Uropathogenic Escherichia coli (UPEC) is known to display bimodal virulence strategies during bladder infection. In the course of acute cystitis, UPEC is known to invade the superficial bladder epithelia and replicate within the host cell cytoplasm to form intracellular bacterial communities (IBCs) and subsequently flux out of the bladder facet cells as filaments. Progression to chronic urinary tract infection, however, involves invasion of the deeper cell layers of the urothelium and formation of quiescent intracellular reservoirs (QIRs).
Recent years have seen considerable efforts dedicated to understanding the strategies that intracellular pathogens adopt, and the extent to which small RNAs (sRNAs) are involved. sRNAs, with their short half-life, provide a means of rapidly adjusting gene expression to meet the environmental changes associated with host invasion. A vast majority of sRNAs discovered so far, are trans-acting and exert their function via interaction with Hfq- a homohexameric RNA chaperone. Discovery of novel sRNAs that have a role to play in the complex scheme of infection and intracellular survival constitutes the premise of our study and involves an exploratory technique within an intracellular niche that is presently underrepresented in the literature.
In order to study the repository of sRNAs expressed by intracellular UPEC infecting human bladder epithelial cells in culture, we adopted an Hfq co-immunoprecipitation and a next-generation RNA sequencing approach. Our sequence data revealed a snapshot view of previously reported Hfq binding sRNAs and mRNAs differentially expressed during intracellular survival, but more importantly, unveiled three novel sRNAs that are conserved among ExPEC strains and play an important role in infection – RipA, RipB and RipC. We found RipA and RipB to be involved in regulation of P fimbrial phase variation and bacterial flagellation respectively. The presence of these novel sRNAs adds new dimension to already complex regulatory systems of the flagellar cascade and P fimbria; and possibly helps the intracellular pathogens to successfully adapt to their niche.