Impact of overexpressing IS200 transposase mRNA on Salmonella Typhimurium gene expression. Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Bacterial sRNAs play an important role in regulating many cellular processes including metabolism, outer membrane homeostasis, and virulence. Although sRNAs were initially found in intergenic regions, there is emerging evidence that protein coding regions of the genome are a rich reservoir of sRNAs. Here we report that the 5’UTR of IS200 transposase mRNA (tnpA) is processed to produce a regulatory RNA that affects expression of over 70 genes in Salmonella Typhimurium. We provide evidence that the tnpA derived sRNA base-pairs with invF mRNA to repress expression. As InvF is a transcriptional activator of SPI-1 encoded effector proteins, tnpA indirectly represses these genes. Our work indicates that tnpA acts as an sRNA ‘sponge’ that sets a threshold for activation of SPI-1 effector proteins. Our work identifies a new class of ‘passenger gene’ for bacterial transposons and provides the first example of a bacterial transposon producing a regulatory RNA that controls host gene expression.