Logo of embojLink to Publisher's site
EMBO J. 1995 Jan 3; 14(1): 151–158.
PMCID: PMC398062

The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli.


A statistical analysis of > 2000 Escherichia coli genes suggested that the base following the translational stop codon might be an important feature of the signal for termination. The strengths of each of 12 possible 'four base stop signals' (UAAN, UGAN and UAGN) were tested in an in vivo termination assay that measured termination efficiency by its direct competition with frameshifting. Termination efficiencies varied significantly depending on both the stop codon and the fourth base, ranging from 80 (UAAU) to 7% (UGAC). For both the UAAN and UGAN series, the fourth base hierarchy was U > G > A approximately C. UAG stop codons, which are used rarely in E. coli, showed efficiencies comparable with UAAN and UGAN, but differed in that the hierarchy of the fourth base was G > U approximately A > C. The rate of release factor selection varied 30-fold at UGAN stop signals, and 10-fold for both the UAAN and UAGN series; it correlated well with the frequency with which the different UAAN and UGAN signals are found at natural termination sites. The results suggest that the identity of the base following the stop codon determines the efficiency of translational termination in E. coli. They also provide a rationale for the use of the strong UAAU signal in highly expressed genes and for the occurrence of the weaker UGAC signal at several recording sites.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.7M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Phipps PH. Treatment by H 11. Br Med J. 1949 Jul 09;2(4618):d100–100. [PMC free article]
  • Adamski FM, Donly BC, Tate WP. Competition between frameshifting, termination and suppression at the frameshift site in the Escherichia coli release factor-2 mRNA. Nucleic Acids Res. 1993 Nov 11;21(22):5074–5078. [PMC free article] [PubMed]
  • Adamski FM, McCaughan KK, Jørgensen F, Kurland CG, Tate WP. The concentration of polypeptide chain release factors 1 and 2 at different growth rates of Escherichia coli. J Mol Biol. 1994 May 6;238(3):302–308. [PubMed]
  • Arkov AL, Korolev SV, Kisselev LL. 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):2891–2897. [PMC free article] [PubMed]
  • Atkins JF, Weiss RB, Gesteland RF. Ribosome gymnastics--degree of difficulty 9.5, style 10.0. Cell. 1990 Aug 10;62(3):413–423. [PubMed]
  • Böck A, Forchhammer K, Heider J, Leinfelder W, Sawers G, Veprek B, Zinoni F. Selenocysteine: the 21st amino acid. Mol Microbiol. 1991 Mar;5(3):515–520. [PubMed]
  • 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. [PubMed]
  • Bossi L, Ruth JR. The influence of codon context on genetic code translation. Nature. 1980 Jul 10;286(5769):123–127. [PubMed]
  • Brown CM, Stockwell PA, Trotman CN, Tate WP. The signal for the termination of protein synthesis in procaryotes. Nucleic Acids Res. 1990 Apr 25;18(8):2079–2086. [PMC free article] [PubMed]
  • Brown CM, Dalphin ME, Stockwell PA, Tate WP. The translational termination signal database. Nucleic Acids Res. 1993 Jul 1;21(13):3119–3123. [PMC free article] [PubMed]
  • Brown CM, McCaughan KK, Tate WP. Two regions of the Escherichia coli 16S ribosomal RNA are important for decoding stop signals in polypeptide chain termination. Nucleic Acids Res. 1993 May 11;21(9):2109–2115. [PMC free article] [PubMed]
  • Brown CM, Stockwell PA, Dalphin ME, Tate WP. The translational termination signal database (TransTerm) now also includes initiation contexts. Nucleic Acids Res. 1994 Sep;22(17):3620–3624. [PMC free article] [PubMed]
  • Buckingham RH, Sörensen P, Pagel FT, Hijazi KA, Mims BH, Brechemier-Baey D, Murgola EJ. 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. [PubMed]
  • Craigen WJ, Caskey CT. Expression of peptide chain release factor 2 requires high-efficiency frameshift. Nature. 1986 Jul 17;322(6076):273–275. [PubMed]
  • Craigen WJ, Cook RG, Tate WP, Caskey CT. 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. [PMC free article] [PubMed]
  • Craigen WJ, Lee CC, Caskey CT. Recent advances in peptide chain termination. Mol Microbiol. 1990 Jun;4(6):861–865. [PubMed]
  • Crick FH. The genetic code--yesterday, today, and tomorrow. Cold Spring Harb Symp Quant Biol. 1966;31:1–9. [PubMed]
  • Curran JF. Analysis of effects of tRNA:message stability on frameshift frequency at the Escherichia coli RF2 programmed frameshift site. Nucleic Acids Res. 1993 Apr 25;21(8):1837–1843. [PMC free article] [PubMed]
  • Curran JF, Yarus M. Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2. J Mol Biol. 1988 Sep 5;203(1):75–83. [PubMed]
  • Curran JF, Yarus M. Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J Mol Biol. 1989 Sep 5;209(1):65–77. [PubMed]
