Distribution of prophage-encoded Pas sRNAs across pathogenic Escherichia coli

Abstract

Numerous base pairing small RNAs (sRNAs), which are an integral part of regulatory networks in bacteria, are encoded on mobile genetic elements (MGEs) in pathogenic strains of Escherichia coli. These sRNAs help coordinate the expression of MGE-encoded virulence factors with core genome-encoded cellular pathways. To investigate the evolution of MGE-encoded sRNAs, we queried public databases to characterize the distribution of PasA, PasB, PasC, PasD1, and PasD2, five prophage-encoded sRNAs discovered in enteropathogenic E. coli. We find that while the Pas sRNAs are largely restricted to pathogenic lineages of Escherichia and Shigella, they exhibit diversity in sequence, genomic presence, and copy number across strains. Based on phylogenetic analysis, the Pas sRNAs originate from multiple ancestral lineages and associate with specific E. coli pathovars, consistent with horizontal acquisition followed by retention. Syntenic analysis suggests a phage origin for the Pas sRNAs, likely from Shiga-toxin encoding phages, but the sRNAs appear to have diverged substantially following their integration into bacterial chromosomes. Comparative and structural analyses further suggest that the PasA and PasC sRNAs share a common ancestor as is the case for PasD and STnc100, another prophage-encoded sRNA. These findings add to our understanding of how accessory genome-encoded sRNAs emerge and evolve.