Functional characterization of the antagonistic flagellar late regulators FliA and FlgM of Helicobacter pylori and their effects on the H-pylori transcriptome

Helicobacter pylori is thought to regulate gene expression with a very small set of regulatory genes. We identified a previously unannotated open reading frame (ORF) in the H. pylori 26695 genome (HP1122) as a putative H. pylori fIgM gene (sigma(28) factor antagonist) by a motif-based bioinformatic approach. Deletion of HP1122 resulted in a fourfold increase in transcription of the sigma(28)-dependent major flagellin gene flaA, supporting the function of HP1122 as H. pylori FIgM. Helicobacter pylori FIgM lacks a conserved 20-amino-acid N-terminal domain of enterobacterial FIgM proteins, but was able to interact with the Salmonella typhimurium sigma(28) (FliA) and inhibit the expression of FliA-dependent genes in Salmonella. Helicobacter pylori FIgM inhibited FliA to the same extent in a Salmonella strain with an intact flagellar export system and in an export-deficient strain. Helicobacter pylori FliA was able to drive transcription of FliA-dependent genes in Salmonella. The effects of mutations in the H. pylori fIgM and fliA genes on the H. pylori transcriptome were analysed using whole genome DNA microarrays. The antagonistic roles of FIgM and FliA in controlling the transcription of the major flagellin gene fIaA were confirmed, and two additional FliA/FIgM dependent operons (HP472 and HP1051/HP1052) were identified. None of the three genes contained in these operons has a known function in flagellar biogenesis in other bacteria. Like other motile bacteria, H. pylori has a FliA/FIgM pair of sigma and anti-sigma factors, but the genes controlled by these differ markedly from the Salmonella/Escherichia coli paradigm.