The origin of the biologically coded amino acids

Journal of Theoretical Biology

Volumn 263, Issue 4, 2010, Pages 490-498

  Cleaves II, H James ^a  

^a GEOPHYSICAL LABORATORY   (United States)

Author keywords

Amino acids; Chemical evolution; Genetic code; Natural selections; Origin of life

Indexed keywords

ALPHA AMINO ACID; AMMONIA; RNA;

AMINO ACID; BIOCHEMISTRY; ENZYME; METABOLISM; NATURAL SELECTION; ORIGIN OF LIFE;

AMINO ACID SYNTHESIS; ARTICLE; BIOGENESIS; CATALYST; CHIRALITY; EVOLUTION; GENETIC CODE; METABOLISM; NATURAL SELECTION; POLYMERIZATION; PRIORITY JOURNAL; RNA TRANSLATION;

AMINO ACIDS; BIOCHEMISTRY; BIOGENESIS; CARBON; EVOLUTION; HUMANS; HYDROGEN BONDING; METEOROIDS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, THEORETICAL; ORGANIC CHEMICALS; RNA;

EID: 77649336503     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.12.014     Document Type: Article

References (109)

1. Akashi H., and Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 99 (2002) 3695-3700
2. Albery W.J., and Knowles J.R. Evolution of enzyme function and the development of catalytic efficiency. Biochemistry 15 (1976) 5631-5640
3. Aubrey AD., Cleaves HJ., and Bada J.L. The role of submarine hydrothermal systems in the synthesis of amino acids. Origins Life Evol. Biosphere 39 (2009) 91-108
4. Bada J.L. State-of-the-art instruments for detecting extraterrestrial life. Proc. Natl. Acad. Sci. USA 98 (2001) 797-800
5. Bada J.L., and Hoopes E.A. Alanine enantiomeric ratio in the combined amino acid fraction in seawater. Nature 282 (1979) 822-823
6. Bada J.L., Bigham C., and Miller S.L. Impact melting of frozen oceans on the early Earth: implications for the origin of life. Proc. Natl. Acad. Sci. USA 91 (1994) 1248-1250
7. Bag B.G., and von Kiedrowski G. Templates, autocatalysis and molecular replication. Pure Appl. Chem. 68 (1996) 2145-2152
8. Becerra A., Delaye L., Islas S., and Lazcano A. The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains. Ann. Rