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Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses

Authors
Journal
Gene
0378-1119
Publisher
Elsevier
Publication Date
Volume
300
Identifiers
DOI: 10.1016/s0378-1119(02)01046-6
Keywords
  • Pr2 Biases
  • Dna G+C Content
  • 8-Oxo-Guanine
  • Cpg Methylation/Deamination
  • Preferred Codon
  • Unpreferred Codon
Disciplines
  • Biology

Abstract

Abstract The intra-strand Parity Rule 2 of DNA (PR2) states that A= T and G= C within each strands. Useful corollaries of PR2 are G/( G+ C)= A/( A+ T)=0.5, G/( G+ A)= C/( C+ T)= G+C, G/( G+ T)= C/( C+ A)= G+ C. Here. A, T, G, and C represent relative contents of the four nucleotide residues in a specific strand of DNA, so that A+ T+ G+ C=1. Thus, deviations from the PR2 is a sign of strand-specific (or asymmetric) mutation and/or selection pressures. The present study delineates the symmetric and asymmetric effects of mutations on the intra-genomic heterogeneity of the G+C content in the human genome. The results of this study on the human genome are: (1) When both two- and four-codon amino acids were combined, only slight departures from the PR2 were observed in the total ranges of G+C content of the third-codon position. Thus, the G+C heterogeneity is likely to be caused by symmetric mutagenesis between the two strands. (2) The above result makes the deamination of cytosine due to double-strand breathing of DNA [Mol. Biol. Evol. 17 (2000) 1371] and/or incorporation of the oxidized guanine (8-oxo-guanine) opposite adenine during DNA replication (dGTP-oxidation hypothesis) as the most likely candidates for the major cause of the diversities of the G+C content. (3) Patterns of amino acid-specific PR2-biases detected by plotting PR2 corollaries against the G+C content of third codon position revealed that eight four-codon amino acids can be divided into three types by the second codon letter: (a) C 2-type (Ala, Pro, Ser4, and Thr), (b) G 2-type (Arg4 and Gly), and (c) T 2-type (Leu4 and Val). (4) Most of the asymmetric plot patterns of the above three classes in PR2 biases can be explained by C 2→T 2 deamination of C 2pG 3 of C 2-type to T 2pG 3 (T 2-type) in both human and chicken. This explains the existence of some preferred codons in human and chicken. However, these biases (asymmetric) hardly contribute to the overall G+C content diversity of the third codon position.

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