Methylation-directed acetylation of histone H3 regulates developmental sensitivity to histone deacetylase inhibition.

Hydroxamate-based lysine deacetylase inhibitors (KDACis) are approved for clinical use against certain cancers. However, intrinsic and acquired resistance presents a major problem. Treatment of cells with hydroxamates such as trichostatin A (TSA) leads to rapid preferential acetylation of histone H3 already trimethylated on lysine 4 (H3K4me3), although the importance of this H3K4me3-directed acetylation in the biological consequences of KDACi treatment is not known. We address this utilizing Dictyostelium discoideum strains lacking H3K4me3 due to disruption of the gene encoding the Set1 methyltransferase or mutations in endogenous H3 genes. Loss of H3K4me3 confers resistance to TSA-induced developmental inhibition and delays accumulation of H3K9Ac and H3K14Ac. H3K4me3-directed H3Ac is mediated by Sgf29, a subunit of the SAGA acetyltransferase complex that interacts with H3K4me3 via a tandem tudor domain (TTD). We identify an Sgf29 orthologue in Dictyostelium with a TTD that specifically recognizes the H3K4me3 modification. Disruption of the gene encoding Sgf29 delays accumulation of H3K9Ac and abrogates H3K4me3-directed H3Ac. Either loss or overexpression of Sgf29 confers developmental resistance to TSA. Our results demonstrate that rapid acetylation of H3K4me3 histones regulates developmental sensitivity to TSA. Levels of H3K4me3 or Sgf29 will provide useful biomarkers for sensitivity to this class of chemotherapeutic drug.

Integrating Early Transcriptomic Responses to Rhizotoxins in Rice (Oryza sativa. L.) Reveals Key Regulators and a Potential Early Biomarker of Cadmium Toxicity.

As sessile organisms, plants were constantly challenged with biotic and abiotic stresses. Transcriptional activation of stress-responsive genes is a crucial part of the plant adaptation to environmental changes. Here, early response of rice root to eight rhizotoxic stressors: arsenate, copper, cadmium, mercury, chromate, vanadate, ferulic acid and juglone, was analyzed using published microarray data. There were 539 general stress response (GSR) genes up-regulated under all eight treatments, including genes related to carbohydrate metabolism, phytohormone balance, and cell wall structure. Genes related to transcriptional coactivation showed higher Ka/Ks ratio compared to the other GSR genes. Network analysis discovered complicated interaction within GSR genes and the most connected signaling hubs were WRKY53, WRKY71, and MAPK5. Promoter analysis discovers enriched SCGCGCS cis-element in GSR genes. Moreover, GSR genes tend to be intronless and genes with shorter total intron length were induced in a higher level. Among genes uniquely up-regulated by a single stress, a phosphoenolpyruvate carboxylase kinase (PPCK) was identified as a candidate biomarker for detecting cadmium contamination. Our findings provide insights into the transcriptome dynamics of molecular response of rice to different rhizotoxic stress and also demonstrate potential use of comparative transcriptome analysis in identifying a novel potential early biomarker.

Common Stress Transcriptome Analysis Reveals Functional and Genomic Architecture Differences Between Early and Delayed Response Genes.

To identify the similarities among responses to diverse environmental stresses, we analyzed the transcriptome response of rice roots to three rhizotoxic perturbations (chromium, ferulic acid and mercury) and identified common early-transient, early-constant and delayed gene inductions. Common early response genes were mostly associated with signal transduction and hormones, and delayed response genes with lipid metabolism. Network component analysis revealed complicated interactions among common genes, the most highly connected signaling hubs being PP2C68, MPK5, LRR-RLK and NPR1. Gene architecture studies revealed different conserved promoter motifs and a different ratio of CpG island distribution between early and delayed genes. In addition, early-transient genes had more exons and a shorter first exon. IMEter was used to calculate the transcription regulation effects of introns, with greater effects for the first introns of early-transient than delayed genes. The higher Ka/Ks (non-synonymous/synonymous mutation) ratio of early-constant genes than early-transient, delayed and the genome median demonstrates the rapid evolution of early-constant genes. Our results suggest that finely tuned transcriptional control in response to environmental stress in rice depends on genomic architecture and signal intensity and duration.

Pathways involved in vanadate-induced root hair formation in Arabidopsis.

Root hair formation is controlled by environmental signals. We found significantly increased Arabidopsis root hair density and length in response to low-dose vanadate (V). Reactive oxygen species (ROS) production was induced with V treatment. We investigated the possible role of NADPH oxidase in altering root system architecture induced by V by using diphenylene iodonium (DPI), an inhibitor of NADPH oxidase, and an NADPH oxidase mutant (rhd2/AtrbohC). NADPH oxidase was involved in root hair elongation induced by V. As well, ethylene receptor (ETR1) and ROOT HAIR DEFECTIVE (RHD6) participated in inducing root hair formation induced by V. Furthermore, the kinase inhibitors, genistein (tyrosine kinase inhibitor) and K252a (ser/thr kinase inhibitor), and a phosphatase inhibitor, cantharidin (ser/thr phosphatase inhibitor), suppressed root hair formation induced by V. To elucidate the regulation of gene expression in response to V, we investigated transcriptional changes in roots by microarray assay. Exposure to V triggered changes in transcript levels of genes related to cell wall formation, ROS activity and signaling. Several genes involved in root hair formation were also regulated.

Genomic profiling of rice roots with short- and long-term chromium stress.

Cr(VI) is the most toxic valency form of Cr, but its toxicity targets and the cellular systems contributing to acquisition of tolerance remain to be resolved at the molecular level in plants. We used microarray assay to analyze the transcriptomic profiles of rice roots in response to Cr(VI) stress. Gene ontology analysis revealed that the 2,688 Cr-responsive genes were involved in binding activity, metabolic process, biological regulation, cellular process and catalytic activity. More transcripts were responsive to Cr(VI) during long-term exposure (24 h, 2,097 genes), than short-term exposure (1- and 3-h results pooled, 1,181 genes). Long-term Cr(VI)-regulated genes are involved in cytokinin signaling, the ubiquitin-proteasome system pathway, DNA repair and Cu transportation. The expression of AS2 transcription factors was specifically modulated by long-term Cr(VI) stress. The protein kinases receptor-like cytoplasmic kinase and receptor-like kinase in flowers 3 were significantly upregulated with only short-term Cr(VI) exposure. In addition, 4 mitogen-activated protein kinase kinase kinases, 1 mitogen-activated protein kinase (MAPK) and 1 calcium-dependent protein kinase (CDPK) were upregulated with short-term Cr(VI) treatment. Expression of reactive oxygen species and calcium and activity of MAPKs and CDPK-like kinases were induced with increasing Cr(VI) concentration. These results may provide new insights into understanding the mechanisms of Cr toxicity and tolerance during different stages in rice roots.

Transcriptome profiling and physiological studies reveal a major role for aromatic amino acids in mercury stress tolerance in rice seedlings.

Mercury (Hg) is a serious environmental pollution threat to the planet. The accumulation of Hg in plants disrupts many cellular-level functions and inhibits growth and development, but the mechanism is not fully understood. To gain more insight into the cellular response to Hg, we performed a large-scale analysis of the rice transcriptome during Hg stress. Genes induced with short-term exposure represented functional categories of cell-wall formation, chemical detoxification, secondary metabolism, signal transduction and abiotic stress response. Moreover, Hg stress upregulated several genes involved in aromatic amino acids (Phe and Trp) and increased the level of free Phe and Trp content. Exogenous application of Phe and Trp to rice roots enhanced tolerance to Hg and effectively reduced Hg-induced production of reactive oxygen species. Hg induced calcium accumulation and activated mitogen-activated protein kinase. Further characterization of the Hg-responsive genes we identified may be helpful for better understanding the mechanisms of Hg in plants.

Transcriptome profiling of genes and pathways associated with arsenic toxicity and tolerance in Arabidopsis.

BACKGROUND: Arsenic (As) is a toxic metalloid found ubiquitously in the environment and widely considered an acute poison and carcinogen. However, the molecular mechanisms of the plant response to As and ensuing tolerance have not been extensively characterized. Here, we report on transcriptional changes with As treatment in two Arabidopsis accessions, Col-0 and Ws-2. RESULTS: The root elongation rate was greater for Col-0 than Ws-2 with As exposure. Accumulation of As was lower in the more tolerant accession Col-0 than in Ws-2. We compared the effect of As exposure on genome-wide gene expression in the two accessions by comparative microarray assay. The genes related to heat response and oxidative stresses were common to both accessions, which indicates conserved As stress-associated responses for the two accessions. Most of the specific response genes encoded heat shock proteins, heat shock factors, ubiquitin and aquaporin transporters. Genes coding for ethylene-signalling components were enriched in As-tolerant Col-0 with As exposure. A tolerance-associated gene candidate encoding Leucine-Rich Repeat receptor-like kinase VIII (LRR-RLK VIII) was selected for functional characterization. Genetic loss-of-function analysis of the LRR-RLK VIII gene revealed altered As sensitivity and the metal accumulation in roots. CONCLUSIONS: Thus, ethylene-related pathways, maintenance of protein structure and LRR-RLK VIII-mediated signalling may be important mechanisms for toxicity and tolerance to As in the species. Here, we provide a comprehensive survey of global transcriptional regulation for As and identify stress- and tolerance-associated genes responding to As.