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

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.

Characterization of histone acetyltransferases and deacetylases and their roles in response to dehydration stress in Pyropia yezoensis (Rhodophyta)

Histone acetylation is one of the most pivotal epigenetic mechanisms in eukaryotes and has been tightly linked to the regulation of various genes controlling growth, development and response to environmental stresses in both animals and plants. Till date, the association of histone acetylation to dehydration stress in red algae and genes encoding the enzymes responsible for histone acetylation: histone acetyltransferases (HATs) or histone deacetylases (HDACs), remains largely unknown. In this study, in silico analysis of the red seaweed Pyropia yezoensis identified 6 HAT genes and 10 HDAC genes. These genes displayed good synteny in genome loci with their Pyropia haitanensis orthologs except for a putative gene duplication event in HDAC and a loss of one HAT gene in P. yezoensis. According to the conserved domains and phylogenetic analysis, they encoded three GCNA5-, one TAFII250- and one MYST-HAT, as well as five HDA1-and five SIRT-HDACs. The sirtuin-domain of Py06502 harbored a ~100 aa insert and interestingly, this insertion was specifically observed in Bangiales species. Two nuclear-localized HATs were transcriptionally up-regulated at the early stage of dehydration and so were two nuclear HDA1s when moderate dehydration started, suggesting their potential roles in modulating downstream gene expression to facilitate dehydration adaptation by changing histone acetylation patterns on relevant regulatory elements. This was experimentally confirmed by the increased decline in photosynthesis efficiency during dehydration when HAT and HDAC activities were inhibited by SAHA and MB-3, respectively. Transcriptional patterns of multiple dehydration-responsive genes after water loss were strongly affected by MB-3 or SAHA treatment. This study provides the first insight into the regulation and function of HAT/HDAC during stress adaptation in red algae.

Genome-wide analysis of the CSN genes in land plants and their expression under various abiotic stress and phytohormone conditions in rice

The CONSTITUTIVE PHOTOMORPHOGENIC9 (COP9) signalosome (CSN) is a multi-functional protein complex, which is involved in plant growth and abiotic stress response. However, the evolution and function of the CSN genes in land plants are still largely unclear. Here, we have identified 124 CSN genes and constructed phylogenetic trees of these CSN proteins to elucidate their feature and evolution in twelve land plants. Analysis of gene structure, protein property and protein motif composition shows the evolutional conservation and variation of the CSN proteins in land plants. These CSN genes might evolve through whole genome duplication (WGD)/segmental duplication (SD) and tandem duplication (TD). Analysis of promoter cis-elements shows that the CSN genes are implicated in diverse biological processes and different signaling pathways. RT-qPCR indicates that the transcript abundance of the OsCSN genes is up-regulated or down-regulated in response to abiotic stress and treatment with various hormones in rice. These results provide new insights into the CSN gene evolution and its possible function in land plants.

Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat (Fagopyrum tataricum)

Histone deacetylases (HDACs), widely found in various types of eukaryotic cells, play crucial roles in biological process, including the biotic and abiotic stress responses in plants. However, no research on the HDACs of Fagopyrum tataricum has been reported. Here, 14 putative FtHDAC genes were identified and annotated in Fagopyrum tataricum. Their gene structure, motif composition, cis-acting elements, phylogenetic relationships, protein structure, alternative splicing events, subcellular localization and gene expression pattern were investigated. The gene structure showed FtHDACs were classified into three subfamilies. The promoter analysis revealed the presence of various cis-acting elements responsible for hormone, abiotic stress and developmental regulation for the specific induction of FtHDACs. Two duplication events were identified in FtHDA6-1, FtHDA6-2, and FtHDA19. The expression patterns of FtHDACs showed their correlation with the flavonoid synthesis pathway genes. In addition, alternative splicing, mRNA enrichment profiles and transgenic analysis showed the potential role of FtHDACs in cold responses. Our study characterized FtHDACs, providing a candidate gene family for agricultural breeding and crop improvement.

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.

Heat stress in Marchantia polymorpha: Sensing and mechanisms underlying a dynamic response

Sensing and response to high temperatures are crucial to prevent heat-related damage and to preserve cellular and metabolic functions. The response to heat stress is a complex and coordinated process that involves several subcellular compartments and multi-level regulatory networks that are synchronized to avoid cell damage while maintaining cellular homeostasis. In this review, we provide an insight into the most recent advances in elucidating the molecular mechanisms involved in heat stress sensing and response in Marchantia polymorpha. Based on the signaling pathways and genes that were identified in Marchantia, our analyses indicate that although with specific particularities, the core components of the heat stress response seem conserved in bryophytes and angiosperms. Liverworts not only constitute a powerful tool to study heat stress response and signaling pathways during plant evolution, but also provide key and simple mechanisms to cope with extreme temperatures. Given the increasing prevalence of high temperatures around the world as a result of global warming, this knowledge provides a new set of molecular tools with potential agronomical applications.

PbSRT1 and PbSRT2 regulate pear growth and ripening yet displaying a species-specific regulation in comparison to other Rosaceae spp

Epigenetic regulation is crucial to ensure a coordinated control of the different events that occur during fruit development and ripening. Sirtuins are NAD⁺-dependent histone deacetylases involved in the regulation of gene expression of many biological processes. However, their implications in the Rosaceae family remains unexplored. Accordingly, in this work, we demonstrated the phylogenetic divergence of both sirtuins among Rosaceae species. We then characterized the expression pattern of both SRT1 and SRT2 in selected pome and stone fruit species. Both SRT1 and SRT2 significantly changed during the fruit development and ripening of apple, nectarine and pear fruit, displaying a different expression profile. Such differences could explain in part their different ripening behaviour. To further unravel the role of sirtuins on the fruit development and ripening processes, a deeper analysis was performed using pear as a fruit model. In pear, PbSRT1 gene expression levels were negatively correlated with specific hormones (i.e. abscisic acid, indole-3-acetic acid, gibberellin A1 and zeatin) during the first phases of fruit development. PbSRT2 seemed to directly mediate pear ripening in an ethylene-independent manner. This hypothesis was further reinforced by treating the fruit with the ethylene inhibitor 1-methylcyclopropene (1-MCP). Instead, enhanced PbSRT2 along pear growth/ripening positively correlated with the accumulation of major sugars (R² > 0.94), reinforcing the idea that sugar metabolism may be a target of epigenetic modifications during fruit ripening. Overall, the results from this study point out, for the first time, the importance that sirtuins have in the regulation of fruit growth and ripening of pear fruit by likely regulating hormonal and sugar metabolism.

Zn2+-Dependent Histone Deacetylases in Plants: Structure and Evolution

Zn²⁺-dependent histone deacetylases are widely distributed in archaea, bacteria, and eukaryotes. Through deacetylation of histones and other biomolecules, these enzymes regulate mammalian gene expression, microtubule stability, and polyamine metabolism. In plants, they play essential roles in development and stress response, but little is known about their biochemistry. We provide here a holistic revision of plant histone deacetylase (HDA) phylogeny and translate recent lessons from other organisms. HDA evolution correlates with a gain of structural ductility/disorder, as observed for other proteins. We also highlight two recently identified Brassicaceae-specific HDAs, as well as unprecedented key mutations that would affect the catalytic activity of individual HDAs. This revised phylogeny will contextualize future studies and illuminate research on plant development and adaptation.

H2A.Z acetylation by lincZNF337-AS1 via KAT5 implicated in the transcriptional misregulation in cancer signaling pathway in hepatocellular carcinoma

In eukaryotes, histones and their variants are essential for chromatin structure and function; both play important roles in the regulation of gene transcription, as well as the development of tumors. We aimed to explore the genomics data of hepatocellular carcinoma (HCC), combined with literature analysis, in terms of the histone variant H2A.Z. Cell phenotype assay confirmed the effect of H2A.Z on the proliferation, metastasis, apoptosis, and cell cycle of HCC cells. H2A.Z was shown to function via the tumor dysregulation signaling pathway, with BCL6 as its interacting protein. In addition, the acetylation level of H2A.Z was higher in HCC and was related to tumor formation. We found the acetylation of H2A.Z to be related to and regulated by lincZNF337-AS1. LincZNF337-AS1 was found to bind to H2A.Z and KAT5 at different sites, promoting the acetylation of H2A.Z through KAT5. We concluded that, in HCC, H2A.Z is an oncogene, whose acetylation promotes the transcription of downstream genes, and is regulated by lincZNF331-AS1.

Updated Mechanisms of GCN5-The Monkey King of the Plant Kingdom in Plant Development and Resistance to Abiotic Stresses

Histone modifications are the main epigenetic mechanisms that regulate gene expression, chromatin structure, and plant development, among which histone acetylation is one of the most important and studied epigenetic modifications. Histone acetylation is believed to enhance DNA access and promote transcription. GENERAL CONTROL NON-REPRESSIBLE 5 (GCN5), a well-known enzymatic protein responsible for the lysine acetylation of histone H3 and H4, is a universal and crucial histone acetyltransferase involved in gene transcription and plant development. Many studies have found that GCN5 plays important roles in the different development stages of Arabidopsis. In terms of exogenous stress conditions, GCN5 is also involved in the responses to heat stress, cold stress, and nutrient element deficiency by regulating the related gene expression to maintain the homeostasis of some key metabolites (e.g., cellulose) or ions (e.g., phosphate, iron); in addition, GCN5 is involved in the phytohormone pathways such as ethylene, auxin, and salicylic acid to play various roles during the plant lifecycle. Some of the pathways involved by GCN5 also interwind to regulate specific physiological processes or developmental stages. Here, interactions between various developmental events and stress-resistant pathways mediated by GCN5 are comprehensively addressed and the underlying mechanisms are discussed in the plant. Studies with some interacting factors such as ADA2b provided valuable information for the complicated histone acetylation mechanisms. We also suggest the future focuses for GCN5 functions and mechanisms such as functions in seed development/germination stages, exploration of novel interaction factors, identification of more protein substrates, and application of advanced biotechnology-CRISPR in crop genetic improvement, which would be helpful for the complete illumination of roles and mechanisms of GCN5.

