P-site pairing subtleties revealed by the effects of different tRNAs on programmed translational bypassing where anticodon re-pairing to mRNA is separated from dissociation

J Mol Biol. 2005 Jan 7;345(1):39-49. doi: 10.1016/j.jmb.2004.10.037.

Abstract

Programmed ribosomal bypassing occurs in decoding phage T4 gene 60 mRNA. Half the ribosomes bypass a 50 nucleotide gap between codons 46 and 47. Peptidyl-tRNA dissociates from the "take-off" GGA, codon 46, and re-pairs to mRNA at a matched GGA "landing site" codon directly 5' of codon 47 where translation resumes. The system described here allows the contribution of peptidyl-tRNA re-pairing to be measured independently of dissociation. The matched GGA codons have been replaced by 62 other matched codons, giving a wide range of bypassing efficiencies. Codons with G or C in either or both of the first two codon positions yielded high levels of bypassing. The results are compared with those from a complementary study of non-programmed bypassing, where the combined effects of peptidyl-tRNA dissociation and reassociation were measured. The wild-type, GGA, matched codons are the most efficient in their gene 60 context in contrast to the relatively low value in the non-programmed bypassing study.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Anticodon / genetics
  • Anticodon / metabolism*
  • Arginine / genetics
  • Base Sequence
  • Codon / genetics
  • Codon / metabolism
  • Cytosine / metabolism
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • Guanine / metabolism
  • Inosine / genetics
  • Nucleic Acid Conformation
  • Nucleoside Q / genetics
  • Nucleoside Q / metabolism
  • Protein Biosynthesis*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism*
  • Ribosomes / metabolism
  • Serine / genetics
  • Valine / genetics

Substances

  • Anticodon
  • Codon
  • DNA, Bacterial
  • RNA, Messenger
  • Serine
  • Nucleoside Q
  • Inosine
  • Guanine
  • Cytosine
  • RNA, Transfer
  • Arginine
  • Valine