Role of the alternative sigma factor σ(s) in expression of the alkS regulator of the Pseudomonas oleovorans alkane degradation pathway

Abstract

The AlkS protein activates transcription from the PalkB promoter, allowing the expression of a number of genes required for the assimilation of alkanes in Pseudomonas oleovorans. We have identified the promoter from which the alkS gene is transcribed, PalkS, and analyzed its expression under different conditions and genetic backgrounds. Transcription from PalkS was very low during the exponential phase of growth and increased considerably when cells reached the stationary phase. The PalkS -10 region was similar to the consensus described for promoters recognized by Escherichia coli RNA polymerase bound to the alternative sigma factor σ(s), which directs the expression of many stationary-phase genes. Reporter strains containing PalkS- lacZ transcriptional fusions showed that PalkS promoter is very weakly expressed in a Pseudomonas putida strain bearing an inactivated allele of the gene coding for σ(s), rpoS. When PalkS was transferred to E. coli, transcription started at the same site and expression was higher in stationary phase only if σ(s)-RNA polymerase was present. The low levels of AlkS protein generated in the absence of σ(s) were enough to support a partial induction of the PalkB promoter. The -10 and -35 regions of PalkS promoter also show some similarity to the consensus recognized by σ(D)-RNA polymerase, the primary form of RNA polymerase. We propose that in exponential phase PalkS is probably recognized both by σ(D)-RNA polymerase (inefficiently) and by σ(s)-RNA polymerase (present at low levels), leading to low-level expression of the alkS gene. σ(s)-RNA polymerase would be responsible for the high level of activity of PalkS observed in stationary phase.