RNase L releases a small RNA from HCV RNA that refolds into a potent PAMP

RNA. 2010 Nov;16(11):2108-19. doi: 10.1261/rna.2244210. Epub 2010 Sep 10.


Triggering and propagating an intracellular innate immune response is essential for control of viral infections. RNase L is a host endoribonuclease and a pivotal component of innate immunity that cleaves viral and cellular RNA within single-stranded loops releasing small structured RNAs with 5'-hydroxyl (5'-OH) and 3'-monophosphoryl (3'-p) groups. In 2007, we reported that RNase L cleaves self RNA to produce small RNAs that function as pathogen-associated molecular patterns (PAMPs). However, the precise sequence and structure of PAMP RNAs produced by RNase L is unknown. Here we used hepatitis C virus RNA as substrate to characterize RNase L mediated cleavage products [named suppressor of virus RNA (svRNA)] for their ability to activate RIG-I like receptors (RLR). The NS5B region of HCV RNA was cleaved by RNase L to release an svRNA that bound to RIG-I, displacing its repressor domain and stimulating its ATPase activity while signaling to the IFN-β gene in intact cells. All three of these RIG-I functions were dependent on the presence in svRNA of the 3'-p. Furthermore, svRNA suppressed HCV replication in vitro through a mechanism involving IFN production and triggered a RIG-I-dependent hepatic innate immune response in mice. RNase L and OAS (required for its activation) were both expressed in hepatocytes from HCV-infected patients, raising the possibility that the OAS/RNase L pathway might suppress HCV replication in vivo. It is proposed that RNase L mediated cleavage of HCV RNA generates svRNA that activates RIG-I, thus propagating innate immune signaling to the IFN-β gene.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Cell Line, Tumor
  • DEAD Box Protein 58
  • DEAD-box RNA Helicases / metabolism
  • Endoribonucleases / metabolism*
  • Hepacivirus / chemistry*
  • Hepacivirus / immunology
  • Hepacivirus / metabolism*
  • Humans
  • Immunity, Innate
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Mice
  • Nerve Tissue Proteins / genetics
  • Nerve Tissue Proteins / metabolism
  • Nucleic Acid Conformation*
  • Protein Binding
  • RNA, Viral / chemistry*
  • RNA, Viral / immunology
  • RNA, Viral / metabolism*
  • Receptors, Cell Surface
  • Substrate Specificity
  • Virus Replication


  • Membrane Proteins
  • Nerve Tissue Proteins
  • RNA, Viral
  • Receptors, Cell Surface
  • Robo3 protein, mouse
  • Endoribonucleases
  • 2-5A-dependent ribonuclease
  • DDX58 protein, human
  • DEAD Box Protein 58
  • DEAD-box RNA Helicases