Prebiological Organization of Molecules in Models and in the Matter of the Origin of Life
Keywords:The Origin Of Life, Molecular Evolution, A Replicator, Ribosomal Codons
AbstractThe theoretical model of cell formation in cell selection is considered. The phenomenology of the process shows that molecular evolution did not have a Darwinian basis for development. According to the described model, cell formation is an inevitable process that develops a clear molecular mechanism. This mechanism is observed throughout the entire period of early development, beginning with the stage of initiation of the process, then at the stage of molecular complications and at the final final stage. The mechanism reveals the ideological concept according to which at an early stage there was a group of ribosome structures catalyzing reversible aminoacyltransfer, their activity led to the formation of a self-replicating cycle on a translational basis.
 Agmon I, Bashan A, Zarivach R, Yonath A (2005) Symmetry at the active site of the ribosome: structural and functional implications. Biol. Chem. 386: 833â€“844.
 Atkins JF, Gesteland RF, Cech TR (2011) RNA Worlds: From Lifeâ€™s Origins to Diversity in Gene Regulation. Cold Spring Harb. Lab. Press, p. 366.
 Attwater J, Wochner A, Holliger P (2013) In-ice evolution of RNA polymerase ribozyme activity. Nature Chemistry 5:1011-1018.
 Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (2009) Genome Evolution and Adaptation in a Long-Term Experiment with Escherichia coli. Nature 461:1243â€“1247.
 Belshaw R, Pybus OG, Rambaut A (2007) The evolution of genome compression and genomic novelty in RNA viruses. Genome Res. 17:1496-1504.
 Bokov K, Steinberg S (2009) A hierarchical model for evolution of 23S ribosomal RNA. Nature 457:977-980.
 Briones C, Stitch M, Manrubia SC (2009) The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers. RNA 15:743-749.
 Cairns-Smith AG (1982) Genetic takeover and the mineral origins of life. Cambridge University Press, p. 488.
 Chetverina HV, Demidenko AA, Ugarov VI., Chetverin AB (1999) Spontaneous rearrangements in RNA sequences. FEBS Letters 450:89-94.
 Lawrence AD., Alm EJ (2011) Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469:93-96.
 Dibrova DV, Makarova KS, Galperin MY, Koonin EV, Mulkidjanian AY (2011) Comparative analysis of lipid biosynthesis in archaea, bacteria and eukaryotes: What was the structure of the first membrane lipids? Proceedings of the International Moscow Conference on Computational Molecular Biology, Moscow State University, Moscow, pp. 92-93.
 Doudna JA, Cech TR (2002) The Chemical Repertoire of Natural Ribozymes. Nature 418: 222â€“228.
 Fedor M.J, Williamson JR (2005) The Catalytic Diversity of RNAs. Nature Reviews Molecular Cell Biology 6: 399-412.
 Ferris JP, Hill AR, Liu R, Orgel IE (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381: 59-61.
 Freeland SJ, Hurst LD (1998) The Genetic Code Is One in a Million. J Mol Evol 47:238-248.
 Gorbalenya AE, Koonin EV (1989) Viral Proteins Containing the Purine NTP-Binding Sequence Pattern. Nucleic Acids Res. 17: 8413-8440.
 Ikehara K (2002) Origins of gene, genetic code, protein and life: comprehensive view of life system from a GNC-SNS primitive genetic code hypothesis. J. Biosci 27: 165-186.
 Ikehara K, Omori Y, Arai R, Hirose A (2002) A novel theory on the origin of the genetic code: a GNS-SNS hypothesis. J. Mol. Evol. 54:530-538.
 Koonin EV, Martin W (2005) On the Origin of Genomes and Cells within Inorganic Compartments. Trends Genet. 21:647â€“654.
 Koonin EV (2009) On the Origin of Cells and Viruses: Primordial Virus World Scenario. Ann N Y Acad Sci. 1178: 47-64.
 Koonin EV (2009) Evolution of Genome Architecture. Int J Biochem Cell Biol. 41:298-306.
 Koonin EV (2006) Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol Direct. 1:39.
 Koonin EV (2003) Comparative Genomics, minimal gene-sets and the Last Universal Common Ancestor. Nat. Rev. Microbiol. 1:127-136.
 Levitt M. (2009) Nature of the Protein Universe. Proc. Natl. Acad. Sci. USA 106: 11079-11084.
 Leipe D, Aravind L, Koonin E (1999) Did DNA Replication Evolve Twice Independently? Nucleic Acids Res. 27:3389-3401.
 Lincoln TA, Joyce GF (2009) Self-sustained replication of an RNA enzyme. Science 323:1229-1232.
