An epigenetic switch involving overlapping fur and DNA methylation optimizes expression of a type VI secretion gene cluster

• Published in: PLoS genetics 2011-07, Vol.7 (7), p.e1002205
• Main Authors: Brunet, Yannick R, Bernard, Christophe S, Gavioli, Marthe, Lloubès, Roland, Cascales, Eric
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bacterial Secretion Systems - genetics; Bacteriology; Base Sequence; Binding Sites - genetics; Biochemistry, Molecular Biology; Biology; Consensus Sequence - genetics; DNA methylation; DNA Methylation - genetics; DNA replication; DNA Transposable Elements - genetics; Epigenesis, Genetic; Escherichia coli - genetics; Escherichia coli - metabolism; Gene expression; Gene Expression Regulation, Bacterial; Genes, Bacterial; Genetic aspects; Genomics; Gram-negative bacteria; Life Sciences; Methylation; Microbiology; Microbiology and Parasitology; Models, Biological; Molecular Sequence Data; Multigene Family; Mutagenesis, Site-Directed; Physiological aspects; Promoter Regions, Genetic - genetics; Proteins; Repressor Proteins - genetics; Repressor Proteins - metabolism; Sequence Alignment
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1002205

Type VI secretion systems (T6SS) are macromolecular machines of the cell envelope of Gram-negative bacteria responsible for bacterial killing and/or virulence towards different host cells. Here, we characterized the regulatory mechanism underlying expression of the enteroagregative Escherichia coli sci1 T6SS gene cluster. We identified Fur as the main regulator of the sci1 cluster. A detailed analysis of the promoter region showed the presence of three GATC motifs, which are target of the DNA adenine methylase Dam. Using a combination of reporter fusion, gel shift, and in vivo and in vitro Dam methylation assays, we dissected the regulatory role of Fur and Dam-dependent methylation. We showed that the sci1 gene cluster expression is under the control of an epigenetic switch depending on methylation: fur binding prevents methylation of a GATC motif, whereas methylation at this specific site decreases the affinity of Fur for its binding box. A model is proposed in which the sci1 promoter is regulated by iron availability, adenine methylation, and DNA replication.