title: An antisense RNA inhibits translation by competing with standby ribosomes.
abstract: Most antisense RNAs in bacteria inhibit translation by competing with ribosomes for translation initiation regions (TIRs) on nascent mRNA. We propose a mechanism by which an antisense RNA inhibits translation without binding directly to a TIR. The tisAB locus encodes an SOS-induced toxin, and IstR-1 is the antisense RNA that counteracts toxicity. We show that full-length tisAB mRNA (+1) is translationally inactive and endonucleolytic processing produces an active mRNA (+42). IstR-1 binding inhibits translation of this mRNA, and subsequent RNase III cleavage generates a truncated, inactive mRNA (+106). In vitro translation, toeprinting, and structure mapping suggest that active, but not inactive, tisAB mRNAs contain an upstream ribosome loading or "standby" site. Standby binding is required for initiation at the highly structured tisB TIR. This may involve ribosome sliding to a transiently open tisB TIR. IstR-1 competes with ribosomes by base pairing to the standby site located approximately 100 nucleotides upstream.
authors.affiliation: Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden.
authors.forename: Fabien
authors.initials: F
authors.lastname: Darfeuille
authors.forename: Cecilia
authors.initials: C
authors.lastname: Unoson
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
authors.forename: E Gerhart H
authors.initials: EG
authors.lastname: Wagner
mesh_terms: D001427:Bacterial Toxins / Q000096:biosynthesis / Q000235:genetics; D001483:Base Sequence; D001667:Binding, Competitive; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational / Q000235:genetics*; D014176:Protein Biosynthesis / Q000235:genetics*; D016372:RNA, Antisense / Q000737:chemistry / Q000378:metabolism*; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*; D013014:SOS Response, Genetics / Q000235:genetics / Q000502:physiology; D015534:Trans-Activators
chemical_list: D001427:Bacterial Toxins; D029968:Escherichia coli Proteins; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D015534:Trans-Activators