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Hypothesis of Lithocoding: Origin of the Genetic Code as a “Double Jigsaw Puzzle” of Nucleobase-Containing Molecules and Amino Acids Assembled by Sequential Filling of Apatite Mineral Cellules

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Abstract

The hypothesis of direct coding, assuming the direct contact of pairs of coding molecules with amino acid side chains in hollow unit cells (cellules) of a regular crystal-structure mineral is proposed. The coding nucleobase-containing molecules in each cellule (named “lithocodon”) partially shield each other; the remaining free space determines the stereochemical character of the filling side chain. Apatite-group minerals are considered as the most preferable for this type of coding (named “lithocoding”). A scheme of the cellule with certain stereometric parameters, providing for the isomeric selection of contacting molecules is proposed. We modelled the filling of cellules with molecules involved in direct coding, with the possibility of coding by their single combination for a group of stereochemically similar amino acids. The regular ordered arrangement of cellules enables the polymerization of amino acids and nucleobase-containing molecules in the same direction (named “lithotranslation”) preventing the shift of coding. A table of the presumed “LithoCode” (possible and optimal lithocodon assignments for abiogenically synthesized α-amino acids involved in lithocoding and lithotranslation) is proposed. The magmatic nature of the mineral, abiogenic synthesis of organic molecules and polymerization events are considered within the framework of the proposed “volcanic scenario”.

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References

  • Acevedo OL, Orgel EL (1987) Template-directed ligation of oligonucleotides on hydroxy-apatite: a model for complexation in a primitive ocean. Orig Life 18:441

    Google Scholar 

  • Alvarez-Carreño C, Becerra A, Lazcano A (2013) Norvaline and norleucine may have been more abundant protein components during early stages of cell evolution. Orig Life Evol Biosph 43:363–375. doi:10.1007/s11084-013-9344-3

    Article  PubMed  Google Scholar 

  • Batard P, Jordan M, Wurm F (2001) Transfer of high copy number plasmid into mammalian cells by calcium phosphate transfection. Gene 270:61–68

    Article  CAS  PubMed  Google Scholar 

  • Benetoli LOB, de Souza CMD, da Silva KL, de Souza IG Jr, de Santana H, Paesano A Jr, da Costa ACS, Zaia CTBV, Zaia DAM (2007) amino acid interaction with and adsorption on clays: FT-IR and Mössbauer spectroscopy and X-ray diffractometry investigations. Orig Life Evol Biosph 37(6):479–493

  • Cavalier-Smith T (2001) Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J Mol Evol 53(4–5):555–595

    Article  CAS  PubMed  Google Scholar 

  • Chowdhury EH (2013) pH-responsive magnesium- and carbonate-substituted apatite nano-crystals for efficient and cell-targeted delivery of transgenes. Open J Gen 3:38–44

    Article  CAS  Google Scholar 

  • Chowdhury EH, Kunou M, Nagaoka M, Kundu AK, Hoshiba T, Akaike T (2004) High-efficiency gene delivery for expression in mammalian cells by nanoprecipitates of Ca–Mg phosphate. Gene 341:77–82

    Article  CAS  PubMed  Google Scholar 

  • Copley SD, Smith E, Morowitz HJ (2005) A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc Natl Acad Sci USA 102(12):4442–4447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Costanzo G, Saladino R, Botta G, Giorgi A, Scipioni A, Pino S, Di Mauro E (2012) Generation of RNA molecules by a base-catalysed click-like reaction. ChemBioChem 13(7):999–1008. doi:10.1002/cbic.201200068

    Article  CAS  PubMed  Google Scholar 

  • Ferris JP, Hill AR Jr, Liu R, Orgel LE (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381(6577):59–61

    Article  CAS  PubMed  Google Scholar 

  • Francis BR (2013) Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J Mol Evol 77(4):134–158. doi:10.1007/s00239-013-9567-y

    Article  CAS  PubMed  Google Scholar 

  • Hartman H (1995) Speculations on the origin of the genetic code. J Mol Evol 40(5):541–544

    Article  CAS  PubMed  Google Scholar 

  • Hartman H, Smith TF (2014) The evolution of the ribosome and the genetic code. Life 4:227–249. doi:10.3390/life4020227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hazen MR, Sholl DS (2003) Surface and thin films Chiral selection on inorganic crystalline surfaces. Nat Mater 2:367–374

    Article  CAS  PubMed  Google Scholar 

  • Hoogsteen K (1963) The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr A 16:907–916

    Article  CAS  Google Scholar 

  • Knight R, Landweber L, Yarus M (2003) Tests of a stereochemical genetic code. In: Lapointe J, Brakier-Gingras L (eds) Translation mechanisms. Landes Bioscience, Georgetown, pp 115–128

  • Koonin EV, Novozhilov AS (2009) Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61:99–111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kornberg A, Rao NN, Ault-Riché D (1999) Inorganic polyphosphate: a molecule of many functions. Annu Rev Biochem 68:89–125

    Article  CAS  PubMed  Google Scholar 

  • Kosteckiy EYa (2008) How life had arisen? Bull Pacif State Econ Univ 2:86–103 (in Russian)

    Google Scholar 

  • Kulaev IS, Vagabov VM (1983) Polyphosphate metabolism in microorganisms. Adv Microbiol Physiol 24:83–171

    Article  CAS  Google Scholar 

  • Lambert J-F (2008) Adsorption and polymerization of amino acids on mineral surfaces: a review. Orig Life Evol Biosph. doi:10.1007/s11084-008-9128-3

