Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparison of the expression profiles of 630E JIR8094 strain and a ccpA mutant after 10h of growth in TY with 0.5% glucose.

ABSTRACT: Transcriptionnal profiling of C. difficile 630E JIR8094 strain vs a ccpA mutant after 10h of growth in TY with 0.5% glucose two-conditions experiments, WT strain vs ccpA mutant strain, 4 biological replicates for each condition, in an indirect design using a 8h TY RNA preparation as Reference

ORGANISM(S): [Clostridium] difficile

SUBMITTER: Monot Marc

PROVIDER: E-GEOD-35070 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile.

Antunes Ana A Camiade Emilie E Monot Marc M Courtois Emmanuelle E Barbut Frédéric F Sernova Natalia V NV Rodionov Dmitry A DA Martin-Verstraete Isabelle I Dupuy Bruno B

Nucleic acids research 20120918 21

The catabolite control protein CcpA is a pleiotropic regulator that mediates the global transcriptional response to rapidly catabolizable carbohydrates, like glucose in Gram-positive bacteria. By whole transcriptome analyses, we characterized glucose-dependent and CcpA-dependent gene regulation in Clostridium difficile. About 18% of all C. difficile genes are regulated by glucose, for which 50% depend on CcpA for regulation. The CcpA regulon comprises genes involved in sugar uptake, fermentation ...[more]

PMID: 22989714

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Project description:In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine-containing protein, HPr) binds to operator sites called catabolite responsive elements, cre. Depending on the cre box position relative to the promoter, the CcpA/HPr-Ser-P complex can either act as a positive or a negative regulator. The cre boxes are highly degenerate semi-palindromes with a lowly conserved consensus sequence. So far, studies aimed at revealing how CcpA can bind such diverse sites were focused on the analysis of single cre boxes. In this study, a genome-wide analysis of cre sites was performed in order to identify differences in cre sequence and position, which determine their binding affinity. The transcriptomes of B. subtilis cultures with three different CcpA expression levels were compared. The higher the amount of CcpA in the cells, the more operons possessing cre sites were differentially regulated. The cre boxes that mediated regulation at low CcpA levels were designated as strong (high affinity) and those which responded only to high amounts of CcpA, as weak (low affinity). Differences in the sequence and position in relation to the transcription start site between strong and weak cre boxes were revealed. Certain residues at specific positions in the cre box as well as, to a certain extent, a more palindromic nature of cre sequences and the location of cre in close vicinity to the transcription start site contribute to the strength of CcpA-dependent regulation. The main factors contributing to cre regulatory efficiencies, enabling subtle differential control of various subregulons of the CcpA regulon, are identified. Bacillus subtilis strain MP902 [strain MP901 (Ptet-ccpA, KmR) carrying pWH119 (Pxyl-tetR, EmR)] was grown in presence of three different concentrations of Ptet inducer, anhydrotetracycline (ATc), leading to three levels of ccpA expression induction. The control culture was grown in absence of ATc. The total RNA for transcriptome analyses was isolated at OD600 = 0.8 from 16 ml culture. Three independent cultures of each strain (target strains and controls) were used, and cells were sampled for microarray experiment.

Dataset Information

Comparison of the expression profiles of 630E JIR8094 strain and a ccpA mutant after 10h of growth in TY with 0.5% glucose.

Publications

Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile.

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