PMID:23305111

Citation	Yakhnin, AV, Baker, CS, Vakulskas, CA, Yakhnin, H, Berezin, I, Romeo, T and Babitzke, P (2013) CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage. Mol. Microbiol. 87:851-66
Abstract	Csr is a conserved global regulatory system that controls expression of several hundred Escherichia coli genes. CsrA protein represses translation of numerous genes by binding to mRNA and inhibiting ribosome access. CsrA also activates gene expression, although an activation mechanism has not been reported. CsrA activates flhDC expression, encoding the master regulator of flagellum biosynthesis and chemotaxis, by stabilizing the mRNA. Computer modelling, gel mobility shift and footprint analyses identified two CsrA binding sites extending from positions 1-12 (BS1) and 44-55 (BS2) of the 198 nt flhDC leader transcript. flhD'-'lacZ expression was reduced by mutations in csrA and/or the CsrA binding sites. The position of BS1 suggested that bound CsrA might inhibit 5' end-dependent RNase E cleavage of flhDC mRNA. Consistent with this hypothesis, CsrA protected flhDC leader RNA from RNase E cleavage in vitro and protection depended on BS1 and BS2. Primer extension studies identified flhDC decay intermediates in vivo that correspond to in vitro RNase E cleavage sites. Deletion of these RNase E cleavage sites resulted in increased flhD'-'lacZ expression. Data from mRNA decay studies and quantitative primer extension assays support a model in which bound CsrA activates flhDC expression by inhibiting the 5' end-dependent RNase E cleavage pathway.
Links	PubMed PMC3567230 Online version:10.1111/mmi.12136
Keywords	5' Untranslated Regions; Base Sequence; Binding Sites; Endoribonucleases/genetics; Endoribonucleases/metabolism; Escherichia coli/enzymology; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Gene Expression Regulation, Bacterial; Molecular Sequence Data; Operon; Protein Binding; RNA Processing, Post-Transcriptional; RNA, Bacterial/genetics; RNA, Bacterial/metabolism; RNA, Messenger/genetics; RNA, Messenger/metabolism; RNA-Binding Proteins/chemistry; RNA-Binding Proteins/genetics; RNA-Binding Proteins/metabolism; Repressor Proteins/chemistry; Repressor Proteins/genetics; Repressor Proteins/metabolism; Trans-Activators/chemistry; Trans-Activators/genetics; Trans-Activators/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
ECOLI:CSRA		GO:0048255: mRNA stabilization	ECO:0000315:		P		Figure 6, mRNA half-life reduced in csrA mutant compared to WT	complete CACAO 10962
ECOLI:CSRA		GO:0031438: negative regulation of mRNA cleavage	ECO:0000314:		P		Figure 5A, in vitro experiment using purified RNase E. In the presence of CsrA, the RNA was protected from RNase E cleavage.	complete CACAO 11014

References

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