Substrate recognition and catalysis by the exoribonuclease RNase R

Helen A. Vincent, Murray P Deutscher

Research output: Contribution to journalArticle

139 Citations (Scopus)

Abstract

RNase R is a processive, 3′ to 5′ hydrolytic exoribonuclease that together with polynucleotide phosphorylase plays an important role in the degradation of structured RNAs. However, RNase R differs from other exoribonucleases in that it can by itself degrade RNAs with extensive secondary structure provided that a single-stranded 3′ overhang is present. Using a variety of specifically designed substrates, we show here that a 3′ overhang of at least 7 nucleotides is required for tight binding and activity, whereas optimum binding and activity are achieved when the overhang is 10 or more nucleotides in length. In contrast, duplex RNAs with no overhang or with a 4-nucleotide overhang bind extremely poorly to RNase R and are inactive as substrates. A duplex RNA with a 10-nucleotide 5′ overhang also is not a substrate. Interestingly, this molecule is bound only weakly, indicating that RNase R does not simply recognize single-stranded RNA, but the RNA must thread into the enzyme with 3′ to 5′ polarity. We also show that ribose moieties are required for recognition of the substrate as a whole since RNase R is unable to bind or degrade single-stranded DNA. However, RNA molecules with deoxyribose or dideoxyribose residues at their 3′ termini can be bound and degraded. Based on these data and a homology model of RNase R, derived from the structure of the closely related enzyme, RNase II, we present a model for how RNase R interacts with its substrates and degrades RNA.

Original languageEnglish
Pages (from-to)29769-29775
Number of pages7
JournalJournal of Biological Chemistry
Volume281
Issue number40
DOIs
StatePublished - Oct 6 2006

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Exoribonucleases
Catalysis
RNA
Substrates
Nucleotides
Polyribonucleotide Nucleotidyltransferase
Deoxyribose
Ribose
Single-Stranded DNA
RNA Stability
Molecules
Enzymes
ribonuclease R
Degradation

ASJC Scopus subject areas

  • Biochemistry

Cite this

Substrate recognition and catalysis by the exoribonuclease RNase R. / Vincent, Helen A.; Deutscher, Murray P.

In: Journal of Biological Chemistry, Vol. 281, No. 40, 06.10.2006, p. 29769-29775.

Research output: Contribution to journalArticle

Vincent, Helen A. ; Deutscher, Murray P. / Substrate recognition and catalysis by the exoribonuclease RNase R. In: Journal of Biological Chemistry. 2006 ; Vol. 281, No. 40. pp. 29769-29775.
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