The tri-frame model

Journal of Theoretical Biology

Volumn 251, Issue 4, 2008, Pages 616-627

  Pienaar, Elsje ^a   Viljoen, Hendrik J ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

Error prediction; Frameshifting; Mathematical model; Transcription; Translation

Indexed keywords

AMINO ACID; DNA; MESSENGER RNA; NUCLEOTIDE; POLYPEPTIDE; RNA POLYMERASE;

AMINO ACID; COLIFORM BACTERIUM; DNA; ENZYME; GENE EXPRESSION; MUTATION; NUMERICAL MODEL; PROTEIN; RNA;

ANALYTICAL ERROR; ARTICLE; CODON; ESCHERICHIA COLI; FRAMESHIFT MUTATION; GENE MUTATION; MATHEMATICAL MODEL; OPEN READING FRAME; OPERON; PRIORITY JOURNAL; RIBOSOMAL FRAMESHIFTING; RIBOSOME;

AMINO ACIDS; ANIMALS; FRAMESHIFT MUTATION; HUMANS; MODELS, GENETIC; OPEN READING FRAMES; PROTEIN BIOSYNTHESIS; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 41049117755     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2007.12.003     Document Type: Article

References (33)

1. Andersson S.G.E., and Kurland C.G. Codon preferences in free-living organisms. Microbiol. Rev. 54 (1990) 198-210
2. Antezana M.A., and Kreitman M. The nonrandom location of synonymous codons suggests that reading frame-independent forces have patterned codon preferences. J. Mol. Evol. 49 (1999) 36-43
3. Archetti M. Selection on codon usage for error minimization at the protein level. J. Mol. Evol. 59 (2004) 400-415
4. Crick F.H., Barnett L., Brenner S., and Watts-Tobin R.J. General nature of the genetic code. Nature 192 (1961) 1227-1232
5. Cserzo M., and Simon I. Regularities in the primary structure of proteins. Int. J. Peptide Res. 34 (1989) 184-195
6. Dong H., Nilsson L., and Kurland C.G. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 260 (1996) 649-663
7. Farabaugh P.J. Programmed Alternative Reading of the Genetic Code (1997), Springer, Heidelberg, Germany
8. Fluitt A., Pienaar E., and Viljoen H.J. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput. Biol. Chem. 31 (2007) 335-346
9. Gromadski K.B., and Rodnina M. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13 (2004) 191-200
10. Hansen T.M., Baranov P.V., Ivanov I.P., Gesteland R.F., and Atkins J.F. Maintenance of the correct open reading frame by the ribosome. EMBO Rep. 4 (2003) 499-504
11. Harger J.W., Meskauskas A., and Dinman J.D. An 'integrated model' of programmed ribosomal frameshifting. Trends Biochem. Sci. 27 (2002) 448-454
12. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2 (1985) 13-34
13. Konigsberg W., and Godson N. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc. Natl. Acad. Sci. USA 80 (1983) 687-691
14. Konopka A.K. Theory of degenerate coding and informational parameters of protein coding genes. Biochimie 67 (1985) 455-468
15. Kramer E.B., and Farabaugh P.J. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA 13 (2007) 87-96
16. Kurland C.G. In: Celis J.E., and Smith J.D. (Eds). Nonsense Mutations and tRNA Supressors (1979), Academic Press, New York 97-108
17. Lindsley D., Gallant J., Doneanu C., Nonthuis P., Caldwell S., and Fontelera A. Spontaneous ribosome bypassing in growing cells. J. Mol. Biol. 349 (2005) 261-272
18. Looman A.C., Bodlaender J., Comstock L.J., Eaton D., Jhurani P., de Boer J.A., and van Knippenberg P.H. Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in E. coli. EMBO J. 6 (1987) 2489-2492
19. Manley J.L. Synthesis and degradation of termination and premature-termination fragments of β-galactosidase in vitro and in vivo. J. Mol. Biol. 125 (1978) 407-432
20. Marquez V., Wilson D.N., Tate W.P., Triana-Alonso F., and Nierhaus K.H. Maintaining the ribosomal reading frame: the influence of the E site during translational regulation of release factor 2. Cell 118 (2004) 45-55
21. Marquez R., Smit S., and Knight R. Do universal codon-usage patterns minimize the effects of mutation and translation error?. Genome Biol. 6 (2005) R91
22. Marshall R.E., Caskey C.T., and Nirenberg M. Fine structure of RNA code words recognized by bacterial, amphibian, and mammalian transfer RNA. Science 155 (1967) 820-826
23. Nirenberg M., Caskey T., Marshall R., Brimacombe R., Kellogg D., Doctor B., Hatfield D., Levin J., Rottman F., Pestka S., Wilcox M., and Anderson F. RNA code words and protein synthesis. Cold Spring Harb. Symp. Quant. Biol. 31 (1966) 11-24
24. Parker J. Errors in reading the universal code. Microbiol. Rev. 53 (1989) 273-298
25. Sato T., Terabe M., Watanabe H., Gojobori T., Hori-Takemoto C., and Miura K.-I. Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency. J. Biochem. 129 (2001) 851-860
26. Seligmann H., and Pollock D.D. The ambush hypothesis: off frame stop codons arrest early accidental frameshifted transcription. DNA Cell Biol. 23 (2004) 701-705
27. Sharp P.M., Cow E., Higgins D.G., Shields D.C., Wolfe K.H., and Wright F. Codon usage patterns in Escherichia coli, Bacillus subtilus, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens: a review of the considerable within species diversity. Nucl. Acids Res. 16 (1988) 8207-8211
28. Sipley J., and Goldman E. Increased ribosomal accuracy increases a programmed translational frameshift in Escherichia coli. Proc. Natl. Acad. Sci. USA 90 (1993) 2315-2319
29. Stahl G., McCarty G.P., and Farabaugh P.J. Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding. Trends Biochem. Sci. 27 (2002) 178-183
30. Stenström C.M., and Isaksson L.A. Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3′ side. Gene 288 (2002) 1-8
31. Stenström C.M., Jin H., Major L.L., Tate W.P., and Isaksson L.A. Codon bias at the 3′-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli. Gene 263 (2001) 273-284
32. Tsuchihashi Z. Translational frameshifting in the Escherichia coli dnaX gene in vitro. Nucl. Acids Res. 19 (1991) 2457-2462
33. Weiss R., Dunn D., Atkins J., and Gesteland R. The ribosome rubbish. In: Hill W.E., Dahlberg A., Garrett R.A., Moore P.B., Sclessinger D., and Warner J.R. (Eds). The Ribosome: Structure, Function, and Evolution (1990), American Society of Microbiology, Washington, DC 534-540