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. 1998 Feb 15;26(4):954–960. doi: 10.1093/nar/26.4.954

Translational termination in Escherichia coli: three bases following the stop codon crosslink to release factor 2 and affect the decoding efficiency of UGA-containing signals.

E S Poole 1, L L Major 1, S A Mannering 1, W P Tate 1
PMCID: PMC147352  PMID: 9461453

Abstract

The observations that the Escherichia coli release factor 2 (RF2) crosslinks with the base following the stop codon (+4 N), and that the identity of this base strongly influences the decoding efficiency of stop signals, stimulated us to determine whether there was a more extended termination signal for RF2 recognition. Analysis of the 3' contexts of the 1248 genes in the E.coli genome terminating with UGA showed a strong bias for U in the +4 position and a general bias for A and against C in most positions to +10, consistent with the concept of an extended sequence element. Site-directed crosslinking occurred to RF2 from a thio-U sited at the +4, +5 and +6 bases following the UGA stop codon but not beyond (+7 to +10). Varying the +4 to +6 bases modulated the strength of the crosslink from the +1 invariant U to RF2. A strong selection bias for particular bases in the +4 to +6 positions of certain E. coli UGANNN termination sites correlated in some cases with crosslinking efficiency to RF2 and in vivo termination signal strength. These data suggest that RF2 may recognise at least a hexanucleotide UGA-containing sequence and that particular base combinations within this sequence influence termination signal decoding efficiency.