Characteristic and evolution of HAT and HDAC genes in Gramineae genomes and their expression analysis under diverse stress in Oryza sativa

Comprehensive characterization of Gramineae HATs and HDACs reveals their conservation and variation. The recent WGD/SD gene pairs in the CBP and RPD/HDA1 gene family may confer specific adaptive evolutionary changes. Expression of OsHAT and OsHDAC genes provides a new vision in different aspects of development and response to diverse stress. The histone acetylase (HAT) and histone deacetylase (HDAC) have been proven to be tightly linked to play a crucial role in plant growth, development and response to abiotic stress by regulating histone acetylation levels. However, the evolutionary dynamics and functional differentiation of HATs and HDACs in Gramineae remain largely unclear. In the present study, we identified 37 HAT genes and 110 HDAC genes in seven Gramineae genomes by a detailed analysis. Phylogenetic trees of these HAT and HDAC proteins were constructed to illustrate evolutionary relationship in Gramineae. Gene structure, protein property and protein motif composition illustrated the conservation and variation of HATs and HDACs in Gramineae. Gene duplication analysis suggested that recent whole genome duplication (WGD)/segmental duplication (SD) events contributed to the diversification of the CBP and RPD3/HDA1 gene family in Gramineae. Furthermore, promoter cis-element prediction indicated that OsHATs and OsHDACs were likely functional proteins and involved in various signaling pathways. Expression analysis by RNA-seq data showed that all OsHAT and OsHDAC genes were expressed in different tissues or development stages, revealing that they were ubiquitously expressed. In addition, we found that their expression patterns were altered in response to cold, drought, salt, light, abscisic acid (ABA), and indole-3-acetic acid (IAA) treatments. These findings provide the basis for further identification of candidate OsHAT and OsHDAC genes that may be utilized in regulating growth and development and improving crop tolerance to abiotic stress.

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

The deacetylation of core histones controlled by the action of histone deacetylases (HDACs) plays an important role in the epigenetic regulation of plant gene transcription. However, no systematic analysis of HDAC genes in Dendrobium officinale, a medicinal orchid, has been performed. In the current study, a total of 14 histone deacetylases in D. officinale were identified and characterized using bioinformatics-based methods. These genes were classified into RPD3/HDA1, SIR2, and HD2 subfamilies. Most DoHDAC genes in the same subfamily shared similar structures, and their encoded proteins contained similar motifs, suggesting that the HDAC family members are highly conserved and might have similar functions. Different cis-acting elements in promoters were related to abiotic stresses and exogenous plant hormones. A transient expression assay in onion epidermal cells by Agrobacterium-mediated transformation indicated that all of the detected histone deacetylases such as DoHDA7, DoHDA9, DoHDA10, DoHDT3, DoHDT4, DoSRT1 and DoSRT2, were localized in the nucleus. A tissue-specific analysis based on RNA-seq suggested that DoHDAC genes play a role in growth and development in D. officinale. The expression profiles of selected DoHDAC genes under abiotic stresses and plant hormone treatments were analyzed by qRT-PCR. DoHDA3, DoHDA8, DoHDA10 and DoHDT4 were modulated by multiple abiotic stresses and phytohormones, indicating that these genes were involved in abiotic stress response and phytohormone signaling pathways. These results provide valuable information for molecular studies to further elucidate the function of DoHDAC genes.

Review: The plant sirtuins

The sirtuin family of intracellular enzymes are able to catalyze a unique β-nicotinamide adenine dinucleotide (β-NAD⁺)-dependent N^ε-acyl-lysine deacylation reaction on histone and non-histone protein substrates. Since 2000, the sirtuin family members have been identified in both prokaryotes and eukaryotes; tremendous accomplishments have also been achieved on the mechanistic and functional (pharmacological) understanding of the sirtuin-catalyzed deacylation reaction. Among the eukaryotic organisms, past research has been focused more on the yeast and mammalian sirtuins than on the plant sirtuins, however, the very presence of sirtuins in various plant species and the functional studies on plant sirtuins published thus far attest to the importance of this particular subfamily of eukaryotic sirtuins in regulating the growth and development of plants and their responses to biotic and abiotic stresses. In this review, an integrated and updated account will be presented on the biochemical, cellular, and functional profiles of all the plant sirtuins identified thus far. It is hoped that this article will also set a stage for expanded efforts in the identification, characterization, and functional interrogation of plant sirtuins; and the development and exploration of their chemical modulators (activators and inhibitors) in plant research and agriculture.