The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift

Nucleic Acids Res. 2007;35(16):5581-92. doi: 10.1093/nar/gkm578. Epub 2007 Aug 17.

Abstract

The -1 programmed ribosomal frameshifts (PRF), which are used by many viruses, occur at a heptanucleotide slippery sequence and are currently thought to involve the tRNAs interacting with the ribosomal P- and A-site codons. We investigated here whether the tRNA occupying the ribosomal E site that precedes a slippery site influences -1 PRF. Using the human immunodeficiency virus type 1 (HIV-1) frameshift region, we found that mutating the E-site codon altered the -1 PRF efficiency. When the HIV-1 slippery sequence was replaced with other viral slippery sequences, mutating the E-site codon also altered the -1 PRF efficiency. Because HIV-1 -1 PRF can be recapitulated in bacteria, we used a bacterial ribosome system to select, by random mutagenesis, 16S ribosomal RNA (rRNA) mutations that modify the expression of a reporter requiring HIV-1 -1 PRF. Three mutants were isolated, which are located in helices 21 and 22 of 16S rRNA, a region involved in translocation and E-site tRNA binding. We propose a novel model where -1 PRF is triggered by an incomplete translocation and depends not only on the tRNAs interacting with the P- and A-site codons, but also on the tRNA occupying the E site.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Codon / chemistry
  • Frameshifting, Ribosomal*
  • Genes, Reporter
  • HIV-1 / genetics*
  • Humans
  • Models, Genetic*
  • Mutation
  • Nucleotides / chemistry
  • RNA, Messenger / chemistry
  • RNA, Ribosomal, 16S / chemistry
  • RNA, Transfer / metabolism*
  • RNA, Viral / chemistry*
  • Ribosomes / chemistry*
  • Ribosomes / metabolism

Substances

  • Codon
  • Nucleotides
  • RNA, Messenger
  • RNA, Ribosomal, 16S
  • RNA, Viral
  • RNA, Transfer