Transcriptomics

Dataset Information

26

Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation


ABSTRACT: It is well established that small noncoding RNAs (sRNAs) of bacteria recognize the 5’ regions of target mRNAs, generally at the ribosome binding site. Until now, the translated coding sequence (CDS) of mRNA appeared to be refractory to sRNA interactions. We have discovered that Salmonella MicC RNA silences ompD mRNA by targeting the CDS, at codons 23-26. Analyses of MicC-ompD RNA complexes in vitro, and of chimeric sRNAs and ompD reporter fusions in vivo, show that interactions are confined to the CDS, and that a ≤12 bp RNA duplex involving the conserved 5’ end of MicC is essential and sufficient for target repression. MicC cannot act as a translational repressor at this downstream position being unable to inhibit 30S or 70S ribosome activity on the ompD mRNA. Instead, MicC accelerates RNase E-dependent ompD mRNA decay. The degradosome contributes to target destabilization, and facilitates the efficient degradation of processed ompD mRNA. Our data show that bacterial gene silencing by sRNAs can take place downstream of the translational initiation site by triggering irreversible mRNA decay. This ability of sRNAs allows targets in the CDS to be silenced without interference from the strong RNA helicase activity of elongating ribosomes. Overall design: To determine the targets of the small regulatory RNA MicC in S. Typhimurium, we looked at the effect of a short pulse of MicC over-expression on the Salmonella transcriptome. To achieve over-expression, the micC gene was cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control. 3 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674–1688.

INSTRUMENT(S): IFR_Salmonella_7.3k_v1.0

ORGANISM(S): Salmonella enterica  

SUBMITTER: Sacha Lucchini  

PROVIDER: GSE16540 | GEO |

SECONDARY ACCESSION(S): PRJNA116059

REPOSITORIES: GEO

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