Characterization of the negative elements involved in silencing the bgl operon of Escherichia coli: possible roles for DNA gyrase, H-NS, and CRP-cAMP in regulation

Abstract

The bgl operon of Escherichia coli is rendered cryptic and uninducible in wild-type cells by the presence of DNA structural elements that negatively regulate transcription. We have carried out a detailed analysis of the sequences implicated in negative regulation. Fine-structure deletion analysis of the upstream sequences showed the presence of at least two elements involved in silencing the promoter. Chemical probing of genomic DNA in vivo showed that a region of dyad symmetry, present upstream of the promoter, is hypersensitive to KMnO₄. The hypersensitive region detected corresponds to the potential cruciform structure implicated earlier in negative regulation. Enhancement of transcription from the wild-type promoter, observed in the presence of the gyrase inhibitor novobiocin, was absent in a mutant that carried point mutations in the inverted repeat. This observation suggests that the activation seen in a gyrase mutant is mediated by destabilization of the cruciform because of reduced supercoiling. Deletion of sequences downstream of the potential cruciform also resulted in an increase in transcription, indicating the presence of a second regulatory element. Measurement of transcription from the bgl promoter carrying the deletion, in a strain that has a mutation in the hns gene, indicated that this region is likely to be involved in binding to H-NS or a protein regulated by H-NS, which acts as a non-specific repressor. We also provide evidence which suggests that transcriptional activation by mutations at the cAMP receptor protein (CRP)-binding site is mediated partly by antagonization of the negative effect of H-NS by CRP-cAMP as a result of its increased affinity for the mutant site.