Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli.
The Escherichia coli Sm-like host factor I (Hfq) is thought to play direct and indirect roles in post-transcriptional regulation by targeting small regulatory RNAs and mRNAs. In this study, we have used proteomics to identify new mRNA targets of Hfq. We have identified 11 candidate proteins, synthesis of which was differentially affected in a hfq- background. The effect of Hfq on some of the corresponding mRNAs including fur, gapA, metF, ppiB and sodB mRNA was assessed, using different in vitro and in vivo methods. This allowed us to distinguish between direct and indirect effects of Hfq in modulating the translational activities of these mRNAs. From the collection of mRNAs tested, only fur and sodB mRNA, encoding the master regulator of iron metabolism and the iron superoxide dismutase, respectively, were found to be regulated by Hfq. Fur is known to be a negative regulator of transcription of the small RNA RyhB. Mutations in the sodB leader and compensating mutations in RyhB revealed that RyhB in turn represses translation of sodB mRNA, explaining the previously reported positive control of sodB by Fur. These data assign a role to Hfq in regulation of iron uptake and in switching off of iron scavenger genes.
Vecerek
Branislav
B
Max F. Perutz Laboratories, Department of Microbiology and Genetics, University Department at the Vienna Biocenter, Dr Bohrgasse 9, 1030 Vienna, Austria.
Moll
Isabella
I
Afonyushkin
Taras
T
Kaberdin
Vladimir
V
Bläsi
Udo
U
D045103:5,10-Methylenetetrahydrofolate Reductase (FADH2) / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D002352:Carrier Proteins / Q000235:genetics; D021983:Cyclophilins / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism*; D007501:Iron / Q000378:metabolism*; D018832:Molecular Chaperones / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D019696:Peptidylprolyl Isomerase; D014176:Protein Biosynthesis; D040901:Proteomics / Q000379:methods; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism*; D012342:RNA, Small Nuclear / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism
D001426:Bacterial Proteins; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D018832:Molecular Chaperones; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial; C081786:cyclophilin B; D007501:Iron; D045103:5,10-Methylenetetrahydrofolate Reductase (FADH2); C472209:metf protein, E coli; D021983:Cyclophilins; D019696:Peptidylprolyl Isomerase