AtSRT1 regulates flowering by regulating flowering integrators and energy signals in Arabidopsis.

Epigenetic modifications, such as histone alterations, play crucial roles in regulating the flowering process in Arabidopsis, a typical long-day model plant. Histone modifications are notably involved in the intricate regulation of FLC, a key inhibitor of flowering. Although sirtuin-like protein and NAD+-dependent deacetylases play an important role in regulating energy metabolism, plant stress responses, and hormonal signal transduction, the mechanisms underlying their developmental transitions remain unclear. Thus, this study aimed to reveal how Arabidopsis NAD + -dependent deacetylase AtSRT1 affects flowering by regulating the expression of flowering integrators. Genetic and molecular evidence demonstrated that AtSRT1 mediates histone deacetylation by directly binding near the transcriptional start sites (TSS) of the flowering integrator genes FT and SOC1 and negatively regulating their expression by modulating the expression of the downstream gene LFY to inhibit flowering. Additionally, AtSRT1 directly down-regulates the expression of TOR, a glucose-driven central hub of energy signaling, which controls cell metabolism and growth in response to nutritional and environmental factors. This down-regulation occurs through binding near the TSS of TOR, facilitating the addition of H3K27me3 marks on FLC via the TOR-FIE-PRC2 pathway, further repressing flowering. These results uncover a multi-pathway regulatory network involving deacetylase AtSRT1 during the flowering process, highlighting its interaction with TOR as a hub for the coordinated regulation of energy metabolism and flowering initiation. These findings significantly enhance understanding of the complexity of histone modifications in the regulation of flowering.

Transcriptomic and metabolomic insights into the defense response to HFRs in Arabidopsis.

Tetrabromobisphenol A (TBBPA), Tetrachlorobisphenol A (TCBPA), Tetrabromobisphenol S (TBBPS) and their derivatives as the most widely used halogenated flame retardants (HFR), had been employed in the manufacturing industry to raise fire safety. HFRs have been shown to be developmentally toxic to animals and also affect plant growth. However, little was known about the molecular mechanism responded by when plants were treated with these compounds. In this study, when Arabidopsis was exposed to four HFRs (TBBPA, TCBPA, TBBPS-MDHP, TBBPS), the stress of these compounds had different inhibitory effects on seed germination and plant growth. Transcriptome and metabolome analysis showed that all four HFRs could influence the expression of transmembrane transporters to affect ion transport, Phenylpropanoid biosynthesis, Plant-pathogen interaction, MAPK signalling pathway and other pathways. In addition, the effects of different kinds of HFR on plants also have variant characteristics. It is very fascinating that Arabidopsis shows the response of biotic stress after exposure to these kinds of compounds, including the immune mechanism. Overall, the findings of the mechanism recovered by methods of transcriptome and metabolome analysis supplied a vital insight into the molecular perspective for Arabidopsis response to HFRs stress.

SDG711 Is Involved in Rice Seed Development through Regulation of Starch Metabolism Gene Expression in Coordination with Other Histone Modifications.

SDG711 is a histone H3K27me2/3 transmethylase in rice, a homolog of CLF in Arabidopsis, and plays key roles in regulating flowering time and panicle development. In this work, we investigated the role of SDG711 in rice seed development. Overexpression and downregulation of SDG711 lead to a decrease and increase in the expression level of genes related to starch accumulation, resulting in smaller seeds or even seed abortion. ChIP assay showed that SDG711-mediated H3K27me3 changed significantly in genes related to endosperm development, and SDG711 can directly bind to the gene body region of several starch synthesis genes and amylase genes. In addition, H3K4me3 and H3K9ac modifications also cooperate with H3K27me3 to regulate the development of the endosperm. Our results suggest that the crosstalk between SDG711-mediated H3K27me3 and H3K4me3, and H3K9ac are involved in starch accumulation to control normal seed development.

Inhibition of PHLDA2 transcription by DNA methylation and YY1 in goat placenta.

Pleckstrin homology-like domain family A member 2 (PHLDA2) is essential for placental development in mammals. This study was conducted to investigate transcriptional regulation of goat PHLDA2 in the placenta. Real-time PCR and Western blot analyses showed different expression of the PHLDA2 in goat placentas during gestation with highest expression at 30 and 45 days post coitus (P < 0.05). Luciferase reporter assays demonstrated the highest promoter activity in the region of -1023/+20 (P < 0.05). A CpG island was defined within -631/+379 region, where lower level of CpG-methylation was detected with bisulfite sequencing PCR in the placenta than that in the spleen and liver (P < 0.05). Meanwhile, in vitro experiments showed that 5-AzaC enhanced the gene expression in a dose-dependent manner. Site-directed mutation in vitro demonstrated that transcription factor Ying-yang 1 (YY1) had an inhibitory effect on the PHLDA2 expression, and the inhibition was further confirmed with overexpression and siRNA constructs of YY1. ChIP and RE-ChIP analyses further identified the binding of YY1 to the PHLDA2 promoter by interaction with histone deacetylase 1 (HDAC1) and HDAC3. This study uncovers the negative regulation of the CpG-methylation and YY1 on goat PHLDA2 expression. YY1 prefers binding to CpG-methylation sequences, and inhibits goat PHLDA2 expression via recruiting HDAC1 and 3.

Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response.

Epigenetic regulation of gene expression is important for plant adaptation to environmental changes. Previous results showed that Arabidopsis RPD3-like histone deacetylase HDA9 is known to function in repressing plant response to stress in Arabidopsis. However, how HDA9 targets to specific chromatin loci and controls gene expression networks involved in plant response to stress remains largely unclear. Here, we show that HDA9 represses stress tolerance response by interacting with and regulating the DNA binding and transcriptional activity of WRKY53, which functions as a high-hierarchy positive regulator of stress response. We found that WRKY53 is post-translationally modified by lysine acetylation at multiple sites, some of which are removed by HDA9, resulting in inhibition of WRKY53 transcription activity. Conversely, WRKY53 negatively regulates HDA9 histone deacetylase activity. Collectively, our results indicate that HDA9 and WRK53 are reciprocal negative regulators of each other's activities, illustrating how the functional interplay between a chromatin regulator and a transcription factor regulates stress tolerance in plants.

An Improved Method of Preparing High Efficiency Transformation Escherichia coli with Both Plasmids and Larger DNA Fragments.

The high-throughput, cost-efficient transformation systems determine the success of gene cloning and functional analysis. Among various factors that affect this transformation systems, the competence ability of target cells is one of the most important factors. We found antimicrobial peptides LFcin-B can increase the permeability of the cell membrane, and their lethal antibacterial properties can be inhibited by moderately high concentrations of Ca2+ and Mn2+. In this study, we established a convenient and rapid method (CRM) by adding small concentrations of (0.35 mg/L) and moderately high concentrations of MnCl2 (50 mM) and CaCl2 (30 mM) in transformation buffer. The transformation efficiency of E. coli cells (DH5α, JM109 and TOP10) prepared by CRM were comparable with electroporation for plasmid transformation (3.1 ± 0.3 × 109 cfu/µg). Unlike competent cells prepared using other chemical methods, those obtained using CRM method are extremely competent for receiving larger size DNA fragments (> 5000 bp) into plasmid vectors. The competent E. coli cells prepared by CRM method are particularly useful for most high-efficiency transformation experiments under normal laboratory conditions.

Histone Deacetylase AtSRT1 Links Metabolic Flux and Stress Response in Arabidopsis.

How plant metabolic flux alters gene expression to optimize plant growth and response to stress remains largely unclear. Here, we report that Arabidopsis thaliana NAD+-dependent histone deacetylase AtSRT1 negatively regulates plant tolerance to stress and glycolysis but stimulates mitochondrial respiration. We found that AtSRT1 interacts with Arabidopsis cMyc-Binding Protein 1 (AtMBP-1), a transcriptional repressor produced by alternative translation of the cytosolic glycolytic enolase gene LOS2/ENO2. We demonstrated that AtSRT1 could associate with the chromatin of AtMBP-1 targets LOS2/ENO2 and STZ/ZAT10, both of which encode key stress regulators, and reduce the H3K9ac levels at these genes to repress their transcription. Overexpression of both AtSRT1 and AtMBP-1 had synergistic effects on the expression of glycolytic genes, glycolytic enzymatic activities, and mitochondrial respiration. Furthermore, we found that AtMBP-1 is lysine-acetylated and vulnerable to proteasomal protein degradation, while AtSRT1 could remove its lysine acetylation and significantly enhance its stability in vivo. Taken together, these results indicate that AtSRT1 regulates primary metabolism and stress response by both epigenetic regulation and modulation of AtMBP-1 transcriptional activity in Arabidopsis.

Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis.

Histone modification is an important epigenetic regulation in higher plants adapting to environment changes including salt and drought stresses. In this report, we show that the Arabidopsis RPD3-type histone deacetylase HDA9 is involved in modulating plant responses to salt and drought stresses in Arabidopsis. Loss-of-function mutants of the gene displayed phenotypes (such as seedling root growth and seed germination) insensitive to NaCl and polyethylene glycol (PEG) treatments. HDA9 mutation led to up-regulation of many genes, among which those involved in response to water deprivation stress (GO: 0009414) were enriched. These genes were much more induced in the mutants than wild-type plants when treated with PEG and NaCl. In addition, we found that in the mutants, salt and drought stresses led to much higher levels of histone H3K9 acetylation at promoters of 14 genes randomly selected from those that respond to water-deprivation stress than in wild-type plants. Our study suggested that HDA9 might be a novel chromatin protein that negatively regulates plant sensitivity to salt and drought stresses by regulating histone acetylation levels of a large number of stress-responsive genes in Arabidopsis.