Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB.
Previous work has demonstrated that iron-dependent variations in the steady-state concentration and translatability of sodB mRNA are modulated by the small regulatory RNA RyhB, the RNA chaperone Hfq and RNase E. In agreement with the proposed role of RNase E, we found that the decay of sodB mRNA is retarded upon inactivation of RNase E in vivo, and that the enzyme cleaves within the sodB 5'-untranslated region (5'-UTR) in vitro, thereby removing the 5' stem-loop structure that facilitates Hfq and ribosome binding. Moreover, RNase E cleavage can also occur at a cryptic site that becomes available upon sodB 5'-UTR/RyhB base pairing. We show that while playing an important role in facilitating the interaction of RyhB with sodB mRNA, Hfq is not tightly retained by the RyhB-sodB mRNA complex and can be released from it through interaction with other RNAs added in trans. Unlike turnover of sodB mRNA, RyhB decay in vivo is mainly dependent on RNase III, and its cleavage by RNase III in vitro is facilitated upon base pairing with the sodB 5'-UTR. These data are discussed in terms of a model, which accounts for the observed roles of RNase E and RNase III in sodB mRNA turnover.
Afonyushkin
Taras
T
Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter Dr. Bohrgasse 9/4, A-1030 Vienna, Austria.
Vecerek
Branislav
B
Moll
Isabella
I
Bläsi
Udo
U
Kaberdin
Vladimir R
VR
D020121:5' Untranslated Regions / Q000737:chemistry; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics*; D020029:Base Pairing; D001483:Base Sequence; D004722:Endoribonucleases / Q000502:physiology*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000378:metabolism; D008957:Models, Genetic; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D012329:RNA, Bacterial / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D022661:RNA, Untranslated / Q000378:metabolism*; D043244:Ribonuclease III / Q000502:physiology*; D012270:Ribosomes / Q000378:metabolism; D013482:Superoxide Dismutase / Q000096:biosynthesis / Q000235:genetics*
D020121:5' Untranslated Regions; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated; C087504:SodB protein, Bacteria; D013482:Superoxide Dismutase; D004722:Endoribonucleases; D043244:Ribonuclease III; C022537:ribonuclease E