Sequence and expression analysis of histone deacetylases in rice

Rice (Oryza sativa L.) is one of the most important food crops in the world. In plants, jasmonic acid (JA) plays essential roles in response to biotic and abiotic stresses. As one of the largest transcription factors (TFs), basic region/leucine zipper motif (bZIP) TFs play pivotal roles through the whole life of plant growth. However, the relationship between JA and bZIP TFs were rarely reported, especially in rice. In this study, we found two rice homologues of Arabidopsis VIP1 (VirE2-interacting protein 1), OsbZIP81, and OsbZIP84. OsbZIP81 has at least two alternative transcripts, OsbZIP81.1 and OsbZIP81.2. OsbZIP81.1 and OsbZIP84 are typical bZIP TFs, while OsbZIP81.2 is not. OsbZIP81.1 can directly bind OsPIOX and activate its expression. In OsbZIP81.1 overexpression transgenic rice plant, JA (Jasmonic Acid) and SA (Salicylic acid) were up-regulated, while ABA (Abscisic acid) was down-regulated. Moreover, Agrobacterium, Methyl Jasmonic Acid (MeJA), and PEG6000 can largely induce OsbZIP81. Based on ChIP-Seq and Random DNA Binding Selection Assay (RDSA), we identified a novel cis-element OVRE (Oryza VIP1 response element). Combining ChIP-Seq and RNA-Seq, we obtained 1332 targeted genes that were categorized in biotic and abiotic responses, including α-linolenic acid metabolism and fatty acid degradation. Together, these results suggest that OsbZIP81 may positively regulate JA levels by directly targeting the genes in JA signaling and metabolism pathway in rice.

As sessile organisms, plants must tolerate various environmental stresses. Plant hormones play vital roles in plant responses to biotic and abiotic stresses. Among these hormones, jasmonic acid (JA) and its precursors and derivatives (jasmonates, JAs) play important roles in the mediation of plant responses and defenses to biotic and abiotic stresses and have received extensive research attention. Although some reviews of JAs are available, this review focuses on JAs in the regulation of plant stress responses, as well as JA synthesis, metabolism, and signaling pathways. We summarize recent progress in clarifying the functions and mechanisms of JAs in plant responses to abiotic stresses (drought, cold, salt, heat, and heavy metal toxicity) and biotic stresses (pathogen, insect, and herbivore). Meanwhile, the crosstalk of JA with various other plant hormones regulates the balance between plant growth and defense. Therefore, we review the crosstalk of JAs with other phytohormones, including auxin, gibberellic acid, salicylic acid, brassinosteroid, ethylene, and abscisic acid. Finally, we discuss current issues and future opportunities in research into JAs in plant stress responses.

Brassinosteroids (BRs) are key phytohormones involved in the regulation of major processes of cell metabolism that guide plant growth. In the past decades, new evidence has made it clear that BRs also play a key role in the orchestration of plant responses to many abiotic and biotic stresses. In the present work, we analyzed the impact of foliar treatment with 24-epicastasterone (ECS) on the endogenous content of major phytohormones (auxins, salicylic acid, jasmonic acid, and abscisic acid) and their intermediates in soybean leaves 7 days following the treatment. Changes in the endogenous content of phytohormones have been identified and quantified by LC/MS. The obtained results point to a clear role of ECS in the upregulation of auxin content (indole-3-acetic acid, IAA) and downregulation of salicylic, jasmonic, and abscisic acid levels. These data confirm that under optimal conditions, ECS in tested concentrations of 0.25 µM and 1 µM might promote growth in soybeans by inducing auxin contents. Benzoic acid (a precursor of salicylic acid (SA)), but not SA itself, has also been highly accumulated under ECS treatment, which indicates an activation of the adaptation strategies of cell metabolism to possible environmental challenges.

The occurrence and development of tumors are closely related to histone deacetylases (HDACs). However, their relationship with the overall biology and prognosis of glioma is still unknown. In the present study, we developed and validated a prognostic model for glioma based on HDAC genes. Glioma patients can be divided into two subclasses based on eleven HDAC genes, and patients from the two subclasses had markedly different survival outcomes. Then, using six HDAC genes (HDAC1, HDAC3, HDAC4, HDAC5, HDAC7, and HDAC9), we established a prognostic model for glioma patients, and this prognostic model was validated in an independent cohort. Furthermore, the calculated risk score from six HDACA genes expression was found to be an independent prognostic factor that could predict the five-year overall survival of glioma patients well. High-risk patients have changes in multiple complex functions and molecular signaling pathways, and the gene alterations of high- and low-risk patients were significantly different. We also found that the different survival outcomes of high- and low-risk patients could be related to the differences in immune filtration levels and the tumor microenvironment. Subsequently, we identified several small molecular compounds that could be favorable for glioma patient treatment. Finally, the expression levels of HDAC genes from the prognostic model were validated in glioma and nontumor tissue samples. Our results revealed the clinical utility and potential molecular mechanisms of HDAC genes in glioma. A model based on six HDAC genes can predict the overall survival of glioma patients well, and these genes are potential therapeutic targets.

