title: Positive regulation by small RNAs and the role of Hfq.
abstract: Bacterial small noncoding RNAs carry out both positive and negative regulation of gene expression by pairing with mRNAs; in Escherichia coli, this regulation often requires the RNA chaperone Hfq. Three small regulatory RNAs (sRNAs), DsrA, RprA, and ArcZ, positively regulate translation of the sigma factor RpoS, each pairing with the 5' leader to open up an inhibitory hairpin. In vitro, rpoS interaction with sRNAs depends upon an (AAN)(4) Hfq-binding site upstream of the pairing region. Here we show that both Hfq and this Hfq binding site are required for RprA or ArcZ to act in vivo and to form a stable complex with rpoS mRNA in vitro; both were partially dispensable for DsrA at 37 degrees C. ArcZ sRNA is processed from 121 nt to a stable 56 nt species that contains the pairing region; only the 56 nt ArcZ makes a strong Hfq-dependent complex with rpoS. For each of these sRNAs, the stability of the sRNA*mRNA complexes, rather than their rate of formation, best predicted in vivo activity. These studies demonstrate that binding of Hfq to the rpoS mRNA is critical for sRNA regulation under normal conditions, but if the stability of the sRNA*mRNA complex is sufficiently high, the requirement for Hfq can be bypassed.
authors.affiliation: Johns Hopkins University, Program in Cell, Molecular, Developmental Biology and Biophysics, Baltimore, MD 21218, USA.
authors.forename: Toby
authors.initials: T
authors.lastname: Soper
authors.forename: Pierre
authors.initials: P
authors.lastname: Mandin
authors.forename: Nadim
authors.initials: N
authors.lastname: Majdalani
authors.forename: Susan
authors.initials: S
authors.lastname: Gottesman
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Woodson
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D035001:Host Factor 1 Protein / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism*; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria
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