Codon evolution is governed by linear formulas

Abstract

When nucleotide (G, C, T and A) contents were plotted against each nucleotide, their relationships were clearly expressed by a linear formula, y = alphax + beta in the coding and non-coding regions. This linear relationship was obtained from the complete single-stranded DNA. Similarly, nucleotide contents at all three codon positions were expressed by linear regression lines based on the content of each nucleotide. In addition, 64 codon usages were also expressed by linear formulas against nucleotide content. Thus, the nucleotide content not only in coding sequence but also in non-coding sequence can be expressed by a linear formula, y = alphax + beta, in 145 organisms (112 bacteria, 15 archaea and 18 eukaryotes). Based on these results, the ratio of C/T, G/T, C/A or G/A one can essentially estimate all four nucleotide contents in the complete single-stranded DNA, and the determination of any ratio of two kinds of nucleotides can essentially estimate four nucleotide contents, nucleotide contents at the three different codon positions and codon distributions at 64 codons in the coding region. The maximum and minimum values of G content were approximately 0.35 and approximately 0.15, respectively, among various organisms examined. Codon evolution occurs according to linear formulas between these two values.

Organisms can essentially be classified according to two codon patterns

“…5a-c). The consistent results were obtained from nucleotide alternations in various organisms (Sorimachi and Okayasu 2008a). Thus, biological evolution can be said to progress differently among different kingdoms.…”

“…2), biological evolution progresses under this form of control in all organisms. Correlations between the contents of each nucleotide in a genome can be expressed by linear formulas (Sorimachi and Okayasu 2008a). Eukaryotes, archaea and bacteria behaved differently from each other in respect of correlations of certain amino acid concentrations with nucleotide contents (Fig.…”

“…We recently showed that correlations between the contents of each nucleotide in a genome can be expressed by linear formulas (Sorimachi and Okayasu 2008a). The genomic GC content is strongly correlated with the average amino acid composition of proteins (Sueoka 1961), which is theoretically supported by Lobry (1997).…”

Natural selection in vertebrate evolution under genomic and biosphere biases based on amino acid content: Primitive vertebrate hagfish (<i>Eptatretus burgeri</i>)

“…These results indicated that alternations in nucleotide content were controlled by internal biases that, in the cluster analyses, resulted in the formation of several clusters. Because nucleotide alternations are strictly governed by linear formulae in both the coding and non-coding regions [11], the codon usage pattern of an organism can be estimated by the insertion of its nucleotide content into a specific linear formula [9]. If the nucleotide alternations had occurred at random in the genomes of the selected organisms, such a clear separation between the terrestrial and aquatic vertebrates might not have been observed in the cluster analyses.…”

“…It has been reported that in complete single-stranded DNA genomes, the nucleotide content alternations were strictly controlled, and were expressed by linear regression lines of nucleotide content relationships in both coding and non-coding regions [9]. In addition, Chargaff's second parity rule [10] was confirmed for a large number of complete double-stranded DNA genomes, and the nucleotide content relationships were expressed by linear formulas [11].…”