Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli.
RyhB is a small antisense regulatory RNA that is repressed by the Fur repressor and negatively regulates at least six mRNAs encoding Fe-binding or Fe-storage proteins in Escherichia coli. When Fe is limiting, RyhB levels rise, and target mRNAs are rapidly degraded. RyhB is very stable when measured after treatment of cells with the transcription inhibitor rifampicin, but is unstable when overall mRNA transcription continues. We propose that RyhB turnover is coupled to and dependent on pairing with the target mRNAs. Degradation of both mRNA targets and RyhB is dependent on RNase E and is slowed in degradosome mutants. RyhB requires the RNA chaperone Hfq. In the absence of Hfq, RyhB is unstable, even when general transcription is inhibited; degradation is dependent upon RNase E. Hfq and RNase E bind similar sites on the RNA; pairing may allow loss of Hfq and access by RNase E. Two other Hfq-dependent small RNAs, DsrA and OxyS, are also stable when overall transcription is off, and unstable when it is not, suggesting that they, too, are degraded when their target mRNAs are available for pairing. Thus, this large class of regulatory RNAs share an unexpected intrinsic mechanism for shutting off their action.
Massé
Eric
E
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Escorcia
Freddy E
FE
Gottesman
Susan
S
D001089:Arabinose / Q000235:genetics / Q000378:metabolism; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004251:DNA Transposable Elements; D004722:Endoribonucleases / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism; D007501:Iron / Q000378:metabolism; D009154:Mutation; D011401:Promoter Regions, Genetic; D020871:RNA Stability; D016372:RNA, Antisense / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D038621:Regulatory Sequences, Ribonucleic Acid; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D013482:Superoxide Dismutase / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D058727:RNA, Small Untranslated
D001089:Arabinose; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D004722:Endoribonucleases; D029968:Escherichia coli Proteins; D035001:Host Factor 1 Protein; D007501:Iron; D016372:RNA, Antisense; D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid; D012097:Repressor Proteins; D013482:Superoxide Dismutase; D014157:Transcription Factors; C499660:DrsA protein, E coli; C087373:Hfq protein, E coli; C499686:oxyS small RNA, E coli; D058727:RNA, Small Untranslated; C087504:SodB protein, Bacteria; C022537:ribonuclease E