Functional analysis of the Helicobacter pylori principal sigma subunit of RNA polymerase reveals that the spacer region is important for efficient transcription

We have cloned the rpoD gene encoding the principal sigma (sigma) factor of Helicobacter pylori. The deduced amino acid sequence reveals a predicted polypeptide of 676 residues that has amino acid homology with the principal a factors of a number of divergent prokaryotes. We have designated this factor sigma(80). Amino acid sequence analysis suggests that region 1.1 is missing in sigma(80) and that a region with homology to a regulatory protein from Bacillus subtilis phage SPO1 is present. Genetic studies have indicated that sigma(80) is not compatible with the transcriptional machinery of Escherichia coli. However, in vitro sigma(80) could be assembled into the E. coli RNA polymerase and could bind to E. coli and H. pylori promoters, suggesting that the sigma(80)-containing RNA polymerase has the same stoichiometry as the native complex. By exchanging protein domains between E. coli and H. pylori a factors, we demonstrate that the sigma(80) domain inhibiting transcription from E. coli promoters is confined within the non-conserved spacer region, implying that the spacer region of prokaryotic primary a factors plays an important role in the process of transcription. Consistent with its restricted niche and with the availability of a very restricted number of transcriptional regulators, H. pylori may have evolved a spacer region of the a factor to modulate total transcription and to quickly respond to microenvironmental changes.