Article

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

Laboratoire Pathogenèse des Bactéries Anaérobies, Département de Microbiologie Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, 25 rue du Docteur Roux, Paris 75015, France, Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia and Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.
Nucleic Acids Research (Impact Factor: 9.11). 09/2012; 40(21). DOI: 10.1093/nar/gks864
Source: PubMed

ABSTRACT 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 and amino acids metabolism, confirming the role of CcpA as a link between carbon and nitrogen pathways. Using combination of chromatin immunoprecipitation and genome sequence analysis, we detected 55 CcpA binding sites corresponding to ∼140 genes directly controlled by CcpA. We defined the C. difficile CcpA consensus binding site (cre(CD) motif), that is, 'RRGAAAANGTTTTCWW'. Binding of purified CcpA protein to 19 target cre(CD) sites was demonstrated by electrophoretic mobility shift assay. CcpA also directly represses key factors in early steps of sporulation (Spo0A and SigF). Furthermore, the C. difficile toxin genes (tcdA and tcdB) and their regulators (tcdR and tcdC) are direct CcpA targets. Finally, CcpA controls a complex and extended regulatory network through the modulation of a large set of regulators.

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