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Selected References

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  1. Björnsson A., Isaksson L. A. UGA codon context which spans three codons. Reversal by ms2i6A37 in tRNA, mutation in rpsD(S4) or streptomycin. J Mol Biol. 1993 Aug 20;232(4):1017–1029. doi: 10.1006/jmbi.1993.1457. [DOI] [PubMed] [Google Scholar]
  2. Björnsson A., Mottagui-Tabar S., Isaksson L. A. Structure of the C-terminal end of the nascent peptide influences translation termination. EMBO J. 1996 Apr 1;15(7):1696–1704. [PMC free article] [PubMed] [Google Scholar]
  3. Bonetti B., Fu L., Moon J., Bedwell D. M. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J Mol Biol. 1995 Aug 18;251(3):334–345. doi: 10.1006/jmbi.1995.0438. [DOI] [PubMed] [Google Scholar]
  4. Bossi L. Context effects: translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message. J Mol Biol. 1983 Feb 15;164(1):73–87. doi: 10.1016/0022-2836(83)90088-8. [DOI] [PubMed] [Google Scholar]
  5. Bossi L., Ruth J. R. The influence of codon context on genetic code translation. Nature. 1980 Jul 10;286(5769):123–127. doi: 10.1038/286123a0. [DOI] [PubMed] [Google Scholar]
  6. Brown C. M., Dalphin M. E., Stockwell P. A., Tate W. P. The translational termination signal database. Nucleic Acids Res. 1993 Jul 1;21(13):3119–3123. doi: 10.1093/nar/21.13.3119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Buckingham R. H., Sörensen P., Pagel F. T., Hijazi K. A., Mims B. H., Brechemier-Baey D., Murgola E. J. Third position base changes in codons 5' and 3' adjacent UGA codons affect UGA suppression in vivo. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):259–262. doi: 10.1016/0167-4781(90)90177-4. [DOI] [PubMed] [Google Scholar]
  8. Craigen W. J., Cook R. G., Tate W. P., Caskey C. T. Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2. Proc Natl Acad Sci U S A. 1985 Jun;82(11):3616–3620. doi: 10.1073/pnas.82.11.3616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dalphin M. E., Brown C. M., Stockwell P. A., Tate W. P. The translational signal database, TransTerm: more organisms, complete genomes. Nucleic Acids Res. 1997 Jan 1;25(1):246–247. doi: 10.1093/nar/25.1.246. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fluck M. M., Salser W., Epstein R. H. The influence of the reading context upon the suppression of nonsense codons. Mol Gen Genet. 1977 Mar 7;151(2):137–149. doi: 10.1007/BF00338688. [DOI] [PubMed] [Google Scholar]
  11. Hatfield D., Oroszlan S. The where, what and how of ribosomal frameshifting in retroviral protein synthesis. Trends Biochem Sci. 1990 May;15(5):186–190. doi: 10.1016/0968-0004(90)90159-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ito K., Ebihara K., Uno M., Nakamura Y. Conserved motifs in prokaryotic and eukaryotic polypeptide release factors: tRNA-protein mimicry hypothesis. Proc Natl Acad Sci U S A. 1996 May 28;93(11):5443–5448. doi: 10.1073/pnas.93.11.5443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Jørgensen F., Kurland C. G. Processivity errors of gene expression in Escherichia coli. J Mol Biol. 1990 Oct 20;215(4):511–521. doi: 10.1016/S0022-2836(05)80164-0. [DOI] [PubMed] [Google Scholar]
  14. Kopelowitz J., Hampe C., Goldman R., Reches M., Engelberg-Kulka H. Influence of codon context on UGA suppression and readthrough. J Mol Biol. 1992 May 20;225(2):261–269. doi: 10.1016/0022-2836(92)90920-f. [DOI] [PubMed] [Google Scholar]
  15. Major L. L., Poole E. S., Dalphin M. E., Mannering S. A., Tate W. P. Is the in-frame termination signal of the Escherichia coli release factor-2 frameshift site weakened by a particularly poor context? Nucleic Acids Res. 1996 Jul 15;24(14):2673–2678. doi: 10.1093/nar/24.14.2673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. McCaughan K. K., Brown C. M., Dalphin M. E., Berry M. J., Tate W. P. Translational termination efficiency in mammals is influenced by the base following the stop codon. Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5431–5435. doi: 10.1073/pnas.92.12.5431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Miller J. H., Albertini A. M. Effects of surrounding sequence on the suppression of nonsense codons. J Mol Biol. 1983 Feb 15;164(1):59–71. doi: 10.1016/0022-2836(83)90087-6. [DOI] [PubMed] [Google Scholar]
  18. Moffat J. G., Tate W. P. A single proteolytic cleavage in release factor 2 stabilizes ribosome binding and abolishes peptidyl-tRNA hydrolysis activity. J Biol Chem. 1994 Jul 22;269(29):18899–18903. [PubMed] [Google Scholar]
  19. Mottagui-Tabar S., Björnsson A., Isaksson L. A. The second to last amino acid in the nascent peptide as a codon context determinant. EMBO J. 1994 Jan 1;13(1):249–257. doi: 10.1002/j.1460-2075.1994.tb06255.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Nakamura Y., Ito K., Isaksson L. A. Emerging understanding of translation termination. Cell. 1996 Oct 18;87(2):147–150. doi: 10.1016/s0092-8674(00)81331-8. [DOI] [PubMed] [Google Scholar]
  21. Pedersen W. T., Curran J. F. Effects of the nucleotide 3' to an amber codon on ribosomal selection rates of suppressor tRNA and release factor-1. J Mol Biol. 1991 May 20;219(2):231–241. doi: 10.1016/0022-2836(91)90564-m. [DOI] [PubMed] [Google Scholar]
  22. Poole E. S., Brimacombe R., Tate W. P. Decoding the translational termination signal: the polypeptide chain release factor in Escherichia coli crosslinks to the base following the stop codon. RNA. 1997 Sep;3(9):974–982. [PMC free article] [PubMed] [Google Scholar]
  23. Poole E. S., Brown C. M., Tate W. P. The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J. 1995 Jan 3;14(1):151–158. doi: 10.1002/j.1460-2075.1995.tb06985.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Salser W., Fluck M., Epstein R. The influence of the reading context upon the suppression of nonsense codons. 3. Cold Spring Harb Symp Quant Biol. 1969;34:513–520. doi: 10.1101/sqb.1969.034.01.058. [DOI] [PubMed] [Google Scholar]
  25. Salser W. The influence of the reading context upon the suppression of nonsense codons. Mol Gen Genet. 1969 Oct 13;105(2):125–130. doi: 10.1007/BF00445682. [DOI] [PubMed] [Google Scholar]
  26. Smith D., Yarus M. tRNA-tRNA interactions within cellular ribosomes. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4397–4401. doi: 10.1073/pnas.86.12.4397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Stade K., Rinke-Appel J., Brimacombe R. Site-directed cross-linking of mRNA analogues to the Escherichia coli ribosome; identification of 30S ribosomal components that can be cross-linked to the mRNA at various points 5' with respect to the decoding site. Nucleic Acids Res. 1989 Dec 11;17(23):9889–9908. doi: 10.1093/nar/17.23.9889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Tate W. P., Dalphin M. E., Pel H. J., Mannering S. A. The stop signal controls the efficiency of release factor-mediated translational termination. Genet Eng (N Y) 1996;18:157–182. doi: 10.1007/978-1-4899-1766-9_10. [DOI] [PubMed] [Google Scholar]
  29. Tate W. P., Mannering S. A. Three, four or more: the translational stop signal at length. Mol Microbiol. 1996 Jul;21(2):213–219. doi: 10.1046/j.1365-2958.1996.6391352.x. [DOI] [PubMed] [Google Scholar]
  30. Tate W. P., Poole E. S., Dalphin M. E., Major L. L., Crawford D. J., Mannering S. A. The translational stop signal: codon with a context, or extended factor recognition element? Biochimie. 1996;78(11-12):945–952. doi: 10.1016/s0300-9084(97)86716-8. [DOI] [PubMed] [Google Scholar]
  31. Tate W. P., Poole E. S., Horsfield J. A., Mannering S. A., Brown C. M., Moffat J. G., Dalphin M. E., McCaughan K. K., Major L. L., Wilson D. N. Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon. Biochem Cell Biol. 1995 Nov-Dec;73(11-12):1095–1103. doi: 10.1139/o95-118. [DOI] [PubMed] [Google Scholar]
  32. Tate W., Greuer B., Brimacombe R. Codon recognition in polypeptide chain termination: site directed crosslinking of termination codon to Escherichia coli release factor 2. Nucleic Acids Res. 1990 Nov 25;18(22):6537–6544. doi: 10.1093/nar/18.22.6537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Uno M., Ito K., Nakamura Y. Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2. Biochimie. 1996;78(11-12):935–943. doi: 10.1016/s0300-9084(97)86715-6. [DOI] [PubMed] [Google Scholar]
  34. Weiss R. B., Dunn D. M., Atkins J. F., Gesteland R. F. Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting. Cold Spring Harb Symp Quant Biol. 1987;52:687–693. doi: 10.1101/sqb.1987.052.01.078. [DOI] [PubMed] [Google Scholar]
  35. Zhang S., Rydén-Aulin M., Isaksson L. A. Functional interaction between release factor one and P-site peptidyl-tRNA on the ribosome. J Mol Biol. 1996 Aug 16;261(2):98–107. doi: 10.1006/jmbi.1996.0444. [DOI] [PubMed] [Google Scholar]

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