How RNase R degrades structured RNA

Role of the helicase activity and the S1 domain

Sk Tofajjen Hossain, Arun Malhotra, Murray P Deutscher

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)7877-7887
Number of pages11
JournalJournal of Biological Chemistry
Volume291
Issue number15
DOIs
StatePublished - Apr 8 2016

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RNA Helicases
RNA
Exoribonucleases
RNA Stability
ribonuclease R
Tryptophan
Metabolism
Structural analysis
Adenosine Triphosphate
Fluorescence
Degradation

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

How RNase R degrades structured RNA : Role of the helicase activity and the S1 domain. / Hossain, Sk Tofajjen; Malhotra, Arun; Deutscher, Murray P.

In: Journal of Biological Chemistry, Vol. 291, No. 15, 08.04.2016, p. 7877-7887.

Research output: Contribution to journalArticle

Hossain, Sk Tofajjen ; Malhotra, Arun ; Deutscher, Murray P. / How RNase R degrades structured RNA : Role of the helicase activity and the S1 domain. In: Journal of Biological Chemistry. 2016 ; Vol. 291, No. 15. pp. 7877-7887.
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