The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E.
Numerous small non-coding RNAs (sRNAs) in bacteria modulate rates of translation initiation and degradation of target mRNAs, which they recognize through base-pairing facilitated by the RNA chaperone Hfq. Recent evidence indicates that the ternary complex of Hfq, sRNA and mRNA guides endoribonuclease RNase E to initiate turnover of both the RNAs. We show that a sRNA not only guides RNase E to a defined site in a target RNA, but also allosterically activates the enzyme by presenting a monophosphate group at the 5'-end of the cognate-pairing "seed." Moreover, in the absence of the target the 5'-monophosphate makes the sRNA seed region vulnerable to an attack by RNase E against which Hfq confers no protection. These results suggest that the chemical signature and pairing status of the sRNA seed region may help to both 'proofread' recognition and activate mRNA cleavage, as part of a dynamic process involving cooperation of RNA, Hfq and RNase E.
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England, UK.
Katarzyna J
KJ
Bandyra
Nelly
N
Said
Verena
V
Pfeiffer
Maria W
MW
Górna
Jörg
J
Vogel
Ben F
BF
Luisi
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D004722:Endoribonucleases / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism; D018272:Porins / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D012475:Salmonella / Q000235:genetics / Q000378:metabolism
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; C470933:OmpD protein, Salmonella typhimurium; D018272:Porins; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D004722:Endoribonucleases; C022537:ribonuclease E