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) fact or of Helicobacter pylori. The deduced amino acid sequence reveals a p redicted 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 sugges ts that region 1.1 is missing in sigma(80) and that a region with homo logy to a regulatory protein from Bacillus subtilis phage SPO1 is pres ent. Genetic studies have indicated that sigma(80) is not compatible w ith the transcriptional machinery of Escherichia coli. However, in vit ro sigma(80) could be assembled into the E. coil RNA polymerase and co uld bind to E. coil and H. pylori promoters, suggesting that the sigma (80)-containing RNA polymerase has the same stoichiometry as the nativ e complex. By exchanging protein domains between E. coil and H. pylori a factors, we demonstrate that the sigma(80) domain inhibiting transc ription from E. coli promoters is confined within the non-conserved sp acer region, implying that the spacer region of prokaryotic primary a factors plays an important role in the process of transcription. Consi stent with its restricted niche and with the availability of a very re stricted number of transcriptional regulators, H. pylori may have evol ved a spacer region of the a factor to modulate total transcription an d to quickly respond to microenvironmental changes.