Isolation of a novel rice PR4 type gene whose mRNA expression is modulated by blast pathogen attack and signaling components

Cloning and characterization of a jasmonate inducible rice ( Oryza sativa L.) peroxidase gene, OsPOX, against global signaling molecules and certain inhibitors of kinase-signaling cascade(s)

Chapter 19 - Crosstalk of hormones, second messengers, and MAPK in plant defense

Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor whose activation is dependent on a ligand. PPARγ activation by exogenous ligands, such as thiazolidinediones (TZDs), is a strategy in the treatment of type 2 diabetes mellitus for the improvement of insulin sensitivity. In addition to a ligand, PPARγ function is also regulated by posttranslational modifications, such as phosphorylation, sumoylation, and ubiquitination. Herein, we report that the PPARγ protein is modified by acetylation, which induces the PPARγ function in the absence of an external ligand. We observed that histone deacetylase 3 (HDAC3) interacted with PPARγ to deacetylate the protein. In immunoprecipitation assays, the HDAC3 protein was associated with the PPARγ protein. Inhibition of HDAC3 using RNAi-mediated knockdown or HDAC3 inhibitor increased acetylation of the PPARγ protein. Furthermore, inhibition of HDAC3 enhanced the expression of PPARγ target genes such as adiponectin and aP2. The expression was associated with an increase in glucose uptake and insulin signaling in adipocytes. HDAC3 inhibition enhanced lipid accumulation during differentiation of adipocytes. PPARγ acetylation was also induced by pioglitazone and acetylation was required for PPARγ activation. In the absence of TZDs, the acetylation from HDAC3 inhibition was sufficient to induce the transcriptional activity of PPARγ. Treating diet-induced obesity mice with HDAC3 inhibitor or pioglitazone for 2 weeks significantly improved high-fat-diet-induced insulin resistance. Our results indicate that acetylation of PPARγ is a ligand-independent mechanism of PPARγ activation. HDAC3 inhibitor is a potential PPARγ activator for the improvement of insulin sensitivity.

Expression of two wheat defense-response genes, Hfr-1 and Wci-1, under biotic and abiotic stresses

The phloem-feeding by greenbug (Schizaphis graminum) elicits unique interactions with their host plants. To investigate the expression profiles of sorghum genes responsive to greenbug feeding, two subtractive cDNA libraries were constructed through different combinatorial subtractions in a strong greenbug resistance sorghum M627 line and a susceptible Tx7000 line with or without greenbug infestation. A total of 3,508 cDNAs were selected from the two cDNA libraries, and subsequent cDNA microarray and northern blot analyses were performed for identification of sorghum genes responsive to greenbugs. In total, 157 sorghum transcripts were identified to be differentially expressed by greenbug feeding. The greenbug responsive genes were isolated and classified into nine categories according to the functional roles in plant metabolic pathways, such as defense, signal transduction, cell wall fortification, oxidative burst/stress, photosynthesis, development, cell maintenance, abiotic stress, and unknown function. Overall, the profiles of sorghum genes, responsive to greenbug phloem-feeding shared common identities with other expression profiles known to be elicited by diverse stresses, including pathogenesis, abiotic stress, and wounding. In addition to well-known defense related regulators such as salicylic acid, jasmonic acid, and abscisic acid, auxin and gibberellic acid were also involved in mediation of the defense responses against greenbug phloem-feeding in sorghum.

HDAC2 regulates oocyte maturation in Tan sheep via its strong association with regulating H4K12 acetylation and EREG secretion.

Background: Sodium valproate (NaV) is a widely prescribed antiepileptic and mood-stabilizing drug that also functions as a histone deacetylase inhibitor (HDACi). HDAC deregulation contributes to cancer and neurodegenerative disorders, yet the feedback regulation of HDAC genes under pharmaceutical inhibition remains unclear. Methods: This pilot study evaluated mRNA expression of class I HDACs (HDAC1, HDAC2, HDAC3, HDAC8) and class IIa HDACs (HDAC4, HDAC5, HDAC7, HDAC9) using RT-qPCR in peripheral blood from 50 NaV-treated epileptic patients and 50 age/sex-matched neurological controls. Results: NaV treatment was associated with significant upregulation of HDAC1 (↑2.6-fold) and HDAC3 (↑2.1-fold), alongside downregulation of HDAC7 (↓1.9-fold). HDAC2 expression was unaffected by NaV but significantly reduced in smokers across groups. Obesity was linked to increased HDAC1 and reduced HDAC3 and HDAC9 expression. Conclusions: NaV therapy induces distinct de novo expression changes in HDAC genes, suggesting feedback regulation mechanisms. These findings provide a basis for larger studies examining HDAC superfamily expression as potential biomarkers of treatment response