    PubMed  Google Scholar 

  • Liu R, Orgel LE (1998) Polymerization on the rocks: beta-amino acids and arginine. Orig Life Evol Biosph 28(3):245–257

    Article  CAS  PubMed  Google Scholar 

  • Mellersh AR (1993) A model for the prebiotic synthesis of peptides which throws light on the origin of the genetic code and the observed chirality of life. Orig Life Evol Biosph 23(4):261–274

    Article  CAS  Google Scholar 

  • Mellersh AR, Wilkinson AS (2000) RNA bound to a solid phase can select an amino acid and facilitate subsequent amide bond formation. Orig Life Evol Biosph 30(1):3–7

    Article  CAS  PubMed  Google Scholar 

  • Miller S (1953) A production of amino acids under possible primitive earth conditions. Science 117:528–529

    Article  CAS  PubMed  Google Scholar 

  • Miller SL, Urey HC (1959) Organic compound synthesis on the primitive earth. Science 130(3370):245–251

    Article  CAS  PubMed  Google Scholar 

  • Milner-White EJ, Russell MJ (2010) Polyphosphate-peptide synergy and the organic takeover at the emergence of life. J Cosmol 10:3217–3229

    Google Scholar 

  • 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 109:E821–E830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nelsesteuen GL (1978) Amino acid-directed nucleic acid synthesis. J Mol Evol 11:109–120

    Article  Google Scholar 

  • Norris V, Reusch RN, Igarashi K, Root-Bernstein R (2014) Molecular complementarity between simple, universal molecules and ions limited phenotype space in the precursors of cells. Biol Direct 9:28

    Google Scholar 

  • Okazaki M, Yoshida Y, Yamaguchi S, Kaneno M, Elliott JC (2001) Affinity binding phenomena of DNA onto apatite crystals. Biomaterials 22:2459–2464

    Article  CAS  PubMed  Google Scholar 

  • Pasero M, Kampf AR, Ferraris C, Pekov IV, Rakovan J, White TJ (2010) Nomenclature of the apatite supergroup minerals. Eur J Miner 22:163–179

    Article  CAS  Google Scholar 

  • Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459(7244):239–242

    Article  CAS  PubMed  Google Scholar 

  • Ronto G, Gaspar S, Fekete A, Kerekgyarto T, Berces A, Grof P (2002) Stability of nucleic acid under the effect of UV radiation. Adv Space Res 30(6):1533–1538

    Article  CAS  PubMed  Google Scholar 

  • Root-Bernstein M, Root-Bernstein R (2015) The ribosome as a missing link in the evolution of life. J Theor Biol 367(21):130–158. doi:10.1016/j.jtbi.2014.11.025

    Article  CAS  PubMed  Google Scholar 

  • Saladino R, Crestini C, Ciciriello F, Costanzo G, Di Mauro E (2006) About a formamide-based origin of informational polymers: syntheses of nucleobases and favourable thermodynamic niches for early polymers. Orig Life Evol Biosph 5–6:523–531

    Article  Google Scholar 

  • Schöning K, Scholz P, Guntha S, Wu X, Krishnamurthy R, Eschenmoser A (2000) Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3′ → 2′) oligonucleotide system. Science 290(5495):1347–1351

    Article  PubMed  Google Scholar 

  • Siffert B, Naidja A (1992) Stereoselectivity of montmorillonite in the adsorption and deamination of some amino acids. Clay Min 29:109–118

    Article  Google Scholar 

  • Skoblikow NE, Zimin AA (2015) A search for relict ribonucleotide and amino acid sequences that played a key role in the development of the ribosome and modern protein diversity. Math Biol Bioinform 10(1):116–130. doi:10.17537/2015.10.116

    Article  Google Scholar 

  • Smith JV, Arnold FP Jr, Parsons I, Lee MR (1999) Biochemical evolution III: polymerization on organophilic silica-rich surfaces, crystal–chemical modeling, formation of first cells, and geological clues Proc. Natl Acad Sci USA 96:3479–3485

    Article  CAS  Google Scholar 

  • Yarus M, Widmann JJ, Knight R (2009) RNA-amino acid binding: a stereochemical era for the genetic code. J Mol Evol 69(5):406–429

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Peritz A, Meggers E (2005) A simple glycol nucleic acid. J Am Chem Soc 127(12):4174–4175. doi:10.1021/ja042564z

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We sincerely thank Vladimir Selivanov and Konstantin Shavkunov for providing substantial assistance in preparing the English version of this text.

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Authors and Affiliations

  1. Laboratory of Microbiology, North-Caucasian Research Institute of Animal Husbandry, 4 Pervomayskaya Street, Znamenskiy Settlement, Krasnodar, Russia, 350055

    Nikolai E. Skoblikow

  2. Medical Laboratory “CityLab”, 96 Moskovskaya Street, Krasnodar, Russia, 350000

    Nikolai E. Skoblikow

  3. Laboratory of Molecular Microbiology, Institute of Biochemistry and Physiology of Microorganisms, 5 Prosp. Nauki, Pushchino, Moscow Region, Russia, 142290

    Andrei A. Zimin

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  1. Nikolai E. Skoblikow
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  2. Andrei A. Zimin
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Correspondence to Nikolai E. Skoblikow.

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Skoblikow, N.E., Zimin, A.A. Hypothesis of Lithocoding: Origin of the Genetic Code as a “Double Jigsaw Puzzle” of Nucleobase-Containing Molecules and Amino Acids Assembled by Sequential Filling of Apatite Mineral Cellules. J Mol Evol 82, 163–172 (2016). https://doi.org/10.1007/s00239-016-9736-x

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