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

Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects

Sorghum, renowned for its substantial biomass production and remarkable tolerance to various stresses, possesses extensive gene resources and phenotypic variations. A comprehensive understanding of the genetic basis underlying complex agronomic traits is essential for unlocking the potential of sorghum in addressing food and feed security and utilizing marginal lands. In this context, we provide an overview of the major trends in genomic resource studies focusing on key agronomic traits over the past decade, accompanied by a summary of functional genomic platforms. We also delve into the molecular functions and regulatory networks of impactful genes for important agricultural traits. Lastly, we discuss and synthesize the current challenges and prospects for advancing molecular design breeding by gene-editing and polymerization of the excellent alleles, with the aim of accelerating the development of desired sorghum varieties.

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.

A histone deacetylase, FaSRT1-2, plays multiple roles in regulating fruit ripening, plant growth and stresses resistance of cultivated strawberry

Sirtuins (SRTs) are a group of nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase that target both histone and nonhistone proteins. The biological function of SRT in horticultural plants has been rarely studied. In this study, FaSRT1-2 was identified as a key member of the 8 FaSRTs encoded in cultivated strawberry genome. Transient overexpression of FaSRT1-2 in strawberry fruit accelerated ripening, increased the content of anthocyanins and sugars, enhanced ripening-related gene expression. Moreover, stable transformation of FaSRT1-2 in strawberry plants resulted in enhanced vegetative growth, increased sensitivity to heat stress and increased susceptibility to Botrytis cinerea infection. Interestingly, knocking out the homologous gene in woodland strawberry had the opposite effects. Additionally, we found the content of stress-related hormone abscisic acid (ABA) was decreased, while the growth-related gibberellin (GA) concentration was increased in FaSRT1-2 overexpression lines. Gene expression analysis revealed induction of heat shock proteins, transcription factors, stress-related and antioxidant genes in the FaSRT1-2-overexpressed plants while knocked-out of the gene had the opposite impact. In conclusion, our findings demonstrated that FaSRT1-2 could positively promote strawberry plant vegetative growth and fruit ripening by affecting ABA and GA pathways. However, it negatively regulates the resistance to heat stress and B. cinerea infection by influencing the related gene expression.

The histone deacetylase SRT2 enhances the tolerance of chrysanthemum to low temperatures through the ROS scavenging system

Low temperatures can severely affect plant growth and reduce their ornamental value. A family of plant histone deacetylases allows plants to cope with both biotic and abiotic stresses. In this study, we screened and cloned the cDNA of DgSRT2 obtained from transcriptome sequencing of chrysanthemum leaves under low-temperature stress. Sequence analysis showed that DgSRT2 belongs to the sirtuin family of histone deacetylases. We obtained the stable transgenic chrysanthemum lines OE-2 and OE-12. DgSRT2 showed tissue specificity in wild-type chrysanthemum and was most highly expressed in leaves. Under low-temperature stress, the OE lines showed higher survival rates, proline content, solute content, and antioxidant enzyme activities, and lower relative electrolyte leakage, malondialdehyde, hydrogen peroxide, and superoxide ion accumulation than the wild-type lines. This work suggests that DgSRT2 can serve as an essential gene for enhancing cold resistance in plants. In addition, a series of cold-responsive genes in the OE line were compared with WT. The results showed that DgSRT2 exerted a positive regulatory effect by up-regulating the transcript levels of cold-responsive genes. The above genes help to increase antioxidant activity, maintain membrane stability and improve osmoregulation, thereby enhancing survival under cold stress. It can be concluded from the above work that DgSRT2 enhances chrysanthemum tolerance to low temperatures by scavenging the ROS system.

Epigenetic drugs as new emerging therapeutics: What is the scale's orientation of application and challenges?

Epigenetics is the study of heritable changes in gene expression or function without altering the DNA sequence. Important factors are part of epigenetic events, such as methylation, DNA histone rearrangements, nucleosome transposition, and non-coding RNAs. Dysregulated epigenetic mechanics are associated with various cancers' initiation, development, and metastasis. It is known that the occurrence and development of cancer can be controlled by regulating unexpected epigenetic events. Epi-drugs are used singly or in combination with chemotherapy and enhance antitumor activity, reduce drug resistance, and stimulate the host immune response. Despite these benefits, epigenetic therapy as a single therapy or in combination with other drugs leads to adverse effects. This review article introduces and compares the advantages, disadvantages, and side effects of using these drugs for the first time since their introduction. Also, this article describes the mechanism of action of various epigenetic drugs. Recommendations for future use of epigenetic drugs as cancer therapeutics are suggested as an overall conclusion.

Comparative transcriptome analysis reveals the core molecular network in pattern-triggered immunity in Sorghum bicolor

Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is the first line of defense in plant disease resistance. However, the molecular mechanisms of plant PTI vary across species, making it challenging to identify a core set of trait-associated genes. This study aimed to investigate key factors that influence PTI and identify the core molecular network in Sorghum bicolor, a C4 plant. We performed comprehensive weighted gene co-expression network analysis and temporal expression analysis of large-scale transcriptome data from various sorghum cultivars under different PAMP treatments. Our results revealed that the type of PAMP had a stronger influence on the PTI network than did the sorghum cultivar. Following PAMP treatment, 30 genes with stable downregulated expression and 158 genes with stable upregulated expression were identified, including genes encoding potential pattern recognition receptors whose expression was upregulated within 1 h of treatment. PAMP treatment altered the expression of resistance-related, signaling, salt-sensitive, heavy metal-related, and transporter genes. These findings provide novel insights into the core genes involved in plant PTI and are expected to facilitate the identification and application of resistance genes in plant breeding studies.

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.

Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses

Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.