title: How RNase R Degrades Structured RNA: ROLE OF THE HELICASE ACTIVITY AND THE S1 DOMAIN.
abstract: RNase R, a ubiquitous 3' exoribonuclease, plays an important role in many aspects of RNA metabolism. In contrast to other exoribonucleases, RNase R can efficiently degrade highly structured RNAs, but the mechanism by which this is accomplished has remained elusive. It is known that RNase R contains an unusual, intrinsic RNA helicase activity that facilitates degradation of duplex RNA, but how it stimulates the nuclease activity has also been unclear. Here, we have made use of specifically designed substrates to compare the nuclease and helicase activities of RNase R. We have also identified and mutated several residues in the S1 RNA-binding domain that are important for interacting with duplex RNA and have measured intrinsic tryptophan fluorescence to analyze the conformational changes that occur upon binding of structured RNA. Using these approaches, we have determined the relation of the RNA helicase, ATP binding, and nuclease activities of RNase R. This information has been combined with a structural analysis of RNase R, based on its homology to RNase II, whose structure has been determined, to develop a detailed model that explains how RNase R digests structured RNA and how this differs from its action on single-stranded RNA.
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101.
authors.forename: Sk Tofajjen
authors.initials: ST
authors.lastname: Hossain
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101.
authors.forename: Arun
authors.initials: A
authors.lastname: Malhotra
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101 m.deutscher@med.miami.edu.
authors.forename: Murray P
authors.initials: MP
authors.lastname: Deutscher
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D005095:Exoribonucleases / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D020365:RNA Helicases / Q000737:chemistry / Q000378:metabolism*; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D000255:Adenosine Triphosphate; D005095:Exoribonucleases; C080868:ribonuclease R; D020365:RNA Helicases
keywords: ATP; Escherichia coli (E. coli); P-loop domain; RNA degradation; RNA helicase; conformational change; duplex RNA; ribonuclase