Termination of translation in bacteria may be modulated via specific interaction between peptide chain release factor 2 and the last peptidyl-tRNA(Ser/Phe)

Nucleic Acids Res. 1993 Jun 25;21(12):2891-7. doi: 10.1093/nar/21.12.2891.

Abstract

The 5' context of 671 Escherichia coli stop codons UGA and UAA has been compared with the context of stop-like codons (UAC, UAU and CAA for UAA; UGG, UGC, UGU and CGA for UGA). We have observed highly significant deviations from the expected nucleotide distribution: adenine is over-represented whereas pyrimidines are under-represented in position -2 upstream from UAA. Uridine is over-represented in position -3 upstream from UGA. Lysine codons are preferable immediately prior to UAA. A complete set of codons for serine and the phenylalanine UUC codon are preferable immediately 5' to UGA. This non-random codon distribution before stop codons could be considered as a molecular device for modulation of translation termination. We have found that certain fragment of E. coli release factor 2 (RF2) (amino acids 93-114) is similar to the amino acid sequences of seryl-tRNA synthetase (positions 10-19 and 80-93) and of beta (small) subunit (positions 72-94) of phenylalanyl-tRNA synthetase from E. coli. Three-dimensional structure of E. coli seryl-tRNA synthetase is known [1]: Its N-terminus represents an antiparallel alpha-helical coiled-coil domain and contains a region homologous to RF2. On the basis of the above-mentioned results we assume that a specific interaction between RF2 and the last peptidyl-tRNA(Ser/Phe) occurs during polypeptide chain termination in prokaryotic ribosomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Codon
  • Escherichia coli / enzymology
  • Escherichia coli / genetics*
  • Lysine-tRNA Ligase / chemistry
  • Molecular Sequence Data
  • Peptide Termination Factors / chemistry
  • Peptide Termination Factors / metabolism*
  • Phenylalanine-tRNA Ligase / chemistry
  • Protein Biosynthesis*
  • RNA, Transfer, Phe / metabolism*
  • RNA, Transfer, Ser / metabolism*
  • Sequence Homology, Amino Acid
  • Serine-tRNA Ligase / chemistry

Substances

  • Codon
  • Peptide Termination Factors
  • RNA, Transfer, Phe
  • RNA, Transfer, Ser
  • peptide chain termination release factor 2
  • Serine-tRNA Ligase
  • Phenylalanine-tRNA Ligase
  • Lysine-tRNA Ligase