An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA

Cell. 2013 Mar 28;153(1):166-77. doi: 10.1016/j.cell.2013.02.037.


Many bacteria contain an ortholog of the Ro autoantigen, a ring-shaped protein that binds noncoding RNAs (ncRNAs) called Y RNAs. In the only studied bacterium, Deinococcus radiodurans, the Ro ortholog Rsr functions in heat-stress-induced ribosomal RNA (rRNA) maturation and starvation-induced rRNA decay. However, the mechanism by which this conserved protein and its associated ncRNAs act has been obscure. We report that Rsr and the exoribonuclease polynucleotide phosphorylase (PNPase) form an RNA degradation machine that is scaffolded by Y RNA. Single-particle electron microscopy, followed by docking of atomic models into the reconstruction, suggests that Rsr channels single-stranded RNA into the PNPase cavity. Biochemical assays reveal that Rsr and Y RNA adapt PNPase for effective degradation of structured RNAs. A Ro ortholog and ncRNA also associate with PNPase in Salmonella Typhimurium. Our studies identify another ribonucleoprotein machine and demonstrate that ncRNA, by tethering a protein cofactor, can alter the substrate specificity of an enzyme.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • Deinococcus / chemistry*
  • Deinococcus / genetics
  • Deinococcus / metabolism
  • Exosome Multienzyme Ribonuclease Complex / chemistry*
  • Exosome Multienzyme Ribonuclease Complex / metabolism
  • Molecular Sequence Data
  • Polyribonucleotide Nucleotidyltransferase / chemistry
  • Polyribonucleotide Nucleotidyltransferase / ultrastructure
  • RNA Stability*
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / ultrastructure
  • RNA, Untranslated / metabolism*
  • RNA, Untranslated / ultrastructure
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / genetics
  • Ribonucleoproteins / metabolism*
  • Salmonella typhimurium / metabolism*
  • Xenopus laevis / metabolism


  • RNA, Bacterial
  • RNA, Untranslated
  • Ribonucleoproteins
  • SS-A antigen
  • Polyribonucleotide Nucleotidyltransferase
  • Exosome Multienzyme Ribonuclease Complex

Associated data

  • GENBANK/KC584024
  • GENBANK/KC584025