Enhancer-dependent transcription in Salmonella enterica Typhimurium: new members of the sigmaN regulon inferred from protein sequence homology and predicted promoter sites.

DNA-looping mediated by regulatory proteins is a ubiquitous mode of transcriptional control that allows interactions between genetic elements separated over long distances in DNA. In prokaryotes, one of the best-studied examples of regulatory proteins that use DNA-looping is the NtrC family of enhancer-binding proteins (EBPs), which activate transcription from sigmaN (sigma-N, sigma-54) dependent promoters. The completely sequenced genome of food-borne pathogen Salmonella enterica serovar Typhimurium LT2 contains seven novel EBPs of unknown function. Four of these EBPs have a similar domain organisation to NtrC whilst surprisingly the remaining three resemble LevR in Bacillus subtilis. Probable transcriptional targets are identified for each of the EBPs, including novel homologues of phosphotransferase system Enzyme II (EII) and several virulence-associated functions. Comparisons are made with the related enteric bacteria Salmonella Typhi, Escherichia coli and Yersinia pestis.