Codon evolution in double-stranded organelle DNA: strong regulation of homonucleotides and their analog alternations

Kenji Sorimachi
DOI: 10.4236/ns.2010.28106                

Abstract

In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondria deviated from the rule. On the other hand, plant mitochondria obeyed another different rule after their classification. Complete single DNA strand sequences obtained from chloroplasts, plant mitochondria, and animal mitochondria, were divided into the coding and non-coding regions. The non-coding region, which was the complementary coding region on the reverse strand, was incorporated as a coding region in the forward strand. When the nucleotide contents of the coding region or non-coding regions were plotted against the composition of the four nucleotides in the complete single DNA strand, it was determined that chloroplast and plant mitochondrial DNA obeyed Chargaff’s second parity rule in both the coding and non-coding regions. However, animal mitochondrial DNA deviated from this rule. In chloroplast and plant mitochondrial DNA, which obey Chargaff’s second parity rule, the lines of regression for G (purine) and C (pyrimidine) intersected with regression lines for A (purine) and T (pyrimidines), respectively, at around 0.250 in all cases. On the other hand, in animal mitochondrial DNA, which deviates from Chargaff’s second parity rule, only regression lines due to the content of homonucleotides or their analogs in the coding or non-coding region against those in the complete single DNA strand intersected at around 0.250 at the horizontal axis. Conversely, the intersection of the two lines of regression (G and A or C and T) against the contents of heteronucleotides or their analogs shifted from 0.25 in both coding and non-coding regions. Nucleotide alternations in chloroplasts and plant mitochondria are strictly regulated, not only by the proportion of homonucleotides and their analogs, but also by the heteronucleotides and their analogs. They are strictly regulated in animal mitochondria only by the content of homonucleotides and their analogs.

Keywords

Codon evolution in double-stranded organelle DNA: strong regulation of homonucleotides and their analog alternations

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Rudner, R., Karkas, J.D. and Chargaff, E. (1968) Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proceedings of the National Academy Sciences, 60(3), 921-922.
[2]	Sorimachi, K. (2009) A proposed solution to the historic puzzle of Chargaff’s second parity rule. The Open Genomics Journal, 2(3), 12-14.
[3]	Sorimachi, K. and Okayasu, T. (2004) An evaluation of evolutionary theories based on genomic structures in Saccharomyces cerevisiae and Encephalitozoon cuniculi. Mycoscience, 45(5), 345-350.
[4]	Sorimachi, K. and Okayasu, T. (2008) Codon evolution is governed by linear formulas. Amino Acids, 34(4), 661- 668.
[5]	Chargaff, E. (1950) Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experimentia, 6(6), 201-209.
[6]	Bell, S.J. and Forsdyke, D.R. (1999) Deviations from Chargaff’s second parity rule with direction of transcription. The Journal of Theoretical Biology, 197(1), 63-76.
[7]	Nikolaou, C. and Almirantis, Y. (2006) Deviations from Chargaff’s second parity rule in organelle DNA insights into the evolution of organelle genomes. Gene, 381, 34-41.
[8]	Mitchell, D. and Bridge, R. (2006) A test of Chargaff’s second rule. Biochemical and Biophysical Research Communications, 340(1), 90-94.
[9]	Yang, D., Oyaizu, Y., Oyaizu, H., Olsen, G.J. and Woese, C.R. (1985) Mitochondrial origins. Proceedings of National Academy Sciences, 82(13), 4443-4447.
[10]	Lang, B.F., Burger, G., O’Kelly, C.J., Cedergren, R., Golding, B., Lemieux, C., et al. (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature, 387(6632), 493-497.
[11]	Raven, J.A. and Douglas, A.E. (2003) Genomes at the interface between bacteria and organelles. Philosophical Transactions of Royal Society London. Series B, Biological Science, 358(1429), 5-18.
[12]	Sorimachi, K. (2010) Genomic data provides simple evidence for a single origin of life. Natural Science, 2(5), 521-527.
[13]	Sorimachi, K. and Okayasu, T. (2008) Universal rules governing genome evolution expressed by linear formulas. The Open Genomics Journal, 1(11), 33-43.
[14]	Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409(6822), 860-921.
[15]	Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., et al. (2001) The sequence of the human genome. Science, 291(5507), 1304-1351.
[16]	Sea urchin genome sequencing consortium. (2006) The genome of the sea urchin strongylocentrotus purpuratus. Science, 314(5801), 941-952.
[17]	Szybalski, W., Kubinski, H. and Sheldrick, P. (1966) Pyrimidine clusters on the transcribing strand of DNA and their possible role in the initiation of RNA synthesis. Cold Spring Harbor Symposia on Quantitative Biology, 31, 123-127.
[18]	Sorimachi, K. and Okayasu, T. (2004) Classification of eubacteria based on their complete genome: Where does mycoplasmataceae belong? Proceedings of the Royal Society of London. B (Supplement), 271(4), S127-S130.
[19]	Watson, J.D. and Crick, F.H.C. (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature, 171(4361), 964-967.
[20]	Sorimachi, K. and Okayasu, T. (2003) Gene assembly consisting of small units with similar amino acid composition in the Saacharomyces cerevisiae genome. Mycoscience, 44(5), 415-417.