G and T nucleotide contents show specie-invariant negative correlation for all three codon positions.
The nucleotide contents of the three codon positions show a number of statistical pairwise correlations, some of which are universal for all analysed genomes. Among the most prominent of these correlations are negative correlations between G and T contents found in genes of all species analysed. The pair A/C, which is complementary to G/T shows similar negative correlation in genes of most species. In the genes of several species including all mammalian genes studied, positive correlations between A and T contents, and G and C contents are found. Since these regularities are observed in all three codon positions they are connected with amino-acid content of proteins. Such correlations may origin from features of the mutation process or/and translation reading frame check. The well-known bias of the preference for G in the first codon position and its deficiency in the second is accompanied by opposite bias in T content. In the third codon position there is no general nucleotide preference, but its content is often biased with regard to GC content of the gene. G and T contents in this case are always shifted in the opposite directions Several ideas are drawn to explain this preference.
Frank
G K
GK
V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. gleb@imb.imb.ac.ru
Makeev
V J
VJ
D000818:Animals; D001419:Bacteria / Q000235:genetics; D001482:Base Composition; D003062:Codon / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D005796:Genes; D006147:Guanine / Q000737:chemistry*; D051379:Mice; D008956:Models, Chemical; D013045:Species Specificity; D013941:Thymine / Q000737:chemistry*
D003062:Codon; D006147:Guanine; D004247:DNA; D013941:Thymine