Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms

Nucleic Acids Research

Volumn 34, Issue 7, 2006, Pages 1959-1973

  Cridge, Andrew G ^a   Major, Louise L ^a   Mahagaonkar, Alhad A ^a   Poole, Elizabeth S ^a   Isaksson, Leif A ^b   Tate, Warren P ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; GLYCINE; TRANSFER RNA; TRANSLATION TERMINATION FACTOR; NUCLEOTIDE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; CORRELATION ANALYSIS; ESCHERICHIA COLI; EUKARYOTE; GENE EXPRESSION; GENOME ANALYSIS; MAMMAL CELL; NONHUMAN; PARASITE; PRIORITY JOURNAL; PROKARYOTE; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN SYNTHESIS INHIBITION; SIGNAL TRANSDUCTION; STOP CODON; ANIMAL; BIOLOGY; CELL STRAIN COS1; CERCOPITHECUS; COMPARATIVE STUDY; EUKARYOTIC CELL; GENOMICS; HUMAN; METABOLISM; PROKARYOTIC CELL; RNA TRANSLATION;

ESCHERICHIA COLI; EUKARYOTA; MAMMALIA; PROKARYOTA;

ANIMALS; CERCOPITHECUS AETHIOPS; CODON, TERMINATOR; COMPUTATIONAL BIOLOGY; COS CELLS; EUKARYOTIC CELLS; GENOMICS; HUMANS; NUCLEOTIDES; PEPTIDE CHAIN TERMINATION, TRANSLATIONAL; PEPTIDE TERMINATION FACTORS; PROKARYOTIC CELLS; RNA, TRANSFER;

EID: 33645801951     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl074     Document Type: Article

References (75)

1. Poole,E. and Tate,W. (2000) Release factors and their role as decoding proteins: Specificity and fidelity for termination of protein synthesis. Biochim. Biophys. Acta, 1493, 1-11.
2. Nakamura,Y. and Ito,K. (2003) Making sense of mimic in translation termination. Trends Biochem. Sci., 28, 99-105.
3. Kisselev,L., Ehrenberg,M. and Frolova,L. (2003) Termination of translation: Interplay of mRNA, rRNAs and release factors? EMBO J., 22, 175-182.
4. Buckingham,R.H., Grentzmann,G. and Kisselev,L. (1997) Polypeptide chain release factors. Mol. Microbiol., 24, 449-456.
5. Inge-Vechtomov,S., Zhouravleva,G. and Philippe,M. (2003) Eukaryotic release factors (eRFs) history. Biol. Cell, 95, 195-109.
6. Scolnick,E., Tompkins,R., Caskey,T. and Nirenberg,M. (1968) Release factors differing in specificity for terminator codons. Proc Natl Acad. Sci. USA, 61, 768-774.
7. Frolova,L., Le Goff,X., Rasmussen,H.H., Cheperegin,S., Drugeon,G., Kress,M., Arman,I., Haenni,A.-L., Celis,J.E., Philippe,M. et al. (1994) A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor. Nature, 372, 701-703.
8. Dontsova,M., Frolova,L., Vassilieva,J., Piendl,W., Kisselev,L. and Garber,M. (2000) Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes. FEBS Lett., 472, 213-216.
9. Kisselev,L.L. (1999) Translation termination and yeast prions. Biochemistry, 64, 1337-1341.
10. Tate,W.P., Poole,E.S., Dalphin,M.E., Major,L.L., Crawford,D.J. and Mannering,S.A. (1996) The translational stop signal: Codon with a context, or extended factor recognition element? Biochimie, 78, 945-952.
11. Brown,C.M., Stockwell,P.A., Trotman,C.N. and Tate,W.P. (1990) The signal for the termination of protein synthesis in procaryotes. Nucleic Acids Res., 18, 2079-2086.
12. Arkov,A.L., Korolev,S.V. and Kisselev,L.L. (1993) 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., 21, 2891-2897.
13. Alff-Steinberger,C. and Epstein,R. (1994) Codon preference in the terminal region of E.coli genes and evolution of stop codon usage. J. Theor. Biol., 168, 461-463.
14. Berezovsky,I.N., Kilosanidze,G.T., Tumanyan,V.G. and Kisselev,L. (1997) COOH-terminal decamers in proteins are non-random. FEBS Lett., 404, 140-142.
15. Arkov,A.L., Korolev,S.V. and Kisselev,L.L. (1995) 5′ contexts of Escherichia coli and human termination codons are similar. Nucleic Acids Res., 23, 4712-4716.
16. Gutman,G.A. and Hatfield,G.W. (1989) Nonrandom utilization of codon pairs in Escherichia coli. Proc. Natl Acad. Sci. USA, 86, 3699-3703.
17. Berezovsky,I.N., Kilosanidze,G.T., Tumanyan,V.G. and Kisselev,L.L. (1999) Amino acid composition of protein termini are biased in different manners. Protein Eng., 12, 23-30.
18. Bossi,L. (1983) Context effects: Translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message. J. Mol. Biol., 164, 73-87.
19. Edelmann,P., Martin,R. and Gallant,J. (1987) Nonsense suppression context effects in Escherichia coli bacteriophage T4. Mol. Gen. Genet., 207, 517-518.
20. Miller,J.H. and Albertini,A.M. (1983) Effects of surrounding sequence on the suppression of nonsense codons. J. Mol. Biol., 164, 59-71.
21. Stormo,G.D., Schneider,T.D. and Gold,L. (1986) Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res., 14, 6661-6679.
22. Martin,R., Weiner,M. and Gallant,J. (1988) Effects of release factor context at UAA codons in Escherichia coli. J. Bacteriol., 170, 4714-4717.
23. Poole,E.S., Brimacombe,R. and Tate,W.P. (1997) Decoding the translational termination signal: The polypeptide chain release factor in Escherichia coli crosslinks to the base following the stop codon. RNA, 3, 974-982.
24. Poole,E.S., Major,L.L., Mannering,S.A. and Tate,W.P. (1998) 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. Nucleic Acids Res., 26, 954-960.
25. 6A37 in tRNA, mutation in rpsD(S4) or streptomycin. J. Mol. Biol., 232, 1017-1029.
26. Mottagui-Tabar,S., Bjornsson,A. and Isaksson,L.A. (1994) The second to last amino acid in the nascent peptide as a codon context determinant. EMBO J., 13, 249-257.
