaling and stress response. Although the HDT family's genes have been studied in many plant species, they have not been characterized in Brassicaceae. In this study, 14, 8 and 10 HDT genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the HDTs were divided into four groups: HDT1(HD2A), HDT2(HD2B), HDT3(HD2C) and HDT4(HD2D). There was an expansion of HDT2 orthologous genes in Brassicaceae. Most of the HDT genes were intron-rich and conserved in gene structure, and they coded for proteins with a nucleoplasmin-like (NPL) domain. Expression analysis showed that B. napus, B. rapa, and B. oleracea HDT genes were expressed in different organs at different developmental stages, while different HDT subgroups were specifically expressed in specific organs and tissues. Interestingly, most of the Bna/Br/BoHDT2 members were expressed in flowers, buds and siliques, suggesting they have an important role in the development of reproductive organs in Brassicaceae. Expression of BnaHDT was induced by various hormones, such as ABA and ethylene treatment, and some subgroups of genes were responsive to heat treatment. The expression of most HDT members was strongly induced by cold stress and freezing stress after non-cold acclimation, while it was slightly induced after cold acclimation. In this study, the HDT gene family of Brassicaceae was analyzed for the first time, which helps in understanding the function of BnaHDT in regulating plant responses to abiotic stresses, especially freezing stresses.

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.

Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.

Genomic footprints of selection in early-and late-flowering pearl millet landraces

Pearl millet is among the top three-cereal production in one of the most climate vulnerable regions, sub-Saharan Africa. Its Sahelian origin makes it adapted to grow in poor sandy soils under low soil water regimes. Pearl millet is thus considered today as one of the most interesting crops to face the global warming. Flowering time, a trait highly correlated with latitude, is one of the key traits that could be modulated to face future global changes. West African pearl millet landraces, can be grouped into early- (EF) and late-flowering (LF) varieties, each flowering group playing a specific role in the functioning and resilience of Sahelian smallholders. The aim of this study was thus to detect genes linked to flowering but also linked to relevant traits within each flowering group. We thus investigated genomic and phenotypic diversity in 109 pearl millet landrace accessions, i.e., 66 early-flowering and 43 late-flowering, grown in the groundnut basin, the first area of rainfed agriculture in Senegal dominated by dry cereals (millet, maize, and sorghum) and legumes (groundnuts, cowpeas). We were able to confirm the role of PhyC gene in pearl millet flowering and identify several other genes that appear to be as much as important, such as FSR12 and HAC1. HAC1 and two other genes appear to be part of QTLs previously identified and deserve further investigation. At the same time, we were able to highlight a several genes and variants that could contribute to the improvement of pearl millet yield, especially since their impact was demonstrated across flowering cycles.

Plant Responses to Herbivory, Wounding, and Infection

Plants have various self-defense mechanisms against biotic attacks, involving both physical and chemical barriers. Physical barriers include spines, trichomes, and cuticle layers, whereas chemical barriers include secondary metabolites (SMs) and volatile organic compounds (VOCs). Complex interactions between plants and herbivores occur. Plant responses to insect herbivory begin with the perception of physical stimuli, chemical compounds (orally secreted by insects and herbivore-induced VOCs) during feeding. Plant cell membranes then generate ion fluxes that create differences in plasma membrane potential (Vm), which provokes the initiation of signal transduction, the activation of various hormones (e.g., jasmonic acid, salicylic acid, and ethylene), and the release of VOCs and SMs. This review of recent studies of plant–herbivore–infection interactions focuses on early and late plant responses, including physical barriers, signal transduction, SM production as well as epigenetic regulation, and phytohormone responses.

Genome-wide investigation of histone acetyltransferase gene family and its responses to biotic and abiotic stress in foxtail millet (Setaria italica [L.] P. Beauv)

BACKGROUND

Modification of histone acetylation is a ubiquitous and reversible process in eukaryotes and prokaryotes and plays crucial roles in the regulation of gene expression during plant development and stress responses. Histone acetylation is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT plays an essential regulatory role in various growth and development processes by modifying the chromatin structure through interactions with other histone modifications and transcription factors in eukaryotic cells, affecting the transcription of genes. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana and Oryza sativa. However, little information is available on the HAT genes in foxtail millet (Setaria italica [L.] P. Beauv).

