A conserved small RNA promotes silencing of the outer membrane protein YbfM

Abstract

SummaryIn the past few years an increasing number of small non-coding RNAs (sRNAs) in enterobacteria have been found to negatively regulate the expression of outer membrane proteins (OMPs) at the posttranscriptional level. These RNAs act under various growth and stress conditions, suggesting that one important physiological role of regulatory RNA molecules in Gram-negative bacteria is to modulate the cell surface and/or to prevent accumulation of OMPs in the envelope. Here, we extend the OMP-sRNA network by showing that the expression of the OMP YbfM is silenced by a conserved sRNA, designated MicM (also known as RybC/SroB). The regulation is strictly dependent on the RNA chaperone Hfq, and mutational analysis indicates that MicM sequesters the ribosome binding site of ybfM mRNA by an antisense mechanism. Furthermore, we provide evidence that Hfq strongly enhances the on-rate of duplex formation between MicM and its target RNA in vitro, supporting the idea that a major cellular role of the RNA chaperone is to act as a catalyst in RNA-RNA duplex formation.

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

“…All of the major porins and several outer membrane proteins (OMPs) are targets for regulation by one or more sRNAs. The genes encoding these sRNAs are generally regulated at the transcriptional level, and expressed under specific conditions (Mizuno et al 1984;Chen et al 2004;Douchin et al 2006;Figueroa-Bossi et al 2006;Papenfort et al 2006;Bossi and Figueroa-Bossi 2007; Thompson et al 2007; Udekwu and Wagner 2007;Rasmussen et al 2009). …”

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

“…However, this does not seem to be the case for ChiX. The ChiX RNA is quite abundant under a variety of growth conditions, and no evidence of a regulated promoter has been found (Vogel et al 2003;Mandin and Gottesman 2009;Rasmussen et al 2009). If expressed from an inducible promoter, its half-life in wild-type cells is long (27 min) ).…”

“…FigueroaBossi et al (2009) then proceeded to search for other mutations that could similarly induce the fusion, which is Lac À (tightly repressed) in an hfq + host, by selecting or screening for Lac + colonies. 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).…”

“…Earlier this year, it made its next appearances in studies defining its ability to regulate two different specific targets. In one study, it was found to regulate ybfM, encoding a predicted outer membrane protein (OMP) of unknown function (Rasmussen et al 2009). Because the sRNAs regulating other OMP genes are named mic (mRNA-interfering complementary RNA) followed by the last letter of the OMP gene they regulate, the ybfM-regulating sRNA was renamed MicM (Rasmussen et al 2009).…”

“…In one study, it was found to regulate ybfM, encoding a predicted outer membrane protein (OMP) of unknown function (Rasmussen et al 2009). Because the sRNAs regulating other OMP genes are named mic (mRNA-interfering complementary RNA) followed by the last letter of the OMP gene they regulate, the ybfM-regulating sRNA was renamed MicM (Rasmussen et al 2009). In a second study, the same sRNA was identified in a screen of an overexpression library for down-regulation of the dpiBA operon, which encodes a two-component regulatory system involved in SOS induction in response to sublethal concentration of antibiotics (Mandin and Gottesman 2009).…”