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Evolution from Primitive Life to Homo sapiens Based on Visible Genome Structures: The Amino Acid World

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DOI: 10.4236/ns.2009.12013    5,668 Downloads   10,870 Views   Citations
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It is not too much to say that molecular biology, including genome research, has progressed based on the determination of nucleotide or amino acid sequences. However, these ap-proaches are limited to the analysis of relatively small numbers of the same genes among spe-cies. On the other hand, by graphical presenta-tion of the ratios of the numbers of amino acids present to the total numbers of amino acids presumed from the target gene(s) or genome or those of the numbers of nucleotides present to the total numbers of nucleotides calculated from the target gene(s) or genome, we can readily draw conclusions from extraordinarily huge data sets integrated by human intelli-gence. 1) Assuming polymerization of amino acids or nucleotides in a simulation analysis based on a random choice, proteins were formed by simple amino acid polymerization, while nucleotide polymerization to form nucleic acids encoding specific proteins needed certain specific control. These results proposed that protein formation chronologically preceded codon formation during the establishment of primitive life forms. In the prebiotic phase, amino acid composition was a dominant factor that determined protein characteristics; the “Amino Acid World”. 2) The genome is constructed homogeneou- sly from putative small units displaying similar codon usages and coding for similar amino acid compositions; the unit is a gene assembly en-coding 3,000 - 7,000 amino acid residues and this unit size is independent not only of genome size, but also of species. 3) In codon evolution, all nucleotide alterna-tions are correlated, not only in coding regions, but also in non-coding regions; the correlations can be expressed by linear formulas; y = ax + b, where “y” and “x” represent nucleotide con-tents, and “a” and “b” are constant. 4) The basic pattern of cellular amino acid compositions obtained from whole cell lysates is conserved from bacteria to Homo sapiens, and resembles that calculated from complete genomes. This basic pattern is characterized by a “star-shape” that changes slightly among species, and changes in amino acid composi-tion seem to reflect biological evolution. 5) Organisms can essentially be classified according to two codon patterns. Biological evolution due to nucleotide sub-stitutions can be expressed by simple linear formulas based on mathematical principles, while natural selection must affect species pre- servation after nucleotide alternations. There-fore, although Darwin’s natural selection is not directly involved in nucleotide alternations, it contributes obviously to the selection of nu-cleotide alternations. Thus, Darwin’s natural selection is doubtless an important factor in biological evolution.

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Sorimachi, K. (2009) Evolution from Primitive Life to Homo sapiens Based on Visible Genome Structures: The Amino Acid World. Natural Science, 1, 107-119. doi: 10.4236/ns.2009.12013.


[1] Sanger, F. and Thompson, E.O. (1953) The amino acid sequence in the glycyl chain of insulin. I. The identifica-tion of lower peptides from partial hydrolysates. Biochem. J., 53, 353-366.
[2] Sanger F. and Thompson, E.O. (1953) The amino acid sequence in the glycyl chain of insulin. II. The investiga-tion of peptides from enzymic hydrolysates. Biochem. J , 53, 366-374.
[3] Sanger, F. and Coulson, A.R. (1975) A rapid method for determing sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol., 94, 441-446.
[4] Maxam, A.M. and Gilbert, W. (1977) A new method for sequencing DNA. Proc. Natl. Acad. Sci., USA 74, 560-564.
[5] Zuckerkandl, E. and Pauling, L.B. (1962) Molecular disease, evolution, and genetic heterogeneity in Kasha M and Pullman B (editors). Horizons in Biochemistry, Aca-demic Press, New York, 189-225.
[6] Sorimachi, K. (2009) A proposed solution to the historic puzzle of Chargaff’s second parity rule. Open Genom. J., 2, 12-14.
[7] Chou, K-C. and Zhang, C.T. (1992) Diagrammatization of codon usage in 339 HIV proteins and its biological implication. AIDS Research and Human Retroviruses, 8, 1967-1976.
[8] Zhang, C-T. and Chou, K-C. (1993) Graphic analysis of codon usage strategy in 1490 human proteins. J. Prot. Chem., 12, 329-335.
[9] Sorimachi, K. and Okayasu, T. (2004) An evolutionary theories based on genomic structures in Saccharomyces cerevisiae and Enchephalitozoon cuniculi. Mycoscience , 45, 345-350.
[10] Sorimachi, K. and Okayasu, T. (2007) Genomic structure is homogeneous based on codon usages. Curr. Top. Pep. Protein Res., 8, 19-24.
[11] Sorimachi, K. and Okayasu, T. (2008) Codon evolution is governed by linear formulas. Amino Acids, 34, 661-668.
[12] Sorimachi, K. and Okayasu, T. (2008) Universal rules governing genome evolution expressed by linear formu-las. Open Genom. J., 1, 33-43.
[13] Chou, K-C. (1983) Advances in graphical methods of enzyme kinetics. Biophys. Chem., 17, 51-55.
[14] Chou, K-C. (1989) Graphical rules in steady and non-steady enzyme kinetics. J. Biol. Chem., 264, 12074- 12079.