RESULTS

In this study, 24 HAT genes (SiHATs) were identified and divided into four groups with conserved gene structures via motif composition analysis. Phylogenetic analysis of the genes was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa, and foxtail millet; 19 and 2 orthologous gene pairs were individually identified. Moreover, all identified HAT gene pairs likely underwent purified selection based on their non-synonymous/synonymous nucleotide substitutions. Using published transcriptome data, we found that SiHAT genes were preferentially expressed in some tissues and organs. Stress responses were also examined, and data showed that SiHAT gene transcription was influenced by drought, salt, low nitrogen, and low phosphorus stress, and that the expression of four SiHATs was altered as a result of infection by Sclerospora graminicola.

CONCLUSIONS

Results indicated that histone acetylation may play an important role in plant growth and development and stress adaptations. These findings suggest that SiHATs play specific roles in the response to abiotic stress and viral infection. This study lays a foundation for further analysis of the biological functions of SiHATs in foxtail millet.

Comprehensive Genome-Wide Analysis of Histone Acetylation Genes in Roses and Expression Analyses in Response to Heat Stress

Roses have high economic values as garden plants and for cut-flower and cosmetics industries. The growth and development of rose plants is affected by exposure to high temperature. Histone acetylation plays an important role in plant development and responses to various stresses. It is a dynamic and reversible process mediated by histone deacetylases (HDAC) and histone acetyltransferases (HAT). However, information on HDAC and HAT genes of roses is scarce. Here, 23 HDAC genes and 10 HAT genes were identified in the Rosa chinensis ‘Old Blush’ genome. Their gene structures, conserved motifs, physicochemical properties, phylogeny, and synteny were assessed. Analyses of the expression of HDAC and HAT genes using available RNAseq data showed that these genes exhibit different expression patterns in different organs of the three analyzed rose cultivars. After heat stress, while the expression of most HDAC genes tend to be down-regulated, that of HAT genes was up-regulated when rose plants were grown at high-temperature conditions. These data suggest that rose likely respond to high-temperature exposure via modification in histone acetylation, and, thus, paves the way to more studies in order to elucidate in roses the molecular mechanisms underlying rose plants development and flowering.

Genome-wide identification of chromatin regulators in Sorghum bicolor

Chromatin regulators play important roles in plant development and stress response. In this study, we identified totally 231 chromatin regulators including 63 histones, 29 histone chaperones, 101 histone modification enzymes, and 38 chromatin remodeling factors from Sorghum bicolor (L.) Moench. Most of these chromatin regulators are homologous to their counterparts in Arabidopsis or rice. However, sorghum genome evolves a few novel histone variants specific to some grass species and a sorghum-unique chromatin remodeling factor that contain the domains belonging to the elongation factor EF-Tu and the histone chaperone SPT16. Finally, we performed co-expression analysis for the chromatin regulator-encoding genes by clustering the expression patterns of these genes. Our results provide useful information for the future studies on the mechanism of epigenetic regulation in sorghum and its roles in development and stress response.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03181-8.

Identification, characterization and expression of rice (Oryza sativa) acetyltransferase genes exposed to realistic environmental contamination of mesotrione and fomesafen

The plant acetyltransferases (ACEs) belong to a super family of proteins that contribute to secondary metabolisms and involve various abiotic and biotic stress responses. However, how rice ACEs respond to toxic agrochemicals is largely unknown. This study demonstrates that 86 and 83 genes coding ACEs in the transcriptome profiling were expressed under mesotrione (MTR) and fomesafen (FSA) exposure, respectively. Of these, 18 and 8 ACE differentially expressed genes (DEGs) were identified in MTR- and FSA-exposed rice transcriptome datasets. Some of the ACE genes were validated by quantitative RT-PCR analysis. Analysis of biochemical properties of ACEs revealed that many genes have various cis-elements and structural domain which may cope with a variety of biotic and abiotic stress responses and detoxification of xenobiotics. Moreover, the ACE activities in rice were induced under MTR and FSA exposure and reached out to the highest value at the 0.1 mg L^-1. The ACE activities in the MTR and FSA treated roots were 2.6 and 3.5 fold over the control and those in shoots with MTR and FSA were 4.0 and 26.1 fold over the control, respectively. These results indicate that the ACE-coding genes can respond to the MTR and FSA stress by increasing their transcriptional level, along with the enhanced specific ACE protein activities in rice tissues.

Characterization of histone deacetylases and their roles in response to abiotic and PAMPs stresses in Sorghum bicolor

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.

Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum

Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.

The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling

After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.

The rice RNase P protein subunit Rpp30 confers broad-spectrum resistance to fungal and bacterial pathogens

RNase P functions either as a catalytic ribonucleoprotein (RNP) or as an RNA-free polypeptide to catalyse RNA processing, primarily tRNA 5' maturation. To the growing evidence of non-canonical roles for RNase P RNP subunits including regulation of chromatin structure and function, we add here a role for the rice RNase P Rpp30 in innate immunity. This protein (encoded by LOC_Os11g01074) was uncovered as the top hit in yeast two-hybrid assays performed with the rice histone deacetylase HDT701 as bait. We showed that HDT701 and OsRpp30 are localized to the rice nucleus, OsRpp30 expression increased post-infection by Pyricularia oryzae (syn. Magnaporthe oryzae), and OsRpp30 deacetylation coincided with HDT701 overexpression in vivo. Overexpression of OsRpp30 in transgenic rice increased expression of defence genes and generation of reactive oxygen species after pathogen-associated molecular pattern elicitor treatment, outcomes that culminated in resistance to a fungal (P. oryzae) and a bacterial (Xanthomonas oryzae pv. oryzae) pathogen. Knockout of OsRpp30 yielded the opposite phenotypes. Moreover, HA-tagged OsRpp30 co-purified with RNase P pre-tRNA cleavage activity. Interestingly, OsRpp30 is conserved in grass crops, including a near-identical C-terminal tail that is essential for HDT701 binding and defence regulation. Overall, our results suggest that OsRpp30 plays an important role in rice immune response to pathogens and provides a new approach to generate broad-spectrum disease-resistant rice cultivars.

Histone Acetylation Changes in Plant Response to Drought Stress

Drought stress causes recurrent damage to a healthy ecosystem because it has major adverse effects on the growth and productivity of plants. However, plants have developed drought avoidance and resilience for survival through many strategies, such as increasing water absorption and conduction, reducing water loss and conversing growth stages. Understanding how plants respond and regulate drought stress would be important for creating and breeding better plants to help maintain a sound ecosystem. Epigenetic marks are a group of regulators affecting drought response and resilience in plants through modification of chromatin structure to control the transcription of pertinent genes. Histone acetylation is an ubiquitous epigenetic mark. The level of histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines whether the chromatin is open or closed, thereby controlling access of DNA-binding proteins for transcriptional activation. In this review, we summarize histone acetylation changes in plant response to drought stress, and review the functions of HATs and HDACs in drought response and resistance.

Protein acetylation and deacetylation in plant-pathogen interactions

Protein acetylation and deacetylation catalysed by lysine acetyltransferases (KATs) and deacetylases (KDACs), respectively, are major mechanisms regulating various cellular processes. During the fight between microbial pathogens and host plants, both apply a set of measures, including acetylation interference, to strengthen themselves while suppressing the other. In this review, we first summarize KATs and KDACs in plants and their pathogens. Next, we introduce diverse acetylation and deacetylation mechanisms affecting protein functions, including the regulation of enzyme activity and specificity, protein-protein or protein-DNA interactions, subcellular localization and protein stability. We then focus on the current understanding of acetylation and deacetylation in plant-pathogen interactions. Additionally, we also discuss potential acetylation-related approaches for controlling plant diseases.

Delineating the epigenetic regulation of heat and drought response in plants

Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.

Histone acetylation dynamics regulating plant development and stress responses

Crop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.

Genome-wide shifts in histone modifications at early stage of rice infection with Meloidogyne graminicola

Epigenetic processes play a crucial role in the regulation of plant stress responses, but their role in plant-pathogen interactions remains poorly understood. Although histone-modifying enzymes have been observed to be deregulated in galls induced by root-knot nematodes (RKN, Meloidogyne graminicola) in rice, their influence on plant defence and their genome-wide impact has not been comprehensively investigated. First, the role of histone modifications in plant-nematode interactions was confirmed by pharmacological inhibition of histone-modifying enzymes, which all significantly affected rice susceptibility to RKN. For a more specific view, three histone marks, H3K9ac, H3K9me2, and H3K27me3, were subsequently studied by chromatin-immunoprecipitation-sequencing on RKN-induced galls at 3 days postinoculation. While levels of H3K9ac and H3K27me3 were strongly enriched, H3K9me2 was generally depleted in galls versus control root tips. Differential histone peaks were generally associated with plant defence-related genes. Transcriptome analysis using RNA-Seq and RT-qPCR-based validation revealed that genes marked with H3K9ac or H3K9me2 showed the expected activation or repression gene expression pattern, but this was not the case for H3K27me3 marks. Our results indicate that histone modifications respond dynamically to RKN infection, and that posttranslational modifications mainly at H3K9 specifically target plant defence-related genes.

