Species wide analysis of Escherichia coli identifies a negative regulatory input that controls flhDC transcription

Abstract

Escherichia coli is a species of bacteria that can be found almost everywhere. It belongs to the family Enterobacteriaceae which, in turn, belongs to gamma subdivision of the phylum Proteobacteria. Genomic plasticity and the ability of genes to transfer across different strains contributed to the division of E. coli into six major phylogenetic lineages: A, B1, B2, D, E and F. The motility organelle of bacteria is the flagellum which consists of: basal body, hook and filament. The flagellar system of E. coli organised into a transcriptional hierarchy strictly dependent on the expression of the flagellar master regulator, FlhD4C2. Bioinformatic analysis of the yecG-flhDC intergenic region showed that the DNA sequence of this region could be grouped into a phylogeny that reflects the phylogenetic clades of E. coli. However, three dominant sequence types of the yecG-flhDC intergenic region mapped to clades: A/B1, B2 and D/E/F. We illustrated the impact of replacing the yecG-flhDC intergenic region of the weakly motile strain MG1655 with the same region of model strains on motility. Our data revealed dramatic increase in motility in the newly created strains. We also dissected the yecG-flhDC intergenic region to investigate the effect of each part on motility. Our analysis revealed that the yecG is a negative regulator of flhDC expression. We tested the impact of host niche environments on the motility phenotype of E. coli. For this reason, we sequenced a collection of bovine strains and aligned them to their phylogenetic groups and compared them to another collection isolated from UTIs. The data showed that the bovine isolates lie mostly in clades B1 and A, whereas UTI isolates mostly occupy clades B2 and D/F. The bovine strains exhibited robust motility compared to the UTI strains. We screened the yecG-flhDC intergenic region for IS elements, and found no isolate has the IS element.