In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses

Arch Virol. 2011 Oct;156(10):1737-47. doi: 10.1007/s00705-011-1043-7. Epub 2011 Jun 17.

Abstract

Foot-and-mouth disease virus (FMDV) uses an internal ribosome entry site (IRES), a highly structured segment of its genomic RNA, to hijack the translational apparatus of an infected host. Computational analysis of 162 type II picornavirus IRES RNA sequences yielded secondary structures that included only base pairs supported by comparative or experimental evidence. The deduced helical sections provided the foundation for a hypothetical three-dimensional model of FMDV IRES RNA. The model was further constrained by incorporation of data derived from chemical modification and enzymatic probing of IRES RNAs as well as high-resolution information about IRES RNA-bound proteins.

Publication types

  • Comparative Study
  • 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

  • Base Sequence
  • Binding Sites
  • Foot-and-Mouth Disease Virus / chemistry
  • Foot-and-Mouth Disease Virus / genetics*
  • Foot-and-Mouth Disease Virus / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptide Chain Initiation, Translational*
  • Picornaviridae / chemistry
  • Picornaviridae / genetics
  • Picornaviridae / metabolism
  • RNA, Viral / chemistry
  • RNA, Viral / genetics*
  • RNA, Viral / metabolism
  • Ribosomes / genetics
  • Ribosomes / metabolism*

Substances

  • RNA, Viral