title: PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action.
abstract: Major bacterial small RNAs (sRNAs) regulate the translation and stability of target mRNAs through base pairing with the help of the RNA chaperone Hfq. The Hfq-dependent sRNAs consist of three basic elements, mRNA base-pairing region, Hfq-binding site, and rho-independent terminator. Although the base-pairing region and the terminator are well documented in many sRNAs, the Hfq-binding site is less well-defined except that Hfq binds RNA with a preference for AU-rich sequences. Here, we performed mutational and biochemical studies to define the sRNA site required for Hfq action using SgrS as a model sRNA. We found that shortening terminator polyU tail eliminates the ability of SgrS to bind to Hfq and to silence ptsG mRNA. We also demonstrate that the SgrS terminator can be replaced with any foreign rho-independent terminators possessing a polyU tail longer than 8 without losing the ability to silence ptsG mRNA in an Hfq-dependent manner. Moreover, we found that shortening the terminator polyU tail of several other sRNAs also eliminates the ability to bind to Hfq and to regulate target mRNAs. We conclude that the polyU tail of sRNAs is essential for Hfq action in general. The data also indicate that the terminator polyU tail plays a role in Hfq-dependent stabilization of sRNAs.
authors.affiliation: Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan.
authors.forename: Hironori
authors.initials: H
authors.lastname: Otaka
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Ishikawa
authors.forename: Teppei
authors.initials: T
authors.lastname: Morita
authors.forename: Hiroji
authors.initials: H
authors.lastname: Aiba
mesh_terms: D020856:AT Rich Sequence / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D048168:Escherichia coli K12 / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D020868:Gene Silencing; D035001:Host Factor 1 Protein / Q000378:metabolism*; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000378:metabolism; D009690:Nucleic Acid Conformation; D011072:Poly U / Q000378:metabolism*; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013728:Terminator Regions, Genetic / Q000235:genetics*
chemical_list: D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D050505:Mutant Proteins; D012329:RNA, Bacterial; C534627:Rho protein, E coli; D011072:Poly U