title: The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes.
abstract: In all bacterial species examined thus far, small regulatory RNAs (sRNAs) contribute to intricate patterns of dynamic genetic regulation. Many of the actions of these nucleic acids are mediated by well-characterized chaperones such as the Hfq protein, but genetic screens have also recently identified the 3'-to-5' exoribonuclease polynucleotide phosphorylase (PNPase) as an unexpected stabilizer and facilitator of sRNAs in vivo. To understand how a ribonuclease might mediate these effects, we tested the interactions of PNPase with sRNAs and found that the enzyme can readily degrade these nucleic acids in vitro but, nonetheless, copurifies from cell extracts with the same sRNAs without discernible degradation or modification to their 3' ends, suggesting that the associated RNA is protected against the destructive activity of the ribonuclease. In vitro, PNPase, Hfq, and sRNA can form a ternary complex in which the ribonuclease plays a nondestructive, structural role. Such ternary complexes might be formed transiently in vivo, but could help to stabilize particular sRNAs and remodel their population on Hfq. Taken together, our results indicate that PNPase can be programmed to act on RNA in either destructive or stabilizing modes in vivo and may form complex, protective ribonucleoprotein assemblies that shape the landscape of sRNAs available for action.
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.
authors.forename: Katarzyna J
authors.initials: KJ
authors.lastname: Bandyra
authors.affiliation: Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas 77030, USA.
authors.forename: Dhriti
authors.initials: D
authors.lastname: Sinha
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.
authors.forename: Johanna
authors.initials: J
authors.lastname: Syrjanen
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.
authors.forename: Ben F
authors.initials: BF
authors.lastname: Luisi
authors.affiliation: Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas 77030, USA Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas 77030, USA.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: De Lay
mesh_terms: D006868:Hydrolysis; D011117:Polyribonucleotide Nucleotidyltransferase / Q000378:metabolism*; D011485:Protein Binding; D012313:RNA / Q000378:metabolism*
chemical_list: D012313:RNA; D011117:Polyribonucleotide Nucleotidyltransferase
keywords: Hfq; RNA degradation; RNase E; polynucleotide phosphorylase; small regulatory RNA