title: Ribonuclease III processing of coaxially stacked RNA helices.
abstract: The RNase III family of endoribonucleases participates in maturation and decay of cellular and viral transcripts by processing of double-stranded RNA. RNase III degradation is inherent to most antisense RNA-regulated gene systems in Escherichia coli. In the hok/sok system from plasmid R1, Sok antisense RNA targets the hok mRNA for RNase III-mediated degradation. An intermediate in the pairing reaction between Sok RNA and hok mRNA forms a three-way junction. A complex between a chimeric antisense RNA and hok mRNA that mimics the three-way junction was cleaved by RNase III both in vivo and in vitro. Footprinting using E117A RNase III binding to partially complementary RNAs showed protection of the 13 base pairs of interstrand duplex and of the bottom part of the transcriptional terminator hairpin of the antisense RNA. This suggests that the 13 base pairs of RNA duplex are coaxially stacked on the antisense RNA terminator stem-loop and that each stem forms a monomer half-site, allowing symmetrical binding of the RNase III dimer. This processing scheme shows an unanticipated diversity in RNase III substrates and may have a more general implication for RNA metabolism.
authors.affiliation: Department of Molecular Biology, Odense University, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: T
authors.initials: T
authors.lastname: Franch
authors.forename: T
authors.initials: T
authors.lastname: Thisted
authors.forename: K
authors.initials: K
authors.lastname: Gerdes
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001427:Bacterial Toxins; D001483:Base Sequence; D017931:DNA Primers; D004722:Endoribonucleases / Q000378:metabolism*; D029968:Escherichia coli Proteins; D006868:Hydrolysis; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012323:RNA Processing, Post-Transcriptional; D016372:RNA, Antisense / Q000737:chemistry / Q000378:metabolism*; D043244:Ribonuclease III; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D001427:Bacterial Toxins; D017931:DNA Primers; D029968:Escherichia coli Proteins; C087025:Hok protein, E coli; D016372:RNA, Antisense; D004722:Endoribonucleases; D043244:Ribonuclease III; C468366:ribonuclease III, E coli