The methyltransferase domain of the Respiratory Syncytial Virus L protein catalyzes cap N7 and 2'-O-methylation

PLoS Pathog. 2021 May 6;17(5):e1009562. doi: 10.1371/journal.ppat.1009562. eCollection 2021 May.

Abstract

Respiratory syncytial virus (RSV) is a negative sense single-stranded RNA virus and one of the main causes of severe lower respiratory tract infections in infants and young children. RSV RNA replication/transcription and capping are ensured by the viral Large (L) protein. The L protein contains a polymerase domain associated with a polyribonucleotidyl transferase domain in its N-terminus, and a methyltransferase (MTase) domain followed by the C-terminal domain (CTD) enriched in basic amino acids at its C-terminus. The MTase-CTD of Mononegavirales forms a clamp to accommodate RNA that is subsequently methylated on the cap structure and depending on the virus, on internal positions. These enzymatic activities are essential for efficient viral mRNA translation into proteins, and to prevent the recognition of uncapped viral RNA by innate immunity sensors. In this work, we demonstrated that the MTase-CTD of RSV, as well as the full-length L protein in complex with phosphoprotein (P), catalyzes the N7- and 2'-O-methylation of the cap structure of a short RNA sequence that corresponds to the 5' end of viral mRNA. Using different experimental systems, we showed that the RSV MTase-CTD methylates the cap structure with a preference for N7-methylation as first reaction. However, we did not observe cap-independent internal methylation, as recently evidenced for the Ebola virus MTase. We also found that at μM concentrations, sinefungin, a S-adenosylmethionine analogue, inhibits the MTase activity of the RSV L protein and of the MTase-CTD domain. Altogether, these results suggest that the RSV MTase domain specifically recognizes viral RNA decorated by a cap structure and catalyzes its methylation, which is required for translation and innate immune system subversion.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Methylation*
  • Humans
  • Immunity, Innate
  • Methyltransferases / genetics
  • Methyltransferases / metabolism*
  • RNA Caps / genetics
  • RNA Caps / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • Respiratory Syncytial Virus Infections / metabolism
  • Respiratory Syncytial Virus Infections / virology*
  • Respiratory Syncytial Virus, Human / metabolism*
  • Viral Nonstructural Proteins / genetics
  • Viral Nonstructural Proteins / metabolism*
  • Virus Replication

Substances

  • RNA Caps
  • RNA, Messenger
  • RNA, Viral
  • Viral Nonstructural Proteins
  • Methyltransferases

Grants and funding

The research was funded by JANSSEN-CILAG S.A., a Company of Johnson & Johnson and the National Research Agency (ANR) under the program ANR DecRisP-cap (ANR-19_CE11_0017) awarded to JFE. The funding organization had no role in study design, data collection and analysis. P.R., N.Y., P.A, and D.R. are employees of Janssen Pharmaceutical Companies of Johnson & Johnson and participated to the decision to publish and to the manuscript proofreading.