Genome-wide identification of the histone acetyltransferase gene family in Triticum aestivum

Background

Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene transcription and thereby playing a crucial regulatory role in plant development. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana, Oryza sativa, barley, grapes, tomato, litchi and Zea mays, but comparable identification and analyses have not been conducted in wheat (Triticum aestivum).

Results

In this study, 31 TaHATs were identified and divided into six groups with conserved gene structures and motif compositions. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa and Triticum aestivum HAT genes. The TaHATs appeared to be regulated by cis-acting elements such as LTR and TC-rich repeats. The qRT–PCR analysis showed that the TaHATs were differentially expressed in multiple tissues. The TaHATs in expression also responded to temperature changes, and were all significantly upregulated after being infected by barley streak mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV) and wheat yellow mosaic virus (WYMV).

Conclusions

These results suggest that TaHATs may have specific roles in the response to viral infection and provide a basis for further study of TaHAT functions in T. aestivum plant immunity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07348-6.

Salt induced programmed cell death in rice: evidence from chloroplast proteome signature

Soil salinity, depending on its intensity, drives a challenged plant either to death, or survival with compromised productivity. On exposure to moderate salinity, plants can often survive by sacrificing some of their cells 'in target' following a route called programmed cell death (PCD). In animals, PCD has been well characterised, and involvement of mitochondria in the execution of PCD events has been unequivocally proven. In plants, mechanistic details of the process are still in grey area. Previously, we have shown that in green tissues of rice, for salt induced PCD to occur, the presence of active chloroplasts and light are equally important. In the present work, we have characterised the chloroplast proteome in rice seedlings at 12 and 24 h after salt exposure and before the time point where the signature of PCD was observed. We identified almost 100 proteins from chloroplasts, which were divided in to 11 categories based on the biological functions in which they were involved. Our results concerning the differential expression of chloroplastic proteins revealed involvement of some novel candidates. Moreover, we observed maximum phosphorylation pattern of chloroplastic proteins at an early time point (12 h) of salt exposure.

Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance

BACKGROUND

Drought-tolerance ensures a crop to maintain life activities and protect cell from damages under dehydration. It refers to diverse mechanisms temporally activated when the crop adapts to drought. However, knowledge about the temporal dynamics of rice transcriptome under drought is limited.

RESULTS

Here, we investigated temporal transcriptomic dynamics in 12 rice genotypes, which varied in drought tolerance (DT), under a naturally occurred drought in fields. The tolerant genotypes possess less differentially expressed genes (DEGs) while they have higher proportions of upregulated DEGs. Tolerant and susceptible genotypes have great differences in temporally activated biological processes (BPs) during the drought period and at the recovery stage based on their DEGs. The DT-featured BPs, which are activated specially (e.g. raffinose, fucose, and trehalose metabolic processes, etc.) or earlier in the tolerant genotypes (e.g. protein and histone deacetylation, protein peptidyl-prolyl isomerization, transcriptional attenuation, ferric iron transport, etc.) shall contribute to DT. Meanwhile, the tolerant genotypes and the susceptible genotypes also present great differences in photosynthesis and cross-talks among phytohormones under drought. A certain transcriptomic tradeoff between DT and productivity is observed. Tolerant genotypes have a better balance between DT and productivity under drought by activating drought-responsive genes appropriately. Twenty hub genes in the gene coexpression network, which are correlated with DT but without potential penalties in productivity, are recommended as good candidates for DT.

CONCLUSIONS

Findings of this study provide us informative cues about rice temporal transcriptomic dynamics under drought and strengthen our system-level understandings in rice DT.

