By binding to the 5′ untranslated region (UTR) of an mRNA, bacterial small non-coding RNAs (sRNAs) can inhibit ribosome loading onto the transcript and thereby repress its translation. The mRNA is then targeted for degradation by endonucleases such as RNaseE, although the inhibition of translation is thought to be the crucial step in this process. Now Pfeiffer et al. show that in Salmonella enterica subsp. enterica serovar Typhimurium the sRNA MicC binds in the coding sequence rather than in the 5′ UTR of outer membrane protein D (ompD) mRNA. In doing so, MicC regulates OmpD expression not by inhibiting translation but instead by mediating endonucleolytic degradation of its transcript.
In
Escherichia coli
, MicC regulates the expression of OmpC by binding to a 17 bp region near the start codon in the ompC mRNA 5′ UTR. To identify MicC targets in S. Typhimurium, Pfeiffer and colleagues examined the changes in the global mRNA profile following the induction of exogenous MicC expression. Only two transcripts showed a decrease in their steady state levels following MicC induction, those of ompC and ompD. To identify the binding site for MicC in the ompD transcript, the authors fused the ompD 5′ UTR to a GFP reporter. Intriguingly, they found that MicC failed to downregulate the reporter. However, when the fusion was extended to include the first 33 codons of the ompD open reading frame, MicC was able to downregulate expression of the reporter fusion, suggesting that the binding site for MicC was not in the 5′ UTR but in the coding sequence instead. Structural analyses confirmed that MicC formed a 12 bp RNA duplex with ompD codons 23–26.
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