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E-GEOD-48221 - A small RNA activates CFA synthase by a reprogrammable mechanism of mRNA stabilization

Status
Released on 24 June 2013, last updated on 3 June 2014
Organism
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Samples (8)
Array (1)
Protocols (7)
Description
Small RNAs use a diversity of well-characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq-associated small RNAs has been translational control whereby base-pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation-independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of cfa mRNA (encoding cyclopropane fatty acid synthase) in Salmonella enterica. Target activation is achieved through seed pairing of the pseudoknot-exposed, conserved 5' end of RydC to an upstream region of the cfa mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E-mediated decay in the 5' untranslated region. Intriguingly, this activation mechanism is fully generic in that it can be reprogrammed to other seed pairing small RNAs, suggesting this mechanism may be utilised in the design of RNA-controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability. To determine the targets of the small regulatory RNA RydC in S. Typhimurium, we looked at the effect of a short pulse of RydC over-expression on the Salmonella transcriptome. To achieve over-expression, the rydC 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 (also induced by L-arabinose). 2 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674–1688.
Experiment type
transcription profiling by array 
Contacts
Kai Papenfort <geo@ncbi.nlm.nih.gov>, Agnes Fekete, Jörg Vogel, Kathrin S Fröhlich
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-48221.idf.txt
Sample and data relationshipE-GEOD-48221.sdrf.txt
Raw data (1)E-GEOD-48221.raw.1.zip
Processed data (1)E-GEOD-48221.processed.1.zip
Array designA-GEOD-11416.adf.txt
Links