Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

Abstract

A relevant, yet little recognized feature of antisense regulation is the possibility of switching roles between regulatory and regulated RNAs. Here we show that induction of a Salmonella gene relies on the conversion of a small RNA from effector to regulatory target. The chiP gene (formerly ybfM), identified and characterized in the present study, encodes a conserved enterobacterial chitoporin required for uptake of chitin-derived oligosaccharides. In the absence of inducer, chiP is kept silent by the action of a constitutively made small RNA, ChiX (formerly SroB, RybC), which pairs with a sequence at the 59 end of chiP mRNA. Silencing is relieved in the presence of chitooligosaccharides due to the accumulation of an RNA that pairs with ChiX and promotes its degradation. Anti-ChiX RNA originates from an intercistronic region of the chb operon, which comprises genes for chitooligosaccharide metabolism and whose transcription is activated in the presence of these sugars. We present evidence suggesting that the chb RNA destabilizes ChiX sRNA by invading the stem of its transcription terminator hairpin. Overall, our findings blur the distinction between effector and target in sRNA regulation, raising the possibility that some of the currently defined targets could actually be inhibitors of sRNA function.[Keywords: Antisense regulation; chitoporin; chitobiose; Hfq; small RNA] Supplemental material is available at http://www.genesdev.org.

Regulating the regulator: an RNA decoy acts as an OFF switch for the regulation of an sRNA: Figure 1.

“…Figueroa-Bossi et al (2009) isolated mutations inactivating hfq, mutations inactivating the sRNA, and mutations in the fusion, within the pairing region with the sRNA, that all relieved ybfM repression, as expected. In the overproduction screen, genes for the 59 pyrophosphohydrolase rppH and the polyA polymerase pcnB were identified; these should lead to increased sRNA degradation ).…”

“…This stoichiometric destruction of an sRNA by pairing with a target raises the intriguing possibility that one target, made in high amounts, might titrate away an sRNA from other targets by causing degradation. The work by Figueroa-Bossi et al (2009) and Overgaard et al (2009) demonstrates a number of new twists on this idea.…”

“…Initially, ChiX, the Salmonella sRNA under study by Figueroa-Bossi et al (2009) fulfilled most of the expectations for a classical trans-encoded sRNA. It was discovered in E. coli in two different global searches for sRNAs-first as an sRNA binding to Hfq in an immunoprecipitation experiment and named RybC (Zhang et al 2003), and as part of a cloning-based sRNA identification project and named SroB (Vogel et al 2003).…”

“…This powerful selection uncovered the same sRNA regulator found by Rasmussen et al (2009), as well as the network that provides both the biological rationale for the regulation of ybfM and the novel mechanism for regulation of this sRNA. Figueroa-Bossi et al (2009) renamed the sRNA ChiX based on their findings (see below). In a related but complementary approach, Valentin-Hansen and colleagues ) carried out a genetic screen in E. coli for genes that, in multicopy, relieved the very tight regulation of a ybfM translational fusion by the sRNA (called by them MicM); their results uncovered the same unique regulatory network.…”

“…All of this makes regulatory sense if the YbfM porin protein is part of the chitobiose utilization pathway. In fact, YbfM is necessary for growth on some chitin breakdown products, and thus was renamed ChiP (chitoporin) (Figueroa-Bossi et al 2009). In the absence of the ChiX (MicM) sRNA, the basal level of chiP (ybfM) expression is high, but induction by chitobiose increases expression an additional fourfold, consistent with direct action by ChbR on chiP transcription initiation.…”