A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus

EMBO J. 2006 Oct 18;25(20):4933-42. doi: 10.1038/sj.emboj.7601368. Epub 2006 Oct 5.

Abstract

In (+) RNA coronaviruses, replication and transcription of the giant approximately 30 kb genome to produce genome- and subgenome-size RNAs of both polarities are mediated by a cognate membrane-bound enzymatic complex. Its RNA-dependent RNA polymerase (RdRp) activity appears to be supplied by non-structural protein 12 (nsp12) that includes an RdRp domain conserved in all RNA viruses. Using SARS coronavirus, we now show that coronaviruses uniquely encode a second RdRp residing in nsp8. This protein strongly prefers the internal 5'-(G/U)CC-3' trinucleotides on RNA templates to initiate the synthesis of complementary oligonucleotides of <6 residues in a reaction whose fidelity is relatively low. Distant structural homology between the C-terminal domain of nsp8 and the catalytic palm subdomain of RdRps of RNA viruses suggests a common origin of the two coronavirus RdRps, which however may have evolved different sets of catalytic residues. A parallel between the nsp8 RdRp and cellular DNA-dependent RNA primases is drawn to propose that the nsp8 RdRp produces primers utilized by the primer-dependent nsp12 RdRp.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Catalytic Domain / genetics
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Structure, Tertiary / genetics
  • RNA, Viral / biosynthesis
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • RNA-Dependent RNA Polymerase / chemistry
  • RNA-Dependent RNA Polymerase / genetics*
  • RNA-Dependent RNA Polymerase / metabolism
  • Severe acute respiratory syndrome-related coronavirus / chemistry
  • Severe acute respiratory syndrome-related coronavirus / enzymology
  • Severe acute respiratory syndrome-related coronavirus / genetics*
  • Viral Proteins / chemistry
  • Viral Proteins / genetics*
  • Viral Proteins / metabolism

Substances

  • RNA, Viral
  • Viral Proteins
  • RNA-Dependent RNA Polymerase