An evolutionary perspective on synonymous codon usage in unicellular organisms (original) (raw)

• Bennetzen JL, Hall BD (1982) Codon selection in yeast. J Biol Chem 257:3026–3031
  PubMed Google Scholar
• Bernardi G, Bernardi G (1985) Codon usage and genome composition. J Mol Evol 22:363–365
  Google Scholar
• Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953–958
  PubMed Google Scholar
• Bibb MJ, Findlay PR, Johnson MW (1984) The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene 30:157–166
  Article PubMed Google Scholar
• Bonekamp F, Andersen HD, Christensen T, Jensen KF (1985) Codon-defined ribosomal pausing in_Escherichia coli_ detected by using the pyrE attenuator to probe the coupling between transcription and translation. Nucleic Acids Res 13:4113–4123
  PubMed Google Scholar
• Bulmer M (1986) Neighbouring base effects on substitution rates in pseudogenes. Mol Biol Evol 3:322–329
  PubMed Google Scholar
• Fitch WM (1976) Is there selection against wobble in codon-anticodon pairing? Science 194:1173–1774
  PubMed Google Scholar
• Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10:7055–7074
  PubMed Google Scholar
• Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8:r49-r62
  PubMed Google Scholar
• Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 9:r43-r79
  PubMed Google Scholar
• Grantham R, Greenland T, Louail S, Mouchiroud D, Prato JL, Gouy M, Gautier C (1985) Molecular evolution of viruses as seen by nucleic acid sequence study. Bull Inst Pasteur 83:95–148
  Google Scholar
• Gribskov M, Devereux J, Burgess RR (1984) The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res 12:539–549
  PubMed Google Scholar
• Grosjean H, Fiers W (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18:199–209
  Article PubMed Google Scholar
• Hastings KEM, Emerson CP Jr (1983) Codon usage in muscle genes and liver genes. J Mol Evol 19:214–218
  PubMed Google Scholar
• Hinds PW, Blake RD (1985) Delineation of coding areas in DNA sequences through assignment of codon probabilities. J Biomol Struct Dyn 3:543–549
  PubMed Google Scholar
• Honess RW, Bodemer W, Cameron KR, Niller H-H, Fleckenstein B, Randall RE (1986) The A+T-rich genome of_Herpesvirus saimiri_ contains a highly conserved gene for thymidylate synthase. Proc Natl Acad Sci USA 83:3604–3608
  PubMed Google Scholar
• Ikemura T (1981a) Correlation between the abundance of_Escherichia coli_ transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 146:1–21
  Article PubMed Google Scholar
• Ikemura T (1981b) Correlation between the abundance of_Escherichia coli_ transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the_E. coli_ translational system. J Mol Biol 151:389–409
  Article PubMed Google Scholar
• Ikemura T (1982) Correlation between the abundance of yeast tRNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and_Escherichia coli_ with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol 158:573–598
  Article PubMed Google Scholar
• Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2;13–34
  PubMed Google Scholar
• Kimura M (1968) Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral alleles. Genet Res 11:247–269
  PubMed Google Scholar
• Kimura M (1981) Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons. Proc Natl Acad Sci USA 78:5773–5777
  PubMed Google Scholar
• Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England
  Google Scholar
• Kimura M (1986) DNA and the neutral theory. Philos Trans R Soc Lond [Biol] 312:343–354
  Google Scholar
• King JL, Jukes TH (1969) Non-Darwinian evolution. Science 164:788–798
  PubMed Google Scholar
• Konigsberg W, Godson GN (1983) Evidence for use of rare codons in the dnaG gene and other regulatory genes of_Escherichia coli_. Proc Natl Acad Sci USA 80:687–691
  PubMed Google Scholar
• Li W-H (1987) Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J Mol Evol, in press
• Li W-H, Wu C-I, Luo C-C (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol 21:58–71
  PubMed Google Scholar
• Li W-H, Luo C-C, Wu C-I (1985a) Evolution of DNA sequences. In: MacIntyre RJ (ed) Molecular evolutionary genetics. Plenum, New York, pp 1–94
  Google Scholar
• Li W-H, Wu C-I, Luo C-C (1985b) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150–174
  PubMed Google Scholar
• Lipman DJ, Wilbur WJ (1985) Interaction of silent and replacement changes in eucaryotic coding sequences. J Mol Evol 21:161–167
  Google Scholar
• Lopes JM, Lawther RP (1986) Analysis and comparison of the internal promoter, pE, of the ilvGMEDA operons from_Escherichia coli_ and_Salmonella typhimurium_. Nucleic Acids Res 14:2779–2798
  PubMed Google Scholar
• McConnell DJ, Cantwell BA, Devine KM, Forage AJ, Laoide BM, O'Kane C, Ollington JF, Sharp PM (1986) Genetic engineering of extracellular enzyme systems of Bacilli. Ann NY Acad Sci 469:1–17
  Google Scholar
• Normore WM (1973) Guanine-plus-cytosine (GC) composition of the DNA of bacteria, fungi, algae and protozoa. In: Laskin AI, Lechevalier HA (eds) Handbook of microbiology, vol 2: microbial components. CRC Press, Cleveland, pp 585–740
  Google Scholar
• Nussinov R (1984) Doublet frequencies in evolutionary distinct groups. Nucleic Acids Res 12:1749–1763
  PubMed Google Scholar
• Ogasawara N (1985) Markedly unbiased codon usage in_Bacillus subtilis_. Gene 40:145–150
  Article PubMed Google Scholar
• Robinson M, Lilley R, Little S, Emtage JS, Yarranton G, Stephens P, Millican A, Eaton M, Humphreys G (1984) Codon usage can affect efficiency of translation of genes in_Escherichia coli_. Nucleic Acids Res 12:6663–6671
  PubMed Google Scholar
• Schaaper RM, Danforth BN, Glickman BW (1986) Mechanisms of spontaneous mutagenesis: an analysis of the spectrum of spontaneous mutation in the_Escherichia coli_ lacI gene. J Mol Biol 189:273–284
  Article PubMed Google Scholar
• Sharp PM, Li W-H (1986) Codon usage in regulatory genes in_Escherichia coli_ does not reflect selection for “rare” codons. Nucleic Acids Res 14:7734–7749
  Google Scholar
• Sharp PM, Li W-H (1987) The rate of synonymous substitution in Enterobacterial genes inversely related to codon usage bias. Mol Biol Evol, in press
• Sharp PM, Rogers MS, McConnell DJ (1985) Selection pressures on codon usage in the complete genome of bacteriophage T7. J Mol Evol 21:150–160
  Google Scholar
• Sharp PM, Tuohy TMF, Mosurski KR (1986) Codon usage in yeast: Cluster analysis clearly differentiates between highly and lowly expressed genes. Nucleic Acids Res 14:5125–5143
  PubMed Google Scholar
• Varenne S, Lazdunski C (1986) Effect of distribution of unfavourable codons on the maximum rate of gene expression by an heterologous organism. J Theor Biol 120:99–110
  PubMed Google Scholar