Dataset Information

RNA-Seq analysis and whole genome DNA-binding profile of the Vibrio cholerae histone-like nucleoid structuring protein (H-NS).

ABSTRACT: The data described in this article pertain to the genome-wide transcription profiling of a Vibrio cholerae mutant lacking the histone-like nucleoid structuring protein (H-NS) and the mapping of the H-NS chromosome binding sites [1, 2]. H-NS is a nucleoid-associated protein with two interrelated functions: organization of the bacterial nucleoid and transcriptional silencing [3]. Both functions require DNA binding and protein oligomerization [4, 5]. H-NS commonly silences the expression of virulence factors acquired by lateral gene transfer [6]. The highly pleiotropic nature of hns mutants in V. cholerae indicates that H-NS impacts a broad range of cellular processes such as virulence, stress response, surface attachment, biofilm development, motility and chemotaxis. We used a V. cholerae strain harboring a deletion of hns and a strain expressing H-NS tagged at the C-terminus with the FLAG epitope to generate datasets representing the hns transcriptome and DNA binding profile under laboratory conditions (LB medium, 37°C). The datasets are publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE62785 and GSE64249.

SUBMITTER: Ayala JC

PROVIDER: S-EPMC4470426 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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RNA-Seq analysis and whole genome DNA-binding profile of the <i>Vibrio cholerae</i> histone-like nucleoid structuring protein (H-NS).

Ayala Julio C JC Wang Hongxia H Benitez Jorge A JA Silva Anisia J AJ

Genomics data 20150901

The data described in this article pertain to the genome-wide transcription profiling of a <i>Vibrio cholerae</i> mutant lacking the histone-like nucleoid structuring protein (H-NS) and the mapping of the H-NS chromosome binding sites [1, 2]. H-NS is a nucleoid-associated protein with two interrelated functions: organization of the bacterial nucleoid and transcriptional silencing [3]. Both functions require DNA binding and protein oligomerization [4, 5]. H-NS commonly silences the expression of ...[more]

PMID: 26097806

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Project description:The cholera disease bacterium V. cholerae, can adopt planktonic or biofilm lifestyles depending on the intracellular concentration of the second messenger cyclic diguanylic acid (c-di-GMP). Biofilm formation protects Vibrios from stressful conditions and facilitates disease transmission by enhancing infectivity. The histone-like nucleoid structuring protein (H-NS) is a global regulator of genes associated with pathogenicity and responses to environmental stresses. H-NS represses the transcription of genes vpsT, vpsA and vpsL, which are required for the biosynthesis of the biofilm exopolysacchide matrix. Here we demonstrate that the c-di-GMP-binding protein VpsT disrupts H-NS nucleoprotein complexes at the vpsA and vpsL promoters and that this effect is enhanced by c-di-GMP. We used ChIP coupled with Next Generation Sequencing (ChIP-Seq) and transcriptome analysis (RNA-Seq) to identify additional loci repressed by H-NS affecting biofilm formation. This study showed that H-NS directly represses the transcription of genes encoding proteins present in the biofilm matrix such as the rbmA-F cluster, hemolysin and chitinase. Similar to vpsA and vpsL, the promoter region of vpsU, rbmA and rbmF exhibited overlapping H-NS and VpsT binding motifs. Deletion of vpsT increased H-NS occupancy at the vpsU, vpsA, vpsL, rbmA and rbmF promoters. Conversely, artificially increasing the c-di-GMP pool diminished H-NS occupancy at the above promoters. Deletion of vpsT did not affect H-NS occupancy at its own promoter. However, deletion of genes encoding the regulators AphA and VpsR significantly increased H-NS occupancy at the vpsT promoter. In sum, our study shows that c-di-GMP enhances biofilm formation by acting through VpsT to activate an H-NS anti-repression cascade. The Binding profile of V. cholerae H-NS to the genome was determined by ChIP followed by Next Generation Sequencing (ChIP-Seq) using the Illumina HiSeq2000 platform. V. cholerae C7258 cells expressing H-NS-FLAG fusion protein from the hns transcription and translation signals were collected from LB cultures grown to mid-exponential phase (OD600 0.5). An anti-FLAG Immunoprecipitation (IP) and an Input samples were used for the analysis.

Project description:Cholera is a diarrheal disease caused by Vibrio cholerae of serogroups O1 and O139 that affects impoverished populations worldwide. The histone-like nucleoid structuring protein (H-NS) is a global regulator of environmentally-regulated gene expression that plays a fundamental role in V. cholerae adaptation to disparate ecological niches. We used RNA-seq to characterize the hns transcriptome of El Tor biotype V. cholerae. H-NS affected the expression of 18% of all predicted genes in a growth phase-dependent manner. It silenced the transcription of genes encoding virulence regulators and cytotoxic factors such as the VieSAB regulatory system, the repeat in toxin (RTX) and hemolysin. H-NS was 10 times more effective in silencing the vieSAB promoter in El Tor compared to classical biotype V. cholerae. In the El Tor biotype hns mutant, VieSAB significantly enhanced the expression of cholera toxin genes. For the RTX and hemolysin, we found that overexpression of the transcription activator HlyU diminished H-NS occupancy at the hlyA promoter but not at the rtxCA and rtxBDE promoters. H-NS had a significant impact on the cell envelope and the mutant expressed elevated rpoE encoding the extracytoplamic sigma factor E (sE), though this effect was indirect. A remarkable feature of the hns transcriptome was the down-regulation of numerous methyl-accepting chemotaxis proteins in early stationary phase that translated into diminished chemotaxis toward the amino acids glycine and serine. Our study suggests that H-NS transcriptional silencing can contribute to multiple phenotypic differences observed between V. cholerae biotypes, mainly by differentially repressing the VieSAB sensory pathway. Transcriptome profiles of wild type and M-NM-^Thns mutant cells of the V. cholerae strain C7258 grown in LB medium were generated by Next Generation Sequencing using the Illumina HiSeq2000 platform. Samples from mid-exponential phase (OD600 0.5) and early stationary phase (OD600 2.0) were analyzed in duplicate

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Dataset Information

RNA-Seq analysis and whole genome DNA-binding profile of the Vibrio cholerae histone-like nucleoid structuring protein (H-NS).

Publications

RNA-Seq analysis and whole genome DNA-binding profile of the <i>Vibrio cholerae</i> histone-like nucleoid structuring protein (H-NS).

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