Multiple Xanthomonas campestris pv. campestris 8004 type III effectors inhibit immunity induced by flg22

Xanthomonas campestris pv. campestris 8004 secretes several effector proteins that interfere with plant phosphorylation. Xanthomonas campestris pv. campestris (Xcc) can infect cruciferous plants and cause black rot. The strain Xcc8004 secretes effector proteins that interfere with plant cellular processes into host cells using a type III secretion (T3S) system. Several of the 24 predicted T3S effectors in the Xcc8004 genome have been implicated in the suppression of the Arabidopsis thaliana pattern-triggered immunity (PTI) response. We used an A. thaliana mesophyll protoplast-based assay to identify Xcc8004 T3S effectors that effectively interfere with PTI signalling induced by the bacterial peptide flg22. 11 of the 24 tested effector proteins (XopK, XopQ, HrpW, XopN, XopAC, XopD, XopZ1, XopAG, AvrBs2, XopL and XopX-1) inhibited expression of the flg22-inducible gene FRK1, and five effectors (XopK, XopG, XopQ, XopL and XopX-1) inhibited the expression of the flg22-inducible gene WRKY33. Therefore, there are 12 effector proteins that can inhibit the expression of relevant flg22-inducible genes. It was further investigated whether the 12 effector proteins affect the phosphorylation activation of mitogen-activated protein (MAP) kinases MPK3/MPK6, and four effector proteins (XopK, XopQ, XopZ1 and XopX-1) were found to markedly inhibit MPK3/MPK6 activation. Moreover, a subcellular localisation analysis revealed that the tested effectors were localised within various subcellular compartments. These results indicate that multiple T3S effectors in the Xcc8004 genome interfere with flg22-induced PTI signalling via various molecular mechanisms.

Bioinformatics and expression analysis of histone modification genes in grapevine predict their involvement in seed development, powdery mildew resistance, and hormonal signaling

BACKGROUND

Histone modification genes (HMs) play potential roles in plant growth and development via influencing gene expression and chromatin structure. However, limited information is available about HMs genes in grapes (Vitis vinifera L.).

RESULTS

Here, we described detailed genome-wide identification of HMs gene families in grapevine. We identified 117 HMs genes in grapevine and classified these genes into 11 subfamilies based on conserved domains and phylogenetic relationships with Arabidopsis. We described the genes in terms of their chromosomal locations and exon-intron distribution. Further, we investigated the evolutionary history, gene ontology (GO) analysis, and syntenic relationships between grapes and Arabidopsis. According to results 21% HMs genes are the result of duplication (tandem and segmental) events and all the duplicated genes have negative mode of selection. GO analysis predicted the presence of HMs proteins in cytoplasm, nucleus, and intracellular organelles. According to seed development expression profiling, many HMs grapevine genes were differentially expressed in seeded and seedless cultivars, suggesting their roles in seed development. Moreover, we checked the response of HMs genes against powdery mildew infection at different time points. Results have suggested the involvement of some genes in disease resistance regulation mechanism. Furthermore, the expression profiles of HMs genes were analyzed in response to different plant hormones (Abscisic acid, Jasmonic acid, Salicylic acid, and Ethylene) at different time points. All of the genes showed differential expression against one or more hormones.

CONCLUSION

VvHMs genes might have potential roles in grapevine including seed development, disease resistance, and hormonal signaling pathways. Our study provides first detailed genome-wide identification and expression profiling of HMs genes in grapevine.

Chromatin Regulation in the Response of Ethylene: Nuclear Events in Ethylene Signaling

Plant hormones, produced in response to environmental stimuli, regulate almost all aspects of plant growth and development. Ethylene is a gaseous plant hormone that plays pleotropic roles in plant growth, plant development, fruit ripening, stress responses, and pathogen defenses. After decades of research, the key components of ethylene signaling have been identified and characterized. Although the molecular mechanisms of the sensing of ethylene signal and the transduction of ethylene signaling have been studied extensively, how chromatin influences ethylene signaling and ethylene response is a new area of research. This review describes the current understanding of how chromatin modifications, specifically histone acetylation, regulate ethylene signaling and the ethylene response.

