Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade ds RNA

Proteins. 2011 Jun;79(6):1853-67. doi: 10.1002/prot.23010. Epub 2011 Apr 4.


RNase II and RNase R are the two E. coli exoribonucleases that belong to the RNase II super family of enzymes. They degrade RNA hydrolytically in the 3' to 5' direction in a processive and sequence independent manner. However, while RNase R is capable of degrading structured RNAs, the RNase II activity is impaired by dsRNAs. The final end-product of these two enzymes is also different, being 4 nt for RNase II and 2 nt for RNase R. RNase II and RNase R share structural properties, including 60% of amino acid sequence similarity and have a similar modular domain organization: two N-terminal cold shock domains (CSD1 and CSD2), one central RNB catalytic domain, and one C-terminal S1 domain. We have constructed hybrid proteins by swapping the domains between RNase II and RNase R to determine which are the responsible for the differences observed between RNase R and RNase II. The results obtained show that the S1 and RNB domains from RNase R in an RNase II context allow the degradation of double-stranded substrates and the appearance of the 2 nt long end-product. Moreover, the degradation of structured RNAs becomes tail-independent when the RNB domain from RNase R is no longer associated with the RNA binding domains (CSD and S1) of the genuine protein. Finally, we show that the RNase R C-terminal Lysine-rich region is involved in the degradation of double-stranded substrates in an RNase II context, probably by unwinding the substrate before it enters into the catalytic cavity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli / chemistry
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Exoribonucleases / chemistry*
  • Exoribonucleases / genetics
  • Exoribonucleases / isolation & purification
  • Exoribonucleases / metabolism*
  • Protein Structure, Tertiary
  • RNA, Bacterial / metabolism*
  • RNA, Double-Stranded / metabolism
  • Up-Regulation


  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA, Double-Stranded
  • Exoribonucleases
  • exoribonuclease II
  • ribonuclease R