Termination of translation in bacteria may be modulated via specific interaction between peptide chain release factor 2 and the last peptidyl-tRNA(Ser/Phe).
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.
Arkov
A L
AL
Engelhardt Institute of Molecular Biology, Moscow, Russia.
Korolev
S V
SV
Kisselev
L L
LL
D000595:Amino Acid Sequence; D001483:Base Sequence; D003062:Codon; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D008250:Lysine-tRNA Ligase / Q000737:chemistry; D008969:Molecular Sequence Data; D010454:Peptide Termination Factors / Q000737:chemistry / Q000378:metabolism*; D010652:Phenylalanine-tRNA Ligase / Q000737:chemistry; D014176:Protein Biosynthesis; D012360:RNA, Transfer, Phe / Q000378:metabolism*; D012362:RNA, Transfer, Ser / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D012714:Serine-tRNA Ligase / Q000737:chemistry
D003062:Codon; D010454:Peptide Termination Factors; D012360:RNA, Transfer, Phe; D012362:RNA, Transfer, Ser; C041460:peptide chain termination release factor 2; D012714:Serine-tRNA Ligase; D010652:Phenylalanine-tRNA Ligase; D008250:Lysine-tRNA Ligase