RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.

Abstract We have used a hidden Markov model (HMM) to identify the consensus sequence of the Rpo D promoters in the genome of Campylobacter jejuni . The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved −35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with a period of 10–11 nucleotides. The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended −10 promoter. We predicted a total of 764 presumed Rpo D promoters in the C. jejuni genome, of which 654 were located upstream of annotated genes. A similar promoter was identified in Helicobacter pylori , a close phylogenetic relative of Campylobacter , but not in Escherichia coli , Vibrio cholerae , or six other Proteobacterial genomes, or in Staphylococcus aureus . We used upstream regions of high confidence genes as training data ( n =529, for the C. jejuni genome). We found it necessary to limit the training set to genes that are preceded by an intergenic region of >100 bp or by a gene oriented in the opposite direction to be able to identify a conserved sequence motif, and ended up with a training set of 175 genes. This leads to the conclusion that the remaining genes (354) are more rarely preceded by a ( Rpo D) promoter, and consequently that operon structure may be more widespread in C. jejuni than has been assumed by others. Structural predictions of the regions upstream of the TATA-box indicates a region of highly curved DNA, and we assume that this facilitates the wrapping of the DNA around the RNA polymerase holoenzyme, and offsets the absence of a conserved −35 binding motif.