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

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.

Identification of Endogenous SsrA-tagged Proteins Reveals Tagging at Positions Corresponding to Stop Codons

“…The ybeL gene terminates with a proline sense codon (CCG) and an ochre stop codon (30). Ochre codons are generally thought to be efficient in termination but CCG_UAA is underrepresented in E. coli genes (31). Interestingly P22 c2 repressor, the phage P22 ortholog of repressor, also ends with a proline codon and ochre stop codon (32).…”

The Rate of Peptidyl-tRNA Dissociation from the Ribosome during Minigene Expression Depends on the Nature of the Last Decoding Interaction

“…This non-random codon distribution at the ends of ORFs has been considered as an important factor in the modulation of translation termination (39). This could be explained, because such codons provide an alternative translation termination mechanism including drop-off and Pth-mediated hydrolysis of the final peptidyl-tRNA.…”

Functional Interaction Between Release Factor One and P-site Peptidyl-tRNA on the Ribosome

“…At the 3' side of the stop codon, the first base following the stop codon is of particular importance; this suggests that the signal for the termination factors includes this base in addition to the stop codon itself (Brown et al, 1990;Li & Rice, 1993;Arkov et al, 1993;Poole et al, 1995). Codons at the 5' side can affect termination in several ways.…”

“…Codons at the 5' side can affect termination in several ways. The determinant can be the codon itself, its decoding tRNA, or the nascent peptide it carries (Buckingham et al, 1990;Bjö rnsson & Isaksson, 1993;Arkov et al, 1993;Mottagui-Tabar et al, 1994;Bjö rnsson et al, 1996). If the 5' flanking codon is CGA (Arg), then the I·A anticodon-codon interaction at the wobble base of the peptidyl-tRNA binding site (P-site) tRNA has a negative effect on a suppressor tRNA that decodes the stop codon at the aminoacyl-tRNA acceptor site (A-site).…”