Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella

Escherichia coli and Salmonella can use chitin-derived oligosaccharides as carbon and nitrogen sources. Chitosugars traverse the outer membrane through a dedicated chitoporin, ChiP, and are transported across the cytoplasmic membrane by the chitobiose transporter (ChbBCA). Previous work revealed that synthesis of the chitoporin, ChiP, requires transcription of the chbBCARFG operon. A sequence from the chbBC portion of the transcript was shown to act as a decoy target for a regulatory small RNA, ChiX, that normally blocks chiP expression. ChiX is destabilized and degraded upon pairing with chbBC RNA. Here, we show that the chiP gene, like the chbBCARFG operon, is also downregulated at the transcriptional level by the NagC repressor. NagC repression is critical in maintaining chiP mRNA levels low enough, relative to ChiX, to allow full silencing by this sRNA. We also show that pairing of ChiX to chbBC RNA downregulates chbC under uninduced conditions, that is, when ChiX is in excess to the decoy sequence. Hence, under these conditions, chbBC RNA is not just a decoy, but a true target of ChiX regulation. Altogether these findings underscore the importance of stoichiometry in dictating the strength of the sRNA response and in differentiating the regulator from the regulatory target.