Evolutionary conservation and lineage-specific virulence repurposing of the core housekeeping gene ushA in...

This study aimed to characterize the genome-wide distribution, evolutionary trajectory, functional conservation of ushA across the Enterobacteriaceae family, and its phylogenomic association with the type III secretion system (T3SS), to clarify its role in bacterial pathogenicity.

We analyzed 12,629 complete Enterobacteriaceae genomes to identify ushA via a dual-validation strategy combining hidden Markov model and Diamond alignment, followed by phylogenetic reconstruction, selection pressure analysis, T3SS co-occurrence testing, and multi-copy strains dissection.

ushA is near-ubiquitous across Enterobacteriaceae (96.38% overall prevalence), with 95.65% of all strains harboring a single copy, showing extreme copy number stability. The gene is under strong genome-wide purifying selection (global ω = 0.045 under the M0 model), with no statistically significant positively selected sites. We identified 92 strains with ushA copy duplications, 94.57% of which were significantly enriched in the genus Shigella (P < 2.2 × 10^-16), with duplicated copies remaining under sustained purifying selection. No universal ushA-T3SS co-evolution was detected, with lineage-specific co-occurrence restricted exclusively to attaching and effacing (A/E) pathogens.

The core housekeeping gene ushA in Enterobacteriaceae is highly conserved under purifying selection. The T3SS-dependent host genotoxic effect of UshA, which has been experimentally validated exclusively in A/E pathogens, likely constitutes a lineage-specific functional co-option rather than a function tied to the gene's conserved core metabolic role.