  • Donly BC, Edgar CD, Adamski FM, Tate WP. Frameshift autoregulation in the gene for Escherichia coli release factor 2: partly functional mutants result in frameshift enhancement. Nucleic Acids Res. 1990 Nov 25;18(22):6517–6522. [PMC free article] [PubMed]
  • Eggertsson G, Söll D. Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli. Microbiol Rev. 1988 Sep;52(3):354–374. [PMC free article] [PubMed]
  • Fluck MM, Salser W, Epstein RH. The influence of the reading context upon the suppression of nonsense codons. Mol Gen Genet. 1977 Mar 7;151(2):137–149. [PubMed]
  • Gesteland RF, Weiss RB, Atkins JF. Recoding: reprogrammed genetic decoding. Science. 1992 Sep 18;257(5077):1640–1641. [PubMed]
  • 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. [PubMed]
  • Hatfield DL, Smith DW, Lee BJ, Worland PJ, Oroszlan S. Structure and function of suppressor tRNAs in higher eukaryotes. Crit Rev Biochem Mol Biol. 1990;25(2):71–96. [PubMed]
  • Hirsh D. Tryptophan transfer RNA as the UGA suppressor. J Mol Biol. 1971 Jun 14;58(2):439–458. [PubMed]
  • Jørgensen F, Kurland CG. Processivity errors of gene expression in Escherichia coli. J Mol Biol. 1990 Oct 20;215(4):511–521. [PubMed]
  • Kawakami K, Inada T, Nakamura Y. Conditionally lethal and recessive UGA-suppressor mutations in the prfB gene encoding peptide chain release factor 2 of Escherichia coli. J Bacteriol. 1988 Nov;170(11):5378–5381. [PMC free article] [PubMed]
  • Kolbe HV, Costello D, Wong A, Lu RC, Wohlrab H. Mitochondrial phosphate transport. Large scale isolation and characterization of the phosphate transport protein from beef heart mitochondria. J Biol Chem. 1984 Jul 25;259(14):9115–9120. [PubMed]
  • 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. [PubMed]
  • Marshall B, Levy SB. Prevalence of amber suppressor-containing coliforms in the natural environment. Nature. 1980 Jul 31;286(5772):524–525. [PubMed]
  • Martin R, Weiner M, Gallant J. Effects of release factor context at UAA codons in Escherichia coli. J Bacteriol. 1988 Oct;170(10):4714–4717. [PMC free article] [PubMed]
  • McClelland M, Bhagwat AS. Biased DNA repair. Nature. 1992 Feb 13;355(6361):595–596. [PubMed]
  • Parker J. Errors and alternatives in reading the universal genetic code. Microbiol Rev. 1989 Sep;53(3):273–298. [PMC free article] [PubMed]
  • Pedersen WT, Curran JF. 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. [PubMed]
  • Phillips GJ, Arnold J, Ivarie R. The effect of codon usage on the oligonucleotide composition of the E. coli genome and identification of over- and underrepresented sequences by Markov chain analysis. Nucleic Acids Res. 1987 Mar 25;15(6):2627–2638. [PMC free article] [PubMed]
  • Prescott CD, Kleuvers B, Göringer HU. A rRNA-mRNA base pairing model for UGA-dependent termination. Biochimie. 1991 Jul-Aug;73(7-8):1121–1129. [PubMed]
  • Purohit P, Stern S. Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature. 1994 Aug 25;370(6491):659–662. [PubMed]
  • Rice CM, Fuchs R, Higgins DG, Stoehr PJ, Cameron GN. The EMBL data library. Nucleic Acids Res. 1993 Jul 1;21(13):2967–2971. [PMC free article] [PubMed]
  • Rydén SM, Isaksson LA. A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors. Mol Gen Genet. 1984;193(1):38–45. [PubMed]
  • Salser W. The influence of the reading context upon the suppression of nonsense codons. Mol Gen Genet. 1969 Oct 13;105(2):125–130. [PubMed]
  • 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. [PubMed]
  • Scolnick E, Tompkins R, Caskey T, Nirenberg M. Release factors differing in specificity for terminator codons. Proc Natl Acad Sci U S A. 1968 Oct;61(2):768–774. [PMC free article] [PubMed]
  • Stormo GD, Schneider TD, Gold L. Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res. 1986 Aug 26;14(16):6661–6679. [PMC free article] [PubMed]
  • Tate WP, Brown CM. Translational termination: "stop" for protein synthesis or "pause" for regulation of gene expression. Biochemistry. 1992 Mar 10;31(9):2443–2450. [PubMed]
  • 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. [PMC free article] [PubMed]
  • Weiss RB, Dunn DM, Atkins JF, Gesteland RF. 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. [PubMed]
  • Weiss RB, Dunn DM, Dahlberg AE, Atkins JF, Gesteland RF. Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J. 1988 May;7(5):1503–1507. [PMC free article] [PubMed]
  • Weiss RB, Dunn DM, Atkins JF, Gesteland RF. Ribosomal frameshifting from -2 to +50 nucleotides. Prog Nucleic Acid Res Mol Biol. 1990;39:159–183. [PubMed]
  • Zinoni F, Birkmann A, Stadtman TC, Böck A. Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4650–4654. [PMC free article] [PubMed]

Articles from The EMBO Journal are provided here courtesy of The European Molecular Biology Organization


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • MedGen
    Related information in MedGen
  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...