title: Small RNA binding to 5' mRNA coding region inhibits translational initiation.
abstract: Small noncoding RNAs (sRNAs) have predominantly been shown to repress bacterial mRNAs by masking the Shine-Dalgarno (SD) or AUG start codon sequence, thereby preventing 30S ribosome entry and, consequently, translation initiation. However, many recently identified sRNAs lack obvious SD and AUG complementarity, indicating that sRNA-mediated translational control could also take place at other mRNA sites. We report that Salmonella RybB sRNA represses ompN mRNA translation by pairing with the 5' coding region. Results of systematic antisense interference with 30S binding to ompN and unrelated mRNAs suggest that sRNAs can act as translational repressors by sequestering sequences within the mRNA down to the fifth codon, even without SD and AUG start codon pairing. This "five codon window" for translational control in the 5' coding region of mRNA not only has implications for sRNA target predictions but might also apply to cis-regulatory systems such as RNA thermosensors and riboswitches.
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, Berlin D-10117, Germany.
authors.forename: Marie
authors.initials: M
authors.lastname: Bouvier
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.forename: Franziska
authors.initials: F
authors.lastname: Mika
authors.forename: Knud H
authors.initials: KH
authors.lastname: Nierhaus
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D003062:Codon / Q000235:genetics; D008969:Molecular Sequence Data; D009692:Nucleic Acid Heteroduplexes / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics*; D014176:Protein Biosynthesis; D016372:RNA, Antisense / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism; D012475:Salmonella / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D009692:Nucleic Acid Heteroduplexes; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated