title: The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail.
abstract: Hfq-dependent sRNAs contain, at least, an mRNA base-pairing region, an Hfq-binding site, and a Rho-independent terminator. Recently, we found that the terminator poly(U) of Escherichia coli sRNAs is essential for Hfq binding and therefore for riboregulation. In this study, we tried to identify additional components within Hfq-binding sRNAs required for efficient Hfq binding by using SgrS as a model. We demonstrate by mutational and biochemical studies that an internal hairpin and an immediately upstream U-rich sequence also are required for efficient Hfq binding. We propose that the functional Hfq-binding module of SgrS consists of an internal hairpin preceded by a U-rich sequence and a Rho-independent terminator with a long poly(U) tail. We also show that the Rho-independent terminator alone can act as a functional Hfq-binding module when it is preceded by an internal U-rich sequence. The 3' region of most known sRNAs share the features corresponding to either a double- or single-hairpin-type Hfq-binding module. We also demonstrate that increasing the spacing between the base-pairing region and the Hfq-binding module reduces or impairs the silencing ability. These findings allowed us to design synthetic Hfq-binding sRNAs to target desired mRNAs.
authors.affiliation: Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Ishikawa
authors.forename: Hironori
authors.initials: H
authors.lastname: Otaka
authors.forename: Kimika
authors.initials: K
authors.lastname: Maki
authors.forename: Teppei
authors.initials: T
authors.lastname: Morita
authors.forename: Hiroji
authors.initials: H
authors.lastname: Aiba
mesh_terms: D001482:Base Composition; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D018388:Codon, Terminator; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D035001:Host Factor 1 Protein / Q000378:metabolism*; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D011072:Poly U / Q000737:chemistry*; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism
chemical_list: D018388:Codon, Terminator; D029968:Escherichia coli Proteins; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012333:RNA, Messenger; C526013:SgrT protein, E coli; D011072:Poly U