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Amino Acid Homochirality may be Linked to the Origin of Phosphate-Based Life

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Abstract

Phosphorylation has to have been one of the key events in prebiotic evolution on earth. In this article, the emergence of phosphoryl amino acid 5′-nucleosides having a P–N bond is described as a model of the origin of amino acid homochirality and Genetic Code. It is proposed that the intramolecular interaction between the nucleotide base and the amino acid side-chain influences the stability of particular amino acid 5′-nucleotides, and the interaction also selects for the chirality of amino acids. The differences between l- and d-conformation energies (ΔE conf) are evaluated by DFT methods at the B3LYP/6-31G(d) level. Although, as expected, these ΔE conf values are not large, they do give differences in energy that can distinguish the chirality of amino acids. Based on our calculations, the chiral selection of the earliest amino acids for l-enantiomers seems to be determined by a clear stereochemical/physicochemical relationship. As later amino acids developed from the earliest amino acids, we deduce that the chirality of these late amino acids was inherited from that of the early amino acids. This idea reaches far back into evolution, and we hope that it will guide further experiments in this area.

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References

  • Adelfinskaya O, Herdewijn P (2007) Amino acid phosphoramidate nucleotides as alternative substrates for HIV-1 reverse transcriptase. Angew Chem Int Ed 46:4356–4358

    Article  CAS  Google Scholar 

  • Arrhenius G, Sales B, Mojzsis S, Lee T (1997) Entropy and charge in molecular evolution-the case of phosphate. J Theor Biol 187:503–522

    Article  CAS  PubMed  Google Scholar 

  • Bailey JM (1998) RNA-directed amino acid homochirality. FASEB J 12:503–507

    CAS  Google Scholar 

  • Bailey J (2000) Chirality and the origin of life. Acta Astronautica 46:627–631

    Article  Google Scholar 

  • Bailey J (2007) The inner solar system cataclysm, the origin of life, and the return to the moon. In: Proceedings of 6th Australian space science conference, Canberra, July 2006, pp 17–22

  • Bonner WA (2000) Parity violation and the evolution of biomolecular homochirality. Chirality 12:114–126

    Article  CAS  PubMed  Google Scholar 

  • Cheng CM, Liu XH, Li YM, Ma Y, Tan B, Wan R, Zhao YF (2004) N-phosphoryl amino acids and biomolecular origins. Orig Life Evol Biosph 34:455–464

    Article  CAS  PubMed  Google Scholar 

  • Chung NM, Lohrmann R, Orgel LE, Rabinowitz J (1971) The mechanism of the trimetaphosphate-induced peptide synthesis. Tetrahedron 27:1205–1210

    Article  CAS  Google Scholar 

  • Di Giulio M (1997) On the origin of the genetic code. J Theor Biol 187:573–581

    Article  CAS  PubMed  Google Scholar 

  • Di Giulio M (1998) Reflections on the origin of the genetic code: a hypothesis. J Theor Biol 191:191–196

    Article  CAS  PubMed  Google Scholar 

  • Di Giulio M (1999) Physicochemical optimization in the genetic code origin as the number of codified amino acids increases. J Mol Evol 49:1–10

    Article  CAS  PubMed  Google Scholar 

  • Di Giulio M (2004) The coevolution theory of the origin of the genetic code. Phys Life Rev 2:128–137

    Article  Google Scholar 

  • Di Giulio M, Medugno M (1998) The historical factor: the biosynthetic relationships between amino acids and their physicochemical properties in the origin of the genetic code. J Mol Evol 46:615–621

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Fu H, Tu GZ, Li ZL, Zhao YF, Zhang RQ (1997) New and efficient approach to the synthesis of pentacoordinate spirobicyclic phosphoranes. J Chem Soc Perkin Trans 1:2021–2022

    Article  Google Scholar 

  • Fu H, Li ZL, Zhao YF, Tu GZ (1999) Oligomerization of N, O-Bis(trimethylsilyl)-α-amino acids into peptides mediated by o-phenylene phosphorochloridate. J Am Chem Soc 121:291–295

    Article  CAS  Google Scholar 

  • Hazen RM (2001) Life’s rocky start. Sci Am 284:77–85

    Article  Google Scholar 

  • Inous H, Baba Y, Furukawa T, Maeda Y, Tsuhako M (1993) Formation of dipeptide in the reaction of amino acids with cyclo-triphosphate. Chem Parm Bull 41:1895–1899

    Google Scholar 

  • Jorissen A, Cerf C (2002) Asymmetric photoreactions as the origin of biomolecular homochirality: a critical review. Orig Life Evol Biosph 32:129–142

    Article  CAS  PubMed  Google Scholar 

  • Kolb V, Zhang SB, Xu Y, Arrhenius G (1997) Mineral induced phosphorylation of glycolate ion—a metaphor in chemical evolution. Orig Life Evol Biosph 27:485–503

    Article  CAS  PubMed  Google Scholar 

  • Li ZL, Fu H, Gong HG, Zhao YF (2004) Convenient solid-phase synthesis of oligopeptides using pentacoordianated phosphoranes with amino acid residue as building blocks. Bioorg Chem 32:170–177

    Article  CAS  PubMed  Google Scholar 

  • Lin CX, Fu H, Tu GZ, Zhao YF (2003) Synthesis and chiral separation of dinucleotides(TpAZT) phosphoramidates. Chin Chem Lett 14:779–782

    CAS  Google Scholar 

  • Lu K, Tu GZ, Guo XF, Sun XB, Liu Y, Feng YP, Zhao YF (2002) Structure and isomerization of O, O-phenylene penta-coordianted phosphoryl serine. J Mol Struct 610:65–72

    Article  CAS  Google Scholar 

  • McGuigan C, Pathirana RN, Balzarini J, De Clercq E (1993) Intracellular delivery of bioactive AZT nucleotides by aryl phosphate derivatives of AZT. J Med Chem 36:1048–1052

    Article  CAS  PubMed  Google Scholar 

  • Ni F, Sun ST, Huang C, Zhao YF (2009) N-phosphorylation of amino acids by trimetaphosphate in aqueous solution-learning from prebiotic synthesis. Green Chem 11:569–573

    Article  CAS  Google Scholar 

  • Pasek MA, Kee TP, Bryant DE, Pavlov AA, Lunine JI (2008) Production of potentially prebiotic condensed phosphates by phosphorus redox chemistry. Angew Chem Int Ed 47:7918–7920

    Article  CAS  Google Scholar 

  • Qin ZH, Lin CX, Chen Y, Ju Y, Zhao YF (2002) Electrospray ionization mass spectrometry of serine/alanine conjugated 5′-UMP and 3′, 5′-dithymidine phosphoramidates. Rapid Commun Mass Spectrom 16:1997–2002

    Article  CAS  PubMed  Google Scholar 

  • Saghatelian A, Yokobayashi Y, Soltani K, Ghadiri MR (2001) A chiroselective peptide replicator. Nature 409:797–801

    Article  CAS  PubMed  Google Scholar 

  • Seligmann H, Amzallag GN (2002) Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code. Naturwissenschaften 89:542–551

    CAS  PubMed  Google Scholar 

  • Speight RE, Hart DJ, Sutherland JD, Blackburn JM (2001) A new plasmid display technology for the in vitro selection of functional phenotype-genotype linked proteins. Chem Biol 8:951–965

    Article  CAS  PubMed  Google Scholar 

  • Szathmary E (1993) Coding coenzyme handles: a hypothesis for the origin of the genetic code. Pro Natl Acad Sci 90:9916–9920

    Article  CAS  Google Scholar 

  • Tan B, Lee MC, Cui M, Liu T, Chen ZZ, Li YM, Ju Y, Zhao YF, Chen KX, Jiang HL (2004) A common intermediate for prebiotic synthesis of proteins and nucleosides: a density functional theory (DFT) study on the formation from N-phosphoryl amino acids. J Mol Struct (Themchem) 672:51–60

    Article  CAS  Google Scholar 

  • Trifonov EN (2000) Consensus temporal order of amino acids and evolution of the triplet code. Gene 261:139–151

    Article  CAS  PubMed  Google Scholar 

  • Tsuhako M, Fujimoto M, Ohashi S, Nariai H, Motooka I (1984) Phosphorylation of nucleosides with cyclo-triphosphate. Bull Chem Soc Jpn 57:3274–3280

    Article  CAS  Google Scholar 

  • Wachtershauser G (1997) The origin of life and its methodological challenge. J Theor Biol 187:483–494

    Article  CAS  PubMed  Google Scholar 

  • Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178

    Article  CAS  PubMed  Google Scholar 

  • Woese CR (1965) On the origin of the genetic code. Proc Natl Acad Sci 54:1546–1552

    Article  CAS  PubMed  Google Scholar 

  • Wong JT (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci 72:1909–1912

    Article  CAS  PubMed  Google Scholar 

  • Yamagata Y, Watanabe H, Saitoh M, Namba T (1991) Volcanic production of polyphosphates and its relevance to prebiotic evolution. Nature 352:516–519

    Article  CAS  PubMed  Google Scholar 

  • Yang P, Han DX (2000) Molecular modeling of the binding mode of chiral metal complexes [Co(phen)2dppz]3 + with B-DNA. Sci China B 43:516–523

    Article  CAS  Google Scholar 

  • Yarus M (1998) Amino acids as RNA ligands: a direct-RNA-template theory for the code’s origin. J Mol Evol 47:109–117

    Article  CAS  PubMed  Google Scholar 

  • Zaia DAM (2004) A review of adsorption of amino acids an minerals: as it important for origin of life? Amino Acids 27:113–118

    Article  CAS  PubMed  Google Scholar 

  • Zhou WH, Ju Y, Zhao YF, Wang QG, Luo GA (1996) Simultaneous formation of peptides and nucleotides from N-phosphothreonine. Orig Life Evol Biosph 26:547–560

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Professor G. Michael Blackburn for useful discussions. This study was supported by the National Science Foundation of China (Grant No. 40976050 and Grant No. 40706043) and the 908 Project Foundation of State Oceanic Administration of China (FJ 908-02-03-05).

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Authors and Affiliations

  1. Department of Pharmacy, Medical College of Xiamen University, Xiamen, 361005, China

    Da Xiong Han

  2. The Third Institute of Oceanography, State Oceanic Administration of China, Xiamen, 361005, China

    Hai Yan Wang

  3. The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China

    Zhi Liang Ji, An Fu Hu & Yu Fen Zhao

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  1. Da Xiong Han
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  2. Hai Yan Wang
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  3. Zhi Liang Ji
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Correspondence to Da Xiong Han.

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Han, D.X., Wang, H.Y., Ji, Z.L. et al. Amino Acid Homochirality may be Linked to the Origin of Phosphate-Based Life. J Mol Evol 70, 572–582 (2010). https://doi.org/10.1007/s00239-010-9353-z

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  • DOI: https://doi.org/10.1007/s00239-010-9353-z

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