 Martin W, Russell MJ (2003) On the Origins of Cells: A Hypothesis for the Evolutionary Transitions from Abiotic Geochemistry to Chemoautotrophic Prokaryotes, and from Prokaryotes to Nucleated Cells. Philos Trans R Soc Lond B Biol Sci. 358: 59-83
 Miller SL (1986) Current status of the prebiotic synthesis of small molecules. Chem. Scr. 26B: 5-11.
 Mulkidjanian AY (2009) On the origin of life in the Zinc world, Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biol Direct. 4:27.
 Mulkidjanian AY, Makarova KS, Galperin MY., Koonin EV (2007) Inventing the Dynamo Machine: The Evolution of the F-type and V-type ATPases. Nature Reviews Microbiology 5: 892-899.
 Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV (2008) Evolutionary primacy of sodium bioenergetics. Biol Direc. 3:13.
 Mulkidjanian AY, Dibrov P, Galperin MY (2008) The past and present of sodium energetics: May the sodiummotive force be with you. Biochimica et Biophysica Acta (BBA) -Bioenergetics 1777. I. 7: P. 985-992.
 Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin MY, Koonin EV (2012) Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci USA Feb 13: 821-830.
 Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289:920â€“930
 Nisbet EG, Fowler. CM (1996) Some liked it hot. Nature 382: 404-405.
 Novozhilov AS, Koonin EV (2009) Exceptional Error Minimization in Putative Primordial Genetic Codes. Biol Direct. 4: 44.
 Oba T, Fukushima J, Maruyama M, Iwamoto R, Ikehara K (2005) Catalytic activities of ï›GADVï-petides. Ori. Life Evol. Bioshph. 35: 447-460.
 Omelchenko MV, Galperin MY, Wolf YI, Koonin EV (2010) Non-Homologous Isofunctional Enzymes: A Systematic Analysis of Alternative Solutions in Enzyme Evolution. Biol Direc. 5:31.
 Orgel LE (1992) Molecular replication and the origin of life. Nature 358: 203-209.
 Pereto J, Lopez-Garcia P, Moreira D (2004) Ancestral Lipid Biosynthesis and Early Membrane Evolution. Trends Biochem Sci. 29:469-477.
 Poole A, Penny D, Sjoberg B-M (2000) Methyl-RNA: an evolutionary bridge between RNA and DNA? Chem Biol. 7: 207-216.
 Root-Bernstein M, Root-Bernstein R (20015) The ribosome as a missing link in the evolution of life. J. Theor. Biol. 367: 130-158.
 Russell MJ, Martin W (2004) The rocky roots of the acetil-CoA pathway.Trends Biochem. Sci. 29:358â€“363.
 Russell MJ, Hall AJ, Cairns-Smith AG, Braterman PS (1988) Submarine hot springs and the origin of life. Nature 336:117.
 Russell MJ (2006) First life. American Scientist 94:32-39.
 Stetter KO (2006) Hyperthermophiles in the history of life. Phil. Trans. R. Soc. B. 361:1837â€“1843.
 Trifonov EN, Gabdank I, Barash D, Sobolevsky Y (2006) Primordia Vita. Deconvolution from Modern Sequences. Orig Life Evol Biosph. 36:559-565.
 Turk RM, Chumachenko NV, Yarus M (2010) Multiple Translational Products from a Five-Nucleotide Ribozyme. Proc. Natl. Acad. Sci. USA 107:4585-4589.
 Vaidya N, Manapat ML, Chen IA, Xulvi-Brunet R, Hayden EJ, Lehman N (2012) Spontaneous network formation among cooperative RNA replicators. Nature 491:72-77.
 Vetsigian K, Woese C, Goldenfeld N (2006) Collective Evolution and the Genetic Code. Proc Natl Acad Sci USA 103:10696-10701.
 Vortler S, Morl M (2010) tRNA-nucleotidyltransferases: Highly unusual RNA polymerases with vital functions. FEBS Letters 584:297-302.
 Wachtershauser G (1990) Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA 87:200-204.
 Wachtershauser G (2006) From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. Phil.Trans. R. Soc. B. 361:1787-1808.
 Wachtershauser G (1992) Groundworks for an evolutionary biochemistry: the ironâ€“sulfur world. Prog. Biophys. Mol.Biol. 58:185-201.
 Wolf YI, Brenner SE, Bash PA, Koonin EV (1999) Distribution of Protein Folds in the Three Superkingdoms of Life. Genome Res 9:17-26.
 Wolf YI, Koonin EV (2007) On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biology Direct. May 31:2-14.
 Wochner A, Attwater J, Coulson A, Holliger P (2011) Ribozyme-Catalyzed Transcription of an Active Ribozyme. Science 332:209â€“212.
 Wolf YI, Koonin EV (2007) On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biology Direct 2:14.
 Woese CR (2002) On the Evolution of Cells. Proc. Natl. Acad. Sci. USA 99:8742-8747.
 Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Soll D (2006) RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc. Natl. Acad. Sci. USA 103: 18923-18927.
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