27. Mottagui-Tabar,S. and Isaksson,L.A. (1997) Only the last amino acids in the nascent peptide influence translation termination in Escherichia coli genes. FEBS Lett., 414, 165-170.
28. Zhang,S., Ryden-Aulin,M. and Isaksson,L.A. (1996) Functional interaction between release factor one and P-site peptidyl-tRNA on the ribosome. J. Mol. Biol., 261, 98-107.
29. Bjornsson,A., Mottagui-Tabar,S. and Isaksson,L.A. (1996) Structure of the C-terminal end of the nascent peptide influences translation termination. EMBO J, 15, 1696-1704.
30. Brown,C.M., Stockwell,P.A., Trotman,C.N. and Tate,W.P. (1990) Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes. Nucleic Acids Res., 18, 6339-6345.
31. Kohli,J. and Grosjean,H. (1981) Usage of the three termination codons: compilation and analysis of the known eukaryotic and prokaryotic translation termination sequences. Mol. Gen. Genet., 182, 430-439.
32. Cavener,D.R. and Ray,S.C. (1991) Eukaryotic start and stop translation sites. Nucleic Acids Res., 19, 3185-3192.
33. Sharp,P.M., Burgess,C.J., Cowe,E., Lloyd,A.T. and Mitchell,K.J. (1992) Selective use of termination codons and variations in codon choice. In Hatfield,D.L., Lee,B.J. and Pirtle,R.M. (eds), Transfer RNA in protein synthesis. CRC Press, Boca Raton, pp. 397-425.
34. Bonetti,B., Fu,L.W., Moon,J. and Bedwell,D.M. (1995) The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol., 251, 334-345.
35. Angenon,G., Van,M.M. and Depicker,A. (1990) Analysis of the stop codon context in plant nuclear genes. FEBS Lett., 271, 144-146.
36. McCaughan,K.K., Brown,C.M., Dalphin,M.E., Berry,M.J. and Tate,W.P. (1995) Translational termination efficiency in mammals is influenced by the base following the stop codon. Proc. Natl Acad. Sci. USA, 92, 5431-5435.
37. Konecki,D.S., Aune,K.C., Tate,W. and Caskey,C.T. (1977) Characterization of reticulocyte release factor. J. Biol. Chem., 252, 4514-4520.
38. 4UGA stop codon located in the A site of eukaryotic ribosomes. Eur. J. Biochem., 268, 2896-2904.
39. Mottagui-Tabar,S., Tuite,M.F. and Isaksson,L.A. (1998) The influence of 5′ codon context on translation termination in Saccharomyces cerevisiae. Eur. J. Biochem., 257, 249-254.
40. Namy,O., Hatin,I. and Rousset,J.P. (2001) Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep., 2, 787-793.
41. Cassan,M. and Rousset,J.P. (2001) UAG readthrough in mammalian cells: effect of upstream and downstream stop codon contexts reveal different signals. BMC Mol. Biol., 2, 3.
42. Tork,S., Hatin,I., Rousset,J.P. and Fabret,C. (2004) The major 5′ determinant in stop codon read-through involves two adjacent adenines. Nucleic Acids Res., 32, 415-421.
43. Brown,C.M., Jacobs,G., Stockwell,P. and Schreiber,M. (2003) Detection of signals in mRNAs that influence translation. Appl. Bioinformatics, 2, S47-51.
44. Sharp,P.M. and Li,W.-H. (1987) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res., 15, 1281-1295.
45. Major,L.L., Edgar,T.D., Yip,P.Y., Isaksson,L.A. and Tate,W.P. (2002) Tandem termination signals: Myth or reality? FEBS Lett., 514, 84-89.
46. Neidhardt,F.C., Bloch,P.L. and Smith,D.F. (1974) Culture medium for enterobacteria. J. Bacteriol., 119, 736-747.
47. Coulondre,C. and Miller,J.H. (1977) Genetic studies of the lac repressor. III. Additional correlation of mutational sites with specific amino acid residues. J. Mol. Biol., 117, 525-567.
48. Grentzmann,G., Ingram,J.A., Kelly,P.J., Gesteland,R.F. and Atkins,J.F. (1998) A dual-luciferase reporter system for studying recoding signals. RNA, 4, 479-486.
49. Bjornsson,A., Mottagui-Tabar,S. and Isaksson,L.A. (1998) The analysis of translational activity using a reporter gene constructed from repeats of an antibody-binding domain from protein A. Methods Mol. Biol., 77, 75-91.
50. Frolova,L.Y., Merkulova,T.I. and Kisselev,L.L. (2000) Translation termination in eukaryotes: Polypeptide release factor eRF1 is composed of functionally and structurally distinct domains. RNA, 6, 381-390.
51. Gluzman,Y. (1981) SV40-transformed simian cells support the replication of early SV40 mutants. Cell, 23, 175-182.
52. Matthews,J.C., Hori,K. and Cormier,M.J. (1977) Purification and properties of Renilla reniformis luciferase. Biochemistry, 16, 85-91.
53. Srikantha,T., Klapach,A., Lorenz,W.W., Tsai,L.K., Laughlin,L.A., Gorman,J.A. and Söll,D.R. (1996) The sea pansy Renilla reniformis luciferase serves as a sensitive bioluminescent reporter for differential gene expression in Candida albicans. J. Bacteriol., 178, 121-129.
54. Tanguay,R.L. and Gallie,D.R. (1996) Translational efficiency is regulated by the length of the 3′ untranslated region. Mol. Cell. Biol., 16, 146-156.
55. Ikemura,T. (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol., 2, 13-34.
56. Percudani,R., Pavesi,A. and Ottonello,S. (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol., 268, 322-330.
57. Wilson,D.N., Guevremont,D. and Tate,W.P. (2000) The ribosomal binding and peptidyl-tRNA hydrolysis functions of Escherichia coli release factor 2 are linked through residue 246. RNA, 6, 1704-1713.
58. Dincbas-Renqvist,V., Engstrom,A., Mora,L., Heurgue-Hamard,V., Buckingham,R. and Ehrenberg,M. (2000) A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation. EMBO J., 19, 6900-6907.
59. Sharp,P.M., Bailes,E., Grocock,R.J., Peden,J.F. and Sockett,R.E. (2005) Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res., 33, 1141-1153.
60. Urbonavicius,J., Qian,O., Durand,J.M.B., Hagervall,T.G. and Bjork,G.R. (2001) Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J., 20, 4863-4873.
61. Fahlman,R.P., Dale,T. and Uhlenbeck,O.C. (2004) Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites. Mol. Cell, 16, 799-805.
62. Lys. Nature Struct. Mol. Biol., 11, 1186-1191.
63. Vestergaard,B., Van,L.B., Andersen,G.R., Nyborg,J., Buckingham,R.H. and Kjeldgaard,M. (2001) Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol. Cell, 8, 1375-1382.
64. Rawat,U.B.S., Zavialov,A.V., Sengupta,J., Valle,M., Grassucci,R.A., Linde,J., Vestergaard,B., Ehrenberg,M. and Frank,J. (2003) A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature, 421, 87-90.
65. Klaholz,B.P., Pape,T., Zavialov,A.V., Myasnikov,A.G., Orlova,E.V., Vestergaard,B., Ehrenberg,M. and Van Heel,M. (2003) Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature, 421, 90-94.
66. Song,H.W., Mugnier,P., Das,A.K., Webb,H.M., Evans,D.R., Tuite,M.F., Hemmings,B.A. and Barford,D. (2000) The crystal structure of human eukaryotic release factor eRF1- Mechanismof stop codon recognition and peptidyl-tRNA hydrolysis. Cell, 100, 311-321.
67. Gly at the ribosomal P-site and RF1 during termination at UAG. J. Mol. Biol., 284, 1243-1246.
68. Petry,S., Broderson,D.E., Murphy,F.V., Dunham,C.M., Selmer,M., Tarry,M.J., Kelley,A.C. and Ramakrishnan,V. (2005) Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell, 123, 1-12.
69. Ozawa,Y., Saito,R., Washio,T. and Tomita,M. (2003) Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes. J. Mol. Evol., 56, 665-672.
70. Liu,Q. (2005) Comparative analysis of biases around stop codons in six eukaryotes. BioSystems, 81, 281-289.
71. Jin,H.N., Bjornsson,A. and Isaksson,L.A. (2002) Cis control of gene expression in E.coli by ribosome queuing at an inefficient translational stop signal. EMBO J., 21, 4357-4367.
72. Sonenberg,N. and Dever,T.E. (2003) Eukaryotic translation initiation factors and regulators. Curr. Opin. Struct. Biol., 13, 56-63.
73. Jacobson,A. and Peltz,S.W. (1996) Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. Annu. Rev. Biochem., 65, 693-739.
74. Amrani,N., Ganesan,R., Kervestin,S., Mangus,D.A., Ghosh,S. and Jacobson,A. (2004) A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature, 432, 112-118.
75. Sprinzl,M. and Vassilenko,K.S. (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 33, D139-140.