A Salmonella-encoded microRNA-like RNA facilitates bacterial invasion and intracellular replication via suppressing host cell inducible nitric oxide synthase (MPF3P.809)

Salmonella has developed a sophisticated machinery to promote virulence and survival. Here we show that Salmonella can hijack mammalian cell non-classical miRNA processing machinery to further process their non-coding RNAs into miRNA-like RNAs that modulate host cell function. Using Solexa deep sequencing, we detected a panel of 19-24nt Salmonella-derived ncRNA fragments in human colonic epithelial HT-29 cells following Salmonella infection. The fragment with the highest copy number, Sal-1, was validated by qRT-PCR and northern blot analysis. With seven copies in the S. enteritidis genome, Sal-1 has a stem structure-containing precursor with a free energy of ΔG= -26.1 kcal/mol. The processing of the Sal-1 “primary” /“precursor” to the mature Sal-1 in Salmonella-infected cells is Dicer-independent but Argonaute 2-dependent. Functionally, Sal-1 targets the expression of epithelial cell inducible nitric oxide synthase (iNOS) and thus reduces the NO production and bacterial resistance of host cells. Expression or depletion of Sal-1 in mouse colonic epithelium significantly enhanced or reduced Salmonella infection in mice, respectively. Finally, the enhancement of Salmonella infection in mice by Sal-1 was completely abolished by expressing a mutant iNOS isoform that had normal NO generation but could not be targeted by Sal-1. Our results show for the first time that Salmonella can produce functional miRNA-like RNAs, which may represent a novel class of virulence factors.