[15] Chou, K-C. (1990). Review: Applications of graph the-ory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophys. Chem., 35, 1-24.
[16] Chou, K-C. (1993) Graphic rule for non-steady-state enzyme kinetics and protein folding kinetics. J. Math. Chem., 12, 97-108.
[17] Lin, S.X. and Neet, K.E. (1990) Demonstration of a slow conformational change in liver glucokinase by fluores-cence spectroscopy. J. Biol. Chem., 265, 9670-5.
[18] Zhou, G.P. and Deng, M.H. (1984) An extension of Chou's graphical rules for deriving enzyme kinetic equa-tions to system involving parallel reaction pathways. Biochem. J., 222, 169-176.
[19] Althaus, I.W., Chou, J.J., Gonzales, A.J. et al. (1993) Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochemistry, 32, 6548-6554.
[20] Chou, K-C., Kezdy, F.J. and Reusser, F. (1994) Review: Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Anal. Biochem., 221, 217- 230.
[21] Qi, X.Q., Wen, J. and Qi, Z.H. (2007) New 3D graphical representation of DNA sequence based on dual nucleo-tides. J. Theoret. Biol., 249, 681–690.
[22] MacGregor, I.M., Truswell, J.F. and Eriksson, K.A. (1974) Filamentous alga from the 2,300 m.y. old Trans-vaal Dolomite. Nature, 247, 538-539.
[23] Nagy, L.A. and Zumberge, J.E. (1976) Fossil microor-ganisms from the approximately 2800 to 2500 million- year-old Bulawayan stromatolite: Application of ultrami-crochemical analyses. Proc. Natl. Acad. Sci. USA, 73, 2973-2976.
[24] Schopf, J.W., Barghoorn, E.S., Maser, M.D. and Gordon, R.O. (1965) Electron microscopy of fossil bacteria two billion years old. Science, 149, 1365-1367.
[25] Johanson, D.C. and Taieb, M. (1976) Plio-Pleistocene hominid discoveries in Hadar, Ethiopia. Nature, 260, 293-297.
[26] Watson, J.D. and Crick, F.H.C. (1953) Genetical implica-tions of the structure of deoxyribonucleic acid. Nature, 171, 964-967.
[27] Sueoka, N. (1961) Correlation between base composition of deoxyribonucleic acid and amino acid composition in proteins. Proc. Natl. Acad. Sci. USA, 47, 1141-1149.
[28] Sorimachi, K. (1999) Evolutionary changes reflected by the cellular amino acid composition. Amino Acids, 17, 207-226.
[29] Sorimachi, K., Itoh, T., Kawarabayasi, Y., Okayasu, T., Akimoto, K. and Niwa, A. (2001) Conservation of the basic pattern of cellular amino acid composition during biological evolution and the putative amino acid compo-sition of primitive life forms. Amino Acids, 21, 393-399.
[30] Sorimachi, K., Okayasu, T., Akimoto, K. and Niwa, A. (2000) Conservation of the basic pattern of cellular amino acid composition during biological evolution in plants. Amino Acids, 18, 193-196.
[31] Sorimachi, K. (2002) The classification of various or-ganisms according to the free amino acid composition change as the result of biological evolution. Amino Acids, 22, 55-69.
[32] Woese, C.R. (1965) Order in the genetic code. Proc. Natl. Acad. Sci. USA, 54, 71-75.
[33] Crick, F.H.C. (1968) The origin of genetic code. J. Mol. Biol., 38, 367-379.
[34] Wong, J.T-F. (1975) A co-evolutionary theory of the genetic code. Proc. Natl. Acad. Sci. USA, 72, 1909-1912.
[35] Lahav, N., White, D. and Chang, S. (1978) Peptide for-mation in the prebiotic era: thermal condensation of gly-cine in fluctuating clay environments. Science, 201, 67-69.
[36] Sorimachi, K. and Okayasu, T. (2007) Mathematical proof of the chronological precedence of protein forma-tion over codon formation. Curr. Top. Pep. Protein Res., 8, 25-34.
[37] Miller, S.L. (1953) A production of amino acids under possible primitive earth conditions. Science, 117, 528- 529.
[38] Kvenvolden, K., Lawless, J., Pering, K., Peterson, E., Flores, J., Ponnamperuma, C., Kaplan, I.R. and Moore, C. (1970) Evidence for extraterrestrial amino-acids and hy-drocarbons in the Murchison meteorite. Nature, 228, 923-926.
[39] Wolman, Y., Haverland, W. and Miller, S.L. (1972) Non-protein amino acids from spark discharges and their comparison with the Muchison meteorite amino acids. Proc. Natl. Acad. Sci. USA, 69, 809-811.
[40] Sorimachi, K. and Ui, N. (1975) Ion-exchange chroma-tographic analysis of iodothyronines. Anal. Biochem., 67, 157-165.
[41] van der Walt, B, Cahnmann, H.J. (1982) Synthesis of thyroid hormone metabolites by photolysis of thyroxine and thyroxine analogs in the near UV. Proc. Natl. Acad. Sci. USA, 79, 1492-1496.
