Structural insights into reptarenavirus cap-snatching machinery

PLoS Pathog. 2017 May 15;13(5):e1006400. doi: 10.1371/journal.ppat.1006400. eCollection 2017 May.

Abstract

Cap-snatching was first discovered in influenza virus. Structures of the involved domains of the influenza virus polymerase, namely the endonuclease in the PA subunit and the cap-binding domain in the PB2 subunit, have been solved. Cap-snatching endonucleases have also been demonstrated at the very N-terminus of the L proteins of mammarena-, orthobunya-, and hantaviruses. However, a cap-binding domain has not been identified in an arena- or bunyavirus L protein so far. We solved the structure of the 326 C-terminal residues of the L protein of California Academy of Sciences virus (CASV), a reptarenavirus, by X-ray crystallography. The individual domains of this 37-kDa fragment (L-Cterm) as well as the domain arrangement are structurally similar to the cap-binding and adjacent domains of influenza virus polymerase PB2 subunit, despite the absence of sequence homology, suggesting a common evolutionary origin. This enabled identification of a region in CASV L-Cterm with similarity to a cap-binding site; however, the typical sandwich of two aromatic residues was missing. Consistent with this, cap-binding to CASV L-Cterm could not be detected biochemically. In addition, we solved the crystal structure of the corresponding endonuclease in the N-terminus of CASV L protein. It shows a typical endonuclease fold with an active site configuration that is essentially identical to that of known mammarenavirus endonuclease structures. In conclusion, we provide evidence for a presumably functional cap-snatching endonuclease in the N-terminus and a degenerate cap-binding domain in the C-terminus of a reptarenavirus L protein. Implications of these findings for the cap-snatching mechanism in arenaviruses are discussed.

MeSH terms

  • Arenaviridae / chemistry
  • Arenaviridae / enzymology*
  • Arenaviridae / genetics
  • Arenaviridae Infections / virology*
  • Crystallography, X-Ray
  • Endonucleases / chemistry
  • Endonucleases / genetics
  • Endonucleases / metabolism*
  • Models, Molecular*
  • Protein Conformation
  • Protein Domains
  • RNA Caps
  • Viral Proteins / chemistry
  • Viral Proteins / genetics
  • Viral Proteins / metabolism

Substances

  • RNA Caps
  • Viral Proteins
  • Endonucleases

Grants and funding

This work was funded by grants from the Deutsche Forschungsgemeinschaft (DFG, http://www.dfg.de): RE 3712/1-1 to SR and GU 883/1-1 and GU 883/4-1 to SG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.