Journal of Molecular Evolution

, Volume 70, Issue 6, pp 572–582 | Cite as

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

  • Da Xiong Han
  • Hai Yan Wang
  • Zhi Liang Ji
  • An Fu Hu
  • Yu Fen Zhao
Article

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 (ΔEconf) are evaluated by DFT methods at the B3LYP/6-31G(d) level. Although, as expected, these ΔEconf 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.

Keywords

Homochirality Genetic codes Phosphate Origin of life Chiral selection 

Notes

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).

References

  1. Adelfinskaya O, Herdewijn P (2007) Amino acid phosphoramidate nucleotides as alternative substrates for HIV-1 reverse transcriptase. Angew Chem Int Ed 46:4356–4358CrossRefGoogle Scholar
  2. Arrhenius G, Sales B, Mojzsis S, Lee T (1997) Entropy and charge in molecular evolution-the case of phosphate. J Theor Biol 187:503–522CrossRefPubMedGoogle Scholar
  3. Bailey JM (1998) RNA-directed amino acid homochirality. FASEB J 12:503–507Google Scholar
  4. Bailey J (2000) Chirality and the origin of life. Acta Astronautica 46:627–631CrossRefGoogle Scholar
  5. 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 17–22Google Scholar
  6. Bonner WA (2000) Parity violation and the evolution of biomolecular homochirality. Chirality 12:114–126CrossRefPubMedGoogle Scholar
  7. 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 34:455–464CrossRefPubMedGoogle Scholar
  8. Chung NM, Lohrmann R, Orgel LE, Rabinowitz J (1971) The mechanism of the trimetaphosphate-induced peptide synthesis. Tetrahedron 27:1205–1210CrossRefGoogle Scholar
  9. Di Giulio M (1997) On the origin of the genetic code. J Theor Biol 187:573–581CrossRefPubMedGoogle Scholar
  10. Di Giulio M (1998) Reflections on the origin of the genetic code: a hypothesis. J Theor Biol 191:191–196CrossRefPubMedGoogle Scholar
  11. Di Giulio M (1999) Physicochemical optimization in the genetic code origin as the number of codified amino acids increases. J Mol Evol 49:1–10CrossRefPubMedGoogle Scholar
  12. Di Giulio M (2004) The coevolution theory of the origin of the genetic code. Phys Life Rev 2:128–137CrossRefGoogle Scholar
  13. 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 46:615–621CrossRefPubMedGoogle Scholar
  14. Ferris JP, Hill AR, Liu RH, Orgel LE (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381:59–61CrossRefPubMedGoogle Scholar
  15. 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 1:2021–2022CrossRefGoogle Scholar
  16. 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 121:291–295CrossRefGoogle Scholar
  17. Hazen RM (2001) Life’s rocky start. Sci Am 284:77–85CrossRefGoogle Scholar
  18. 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 41:1895–1899Google Scholar
  19. Jorissen A, Cerf C (2002) Asymmetric photoreactions as the origin of biomolecular homochirality: a critical review. Orig Life Evol Biosph 32:129–142CrossRefPubMedGoogle Scholar
  20. Kolb V, Zhang SB, Xu Y, Arrhenius G (1997) Mineral induced phosphorylation of glycolate ion—a metaphor in chemical evolution. Orig Life Evol Biosph 27:485–503CrossRefPubMedGoogle Scholar
  21. 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 32:170–177CrossRefPubMedGoogle Scholar
  22. Lin CX, Fu H, Tu GZ, Zhao YF (2003) Synthesis and chiral separation of dinucleotides(TpAZT) phosphoramidates. Chin Chem Lett 14:779–782Google Scholar
  23. 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 610:65–72CrossRefGoogle Scholar
  24. 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 36:1048–1052CrossRefPubMedGoogle Scholar
  25. 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 11:569–573CrossRefGoogle Scholar
  26. 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 47:7918–7920CrossRefGoogle Scholar
  27. 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 16:1997–2002CrossRefPubMedGoogle Scholar
  28. Saghatelian A, Yokobayashi Y, Soltani K, Ghadiri MR (2001) A chiroselective peptide replicator. Nature 409:797–801CrossRefPubMedGoogle Scholar
  29. 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 89:542–551PubMedGoogle Scholar
  30. 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 8:951–965CrossRefPubMedGoogle Scholar
  31. Szathmary E (1993) Coding coenzyme handles: a hypothesis for the origin of the genetic code. Pro Natl Acad Sci 90:9916–9920CrossRefGoogle Scholar
  32. 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) 672:51–60CrossRefGoogle Scholar
  33. Trifonov EN (2000) Consensus temporal order of amino acids and evolution of the triplet code. Gene 261:139–151CrossRefPubMedGoogle Scholar
  34. Tsuhako M, Fujimoto M, Ohashi S, Nariai H, Motooka I (1984) Phosphorylation of nucleosides with cyclo-triphosphate. Bull Chem Soc Jpn 57:3274–3280CrossRefGoogle Scholar
  35. Wachtershauser G (1997) The origin of life and its methodological challenge. J Theor Biol 187:483–494CrossRefPubMedGoogle Scholar
  36. Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178CrossRefPubMedGoogle Scholar
  37. Woese CR (1965) On the origin of the genetic code. Proc Natl Acad Sci 54:1546–1552CrossRefPubMedGoogle Scholar
  38. Wong JT (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci 72:1909–1912CrossRefPubMedGoogle Scholar
  39. Yamagata Y, Watanabe H, Saitoh M, Namba T (1991) Volcanic production of polyphosphates and its relevance to prebiotic evolution. Nature 352:516–519CrossRefPubMedGoogle Scholar
  40. 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 43:516–523CrossRefGoogle Scholar
  41. Yarus M (1998) Amino acids as RNA ligands: a direct-RNA-template theory for the code’s origin. J Mol Evol 47:109–117CrossRefPubMedGoogle Scholar
  42. Zaia DAM (2004) A review of adsorption of amino acids an minerals: as it important for origin of life? Amino Acids 27:113–118CrossRefPubMedGoogle Scholar
  43. Zhou WH, Ju Y, Zhao YF, Wang QG, Luo GA (1996) Simultaneous formation of peptides and nucleotides from N-phosphothreonine. Orig Life Evol Biosph 26:547–560CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Da Xiong Han
    • 1
  • Hai Yan Wang
    • 2
  • Zhi Liang Ji
    • 3
  • An Fu Hu
    • 3
  • Yu Fen Zhao
    • 3
  1. 1.Department of PharmacyMedical College of Xiamen UniversityXiamenChina
  2. 2.The Third Institute of OceanographyState Oceanic Administration of ChinaXiamenChina
  3. 3.The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical EngineeringXiamen UniversityXiamenChina

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