[42] Shizuka, H., Sorimachi, K., Morita, T., Nishiyama, K. and Sato, T. (1971) Photochemical oxidation of 4, 5, 9, 10tetrahydropyrenes. Bull. Chem. Soc. Japan, 44, 1983- 1984.
[43] Sorimachi, K., Morita, T. and Shizuka, H. (1974) Photo-cyclization of 〔2,2〕metacyclophane at 2537 A.. Bull. Chem. Soc. Japan, 47, 987-990.
[44] Gilbert, W. (1986) The RNA World. Nature, 319, 618.
[45] Sorimachi, K. and Okayasu, T. (2003) Gene assembly consisting of small units with similar amino acid compo-sition in the Saccharomyces cerevisiae genome. Myco-science, 44, 415-417.
[46] Hochberg, Y. and Tamhane, A.C. (1987) Multiple com-parison procedures, In Probability and Mathematical Sta-tistics (eds. Y. Hochberg and A.C. Tamhane), John Wiley & Sons, New York, 274-309.
[47] Sorimachi, K., Okayasu, T., Ebara, Y. and Nakagawa, T. (2005) Mathematical proof of genomic amino acid com-position homogeneity based on putative small unts. Dokkyo J. Med. Sci., 32, 99-100.
[48] Bergey’s Mmanual of Systemic Bacteriology.
[49] Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R. et al. (1995) Whole -genome random sequencing and assembly of Haemo-philus influenzae Rd. Science, 269, 496-512.
[50] International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human ge-nome. Nature, 409: 860-921.
[51] Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A. et al. (2001) The sequence of the human ge-nome. Science, 291, 1304-1351.
[52] Sorimachi, K. and Okayasu, T. (2004). Classification of eubacteria based on their complete genome: where does Mycoplasmataceae belong? Proc. R. Soc. Lond. B (Supp l.), 271, S127-S130.
[53] Dayhoff, M.O., Park, C.M. and McLaughlin, P.J. (1977) Building a phylogenetic trees: cytochrome C. In: Atlas of protein sequence and structure. National Biomedical Foundation, Washington, D.C., 5, 7-16.
[54] Sogin, M.L., Elwood, H.J. and Gunderson, J.H. (1986) Evolutionary diversity of eukaryotic small subunit rRNA genes. Proc Natl Acad Sci USA, 83, 1383-1387.
[55] DePouplana, L., Turner, R.J., Steer, B.A. et al. (1998) Genetic code origins: tRNAs older than their synthetases? Proc Natl Acad Sci USA, 95, 11295-11300.
[56] Doolittle, W.F. and Brown, J.R. (1994) Tempo, mode, the progenote, and the universal root. Proc Natl Acad Sci USA, 91, 6721-6728.
[57] Maizels, N. and Weiner, A.M. (1994) Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA, 91, 6729-6734.
[58] Sakagami, M., Nakayama, T., Hashimoto, T. et al. (2006) Phylogeny of the centrohelida inferred from SSU rRNA, tubulin, and actin genes. J. Mol. Evol., 61, 765-775.
[59] Okayasu, T. and Sorimachi, K. (2008) Organisms can essentially be classified according to two codon patterns. Amino Acids, 36, 261-271.
[60] Bentley, S.D., Chater, K.F., Cerde?o-Tárraga, M.A., Challis, G.L., Thompson, N.R., James, K.D., Harris, D.E., Quail, M.A., Kieser, H., Harper, D. et al. (2002) Com-plete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature, 417, 141-147.
[61] Glass, J.I., Lefkowitz, E.J., Glass, J.S., Heiner, C.R., Chen, E.Y. and Cassell, G.H. (2000) The complete se-quence of the mucosal pathogen Ureaplasma urealyticum. Nature, 407, 757-762.
[62] Sueoka, N. (1988) Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA, 85, 2653-2657.
[63] Chargaff, E. (1950) Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experi-entia, VI, 201-209.
[64] Rundner, R., Karkas, J.D., and Chargaff, E. (1968) Sepa-ration of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc. Natl. Acad. Sci. USA, 60, 921-922.
[65] 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.
[66] Bell, S.J. and Forsdyke, D.R. (1999) Deviations from Chargaff’s second parity rule with direction of transcrip-tion. J. Theor. Biol., 197, 63-76.
[67] Mitchell, D. and Bridge, R. (2006) A test of Chargaff’s second rule. Biochem. Biophys. Res. Commun., 340, 90-94.
[68] Gray, M.W., Burger, G. and Lang, B.F. (1999) Mito-chondrial evolution. Science, 283, 1476-1481.
[69] Raven, J.A. and Allen, J.F. (2003) Genomics and chloro-plast evolution: what did cyanobacteria do for plants? Genom. Biol., 4, 209-215.
[70] Brown, W.M., George, Jr.M. and Wilson, A.C. (1979) Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA, 76, 1967-1971.
[71] Kimura M. (1983) The neutral theory of molecular evo-lution. Cambridge, Cambridge Univ. Press.
[72] Van Nimwegen, E., Crutchfield, J.P. and Huynen, M. (1999) Neutral evolution of mutational robustsness. Proc. Natl. Acad. Sci. USA, 96, 9716-9720.

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