Effect of Arsenic Stress on Expression Pattern of a Rice Specific miR156j at Various Developmental Stages and Their Allied Co-expression Target Networks

In plants, arsenic (As) stress modulates metabolic cascades at various developmental stages by influencing the pattern of gene expressions mediated by small non-coding RNAs, especially Micro-RNAs, involved in the moderation of a myriad of cellular processes needed for plant adaptation upon oxidative stress. miR156j of miR156 gene family, involved mainly in the regulation of growth and development in plants. This study was designed to find out the role of arsenic toxicity on Osa-miR156j expression in all physiological growth stages. To better understand the functional role of Osa-miR156j in rice, we observed the expression in different developmental stages (seedlings, tillering and flowering) and various tissues of leaf, stem and root tissues (at 0, 24, 48, and 72 h) under 25 μM arsenite [As (III)] exposure. Additionally, using bioinformatic tools to target genes of Osa-miR156j and the potential co-expressed genes were explored at different development stages in the various tissues of rice under stress conditions. The expression of Osa-miR156j showed its temporal downregulation in various tissues in different developmental stages. Of note, the downregulation was more pronounced in root tissues at seedlings, tillering, and flowering stages during 0-72 h under arsenite exposure as compared to other tissues. Overall, the As stress altered the gene expression more prominently at seedlings developmental stage followed by flowering and tillering. Additionally, through the In silico approach, the target functions and presence of oxidative stress-responsive cis-acting regulatory elements/motifs also confirmed Osa-miR156j involvement in the regulation of arsenic stress in rice. The findings of this study demonstrate the prominent role of Osa-miR156j in rice under arsenite stress, which was found to modulate the metabolic activities in rice plants at different developmental stages, and thus it might be useful for the development of arsenic tolerant varieties.

Genome-Wide Identification of Epigenetic Regulators in Quercus suber L

Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in trees, such as Quercus suber L., is still not available. In this study, eight DNA methyltransferases (DNA Mtases) and three DNA demethylases (DDMEs) were identified in Q. suber. Histone modifiers involved in methylation (35), demethylation (26), acetylation (8), and deacetylation (22) were also identified in Q. suber. In silico analysis showed that some Q. suber DNA Mtases, DDMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. Additional phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork, and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here will be important for future studies exploring the role of epigenetic regulators in this economically important species.

Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferase (HAT) Gene Family in Response to Hormonal Applications, Metal and Abiotic Stresses in Cotton

Post-translational modifications are involved in regulating diverse developmental processes. Histone acetyltransferases (HATs) play vital roles in the regulation of chromation structure and activate the gene transcription implicated in various cellular processes. However, HATs in cotton, as well as their regulation in response to developmental and environmental cues, remain unidentified. In this study, 9 HATs were identified from Gossypium raimondi and Gossypium arboretum, while 18 HATs were identified from Gossypium hirsutum. Based on their amino acid sequences, Gossypium HATs were divided into three groups: CPB, GNAT, and TAF_II250. Almost all the HATs within each subgroup share similar gene structure and conserved motifs. Gossypium HATs are unevenly distributed on the chromosomes, and duplication analysis suggests that Gossypium HATs are under strong purifying selection. Gene expression analysis showed that Gossypium HATs were differentially expressed in various vegetative tissues and at different stages of fiber development. Furthermore, all the HATs were differentially regulated in response to various stresses (salt, drought, cold, heavy metal and DNA damage) and hormones (abscisic acid (ABA) and auxin (NAA)). Finally, co-localization of HAT genes with reported quantitative trait loci (QTL) of fiber development were reported. Altogether, these results highlight the functional diversification of HATs in cotton growth and fiber development, as well as in response to different environmental cues. This study enhances our understanding of function of histone acetylation in cotton growth, fiber development, and stress adaptation, which will eventually lead to the long-term improvement of stress tolerance and fiber quality in cotton.

Molecular cloning and subcellular localization of six HDACs and their roles in response to salt and drought stress in kenaf (Hibiscus cannabinus L.)

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.

Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa

Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of Kac and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localized to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Protein-protein interaction networks of the identified proteins provided further evidence that Kac contributes to a wide range of regulatory functions. Furthermore, we demonstrated that the acetylation level of histone H3 (lysine 27 and 36) is increased in response to cold stress. In summary, our approach comprehensively profiles the regulatory roles of Kac in the growth and development of rice.

Phylogenetic and expression analysis of histone acetyltransferases in Brachypodium distachyon

Histone acetylation is an important post-translational modification in eukaryotes and is regulated by two antagonistic enzymes, namely histone acetyltransferase (HAT) and histone deacetylase (HDAC). However, little has been done on the HAT superfamily in Brachypodium distachyon (B. distachyon), a new model plant of Poaceae. In this study, eight HATs were identified from B. distachyon and classified into four major families. Subcellular localization analysis showed that a majority of BdHATs were predominantly localized in the nucleus. Syntenic and phylogenetic analysis indicated there may be two common ancestral CREB-binding protein (p300/CBP, HAC) genes prior to the separation of monocots and dicots. Expression analysis revealed that the potential roles of BdHATs in B. distachyon development and responses to four abiotic stresses. Protein-protein network analysis identified some potential interactive genes with BdHATs. Thus, our results will provide solid basis for further study the function of HAT genes in B. distachyon and other monocot plants.

Retrospective and perspective of plant epigenetics in China

Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer (two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications (PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato. Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation (RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects. We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.

Molecular identification of histone acetyltransferases and deacetylases in lower plant Marchantia polymorpha

Histone is the core component of nucleosome and modification of amino acid residues on histone tails is one of the most pivotal epigenetic regulatory mechanisms. Histone acetylation or deacetylation is carried out by two groups of proteins: histone acetyltransferases (HATs) or histone deacetylases (HDACs), and has been proven to be tightly linked to regulation of gene expression in animals and vascular plants. The biological functions of HATs and HDACs in non-flowering plants remain largely unknown. We found that there are seven MpHAT genes and twelve MpHDAC genes present in the Marchantia genome, and the comprehensive protein sequence analysis of the HAT and HDAC families was introduced to investigate their potential functions. On the basis of the functional domain analysis, eight MpHATs and twelve MpHDACs contain the conserved functional domains as the defining feature of each family. Phylogenetic trees of all families of MpHATs and MpHDACs along with their homologs from different plant and green algae species were constructed to illustrate evolutionary relationship of HAT and HDAC proteins. We found both SIR2 family and RPD3/HDA1 superfamily possess lower plant-specific proteins indicating the potential unknown functions of HATs and HDACs in Marchantia and other lower plant or algae species. Subcellular localization prediction suggests that MpHATs and MpHDACs are likely functioning in various organelles. Expression analysis shows that all MpHAT and MpHDAC genes are expressed in all tissues with differences at the transcriptional level. In addition, their expression patterns were altered in response to various treatments with plant hormones and environmental stress. We concluded that all MpHATs and MpHDACs are functional proteins in Marchantia and involved in various signaling pathways. Marchantia could have developed a complex histone acetylation epigenetic mechanism to regulate growth and development, as well as responses to environment.

Comparative Proteomic and Physiological Analyses of Two Divergent Maize Inbred Lines Provide More Insights into Drought-Stress Tolerance Mechanisms

Drought stress is the major abiotic factor threatening maize (Zea mays L.) yield globally. Therefore, revealing the molecular mechanisms fundamental to drought tolerance in maize becomes imperative. Herein, we conducted a comprehensive comparative analysis of two maize inbred lines contrasting in drought stress tolerance based on their physiological and proteomic responses at the seedling stage. Our observations showed that divergent stress tolerance mechanisms exist between the two inbred-lines at physiological and proteomic levels, with YE8112 being comparatively more tolerant than MO17 owing to its maintenance of higher relative leaf water and proline contents, greater increase in peroxidase (POD) activity, along with decreased level of lipid peroxidation under stressed conditions. Using an iTRAQ (isobaric tags for relative and absolute quantification)-based method, we identified a total of 721 differentially abundant proteins (DAPs). Amongst these, we fished out five essential sets of drought responsive DAPs, including 13 DAPs specific to YE8112, 107 specific DAPs shared between drought-sensitive and drought-tolerant lines after drought treatment (SD_TD), three DAPs of YE8112 also regulated in SD_TD, 84 DAPs unique to MO17, and five overlapping DAPs between the two inbred lines. The most significantly enriched DAPs in YE8112 were associated with the photosynthesis antenna proteins pathway, whilst those in MO17 were related to C5-branched dibasic acid metabolism and RNA transport pathways. The changes in protein abundance were consistent with the observed physiological characterizations of the two inbred lines. Further, quantitative real-time polymerase chain reaction (qRT-PCR) analysis results confirmed the iTRAQ sequencing data. The higher drought tolerance of YE8112 was attributed to: activation of photosynthesis proteins involved in balancing light capture and utilization; enhanced lipid-metabolism; development of abiotic and biotic cross-tolerance mechanisms; increased cellular detoxification capacity; activation of chaperones that stabilize other proteins against drought-induced denaturation; and reduced synthesis of redundant proteins to help save energy to battle drought stress. These findings provide further insights into the molecular signatures underpinning maize drought stress tolerance.