The foundation for ensuring walnuts of high yield and quality is excellent rootstock. Numerous studies have shown that the walnut rootstock has a major impact on the grafted varieties’ quality, yield, stress resistance, growth, and development. Elucidating the mechanism of grafting affinity in walnuts is crucial, as it paves the way for selecting premium rootstocks to achieve increased production and efficiency. In this study, a combined analysis of the transcriptome, miRNA, and metabolome was conducted to elucidate the molecular mechanisms underlying graft compatibility between different walnut rootstocks (Juglans sigillata cv. ‘Qianhe 7’ and ‘Panzhou’). A total of 44, 41, 50, and 28 differential miRNAs were identified between ‘Qianhe 7’ vs ‘Panzhou’ at 1st d, 11th d, 17th d, and 30th d after grafting, respectively. These miRNAs target genes associated with plant hormone signaling pathways, particularly those related to IAA, SA, and ABA, such as ARF, SAUR, and RAS1-like genes. The most dominant metabolites in both J. sigillata rootstocks (cv. ‘Qianhe 7’ and ‘Panzhou’) at 1st d after grafting were salicylic acid (SA) and Indole-3-acetic acid (IAA). The concentration of SA increased with the extension of time in ‘Qianhe 7’, while IAA decreased significantly on the 30th d. The IAA and abscisic acid (ABA) contents of ‘Qianhe 7’ were markedly higher than those observed in ‘Panzhou’ at 11th d and 30th d post-grafting, respectively. But the concentration of jasmonic acid (JA) in the ‘Panzhou’ was significantly higher than that observed in the ‘Qianhe 7’ at 17th d post-grafting. These results indicated that SA, ABA, and IAA may play a pivotal role in the adaptability of grafted J. sigillata (‘Qianhe 7’ and ‘Panzhou’), which provides a foundation for understanding walnut graft affinity. A deeper exploration of the synergistic regulatory network between the identified miRNAs and plant hormones is warranted to clarify the underlying mechanisms, thereby informing hormone-based breeding strategies for walnut rootstocks and facilitating the sustainable advancement of the walnut industry.

Objective: To explore the effect of human bone marrow mesenchymal stem cells(MSC) on the steroid resistance of human airway epithelial cells. Methods: Ovalbumin (OVA)/lipopolysaccharide (LPS) were used to construct steroid resistant BEAS-2B cells, which were then co-cultured with MSC. Groups were set as follows: blank group, model group, Glucocorticoid group, MSC group, MSC+Glucocorticoid group (MSC+bud group). The expression of interleukin (IL)-8 in the cell supernatant was detected by enzyme-linked immunosorbent assay (ELISA); the expression of reactive oxygen species (ROS) in the cells was detected by flow cytometry; the expression of glucocorticoid receptor α (GRα) and histone deacetylase 2 (HDAC2) protein in the cell was detected by Western blotting; and the expression of GRα and HDAC2 mRNA was detected by reverse transcription-polymerase chain reaction (RTPCR). Results: The expression level of IL-8 in the MSC group was significantly lower than that in the Glucocorticoid group (31.7±0.7 vs. 49.8±3.6, P<0.01). The expression of ROS in the MSC group was significantly lower than that in the Glucocorticoid group (2754±154 vs.4624±228, P<0.05). The expression level of HDAC2 mRNA in the MSC group was significantly higher than that in the Glucocorticoid group(1.749±0.005 vs. 1.283±0.098, P<0.05). The expression level of GRα mRNA in the MSC group was significantly higher than that in the Glucocorticoid group (1.623±0.079 vs.1.047±0.220, P<0.01). The expression of HDAC2 protein in the MSC group was significantly higher than that in the Glucocorticoid group (1.067±0.100 vs. 0.620±0.083, P<0.01). The expression of GRα protein in the MSC group was significantly higher than that in the Glucocorticoid group (0.834±0.053 vs. 0.579±0.017, P<0.01). ROS was positively correlated with the IL-8 expression (r=0.796, P<0.01) and negatively correlated with the HDAC2 and GRα mRNA expression (r=-0.893 3, P<0.01; r=0.931 4, P<0.01, respectively), as well as the HDAC2 and GRα Protein expression (r=-0.929 5, P<0.01;r=-0.864 3, P<0.01, respectively). Conclusions: Human MSC can improve steroid resistance of airway epithelial cells in an exocrine manner. The mechanism may be related to the down-regulation of ROS and up-regulation of HDAC2, which lead to GRα overexpression. In addition, MSC may improve the steroid resistance by reducing the expression of IL-8.

ESTRADIOL AND PHTHALATS INFLUENCES MIGRATION AND PROLIFERATION THROUGH HDAC6 IN ESTROGEN-INDEPENDENT/DEPENDENT BREAST CANCER CELLS