Codon evolution is governed by linear formulas

• Published in: Amino acids 2008-05, Vol.34 (4), p.661-668
• Main Authors: Sorimachi, K, Okayasu, T
• Format: Article
• Language: English
• Subjects: Amino Acids - genetics; Analytical Chemistry; Animals; Arabidopsis - genetics; Base Composition - genetics; Base Sequence; Biochemical Engineering; Biochemistry; Biomedical and Life Sciences; Computational Biology; Computer Simulation; Databases, Genetic; Deoxyribonucleic acid; DNA; DNA - genetics; Escherichia coli - genetics; Evolution, Molecular; Genetic Code - genetics; Life Sciences; Linear Models; Mycobacterium tuberculosis - genetics; Neurobiology; Nucleotides - genetics; Original Article; Plasmodium falciparum - genetics; Proteomics; Reproducibility of Results; Sensitivity and Specificity; Software; Studies; Treponema pallidum - genetics; Ureaplasma urealyticum - genetics
• ISSN: 0939-4451; 1438-2199
• DOI: 10.1007/s00726-007-0024-3

When nucleotide (G, C, T and A) contents were plotted against each nucleotide, their relationships were clearly expressed by a linear formula, y = αx + β 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 = αx + β, 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 ~0.35 and ~0.15, respectively, among various organisms examined. Codon evolution occurs according to linear formulas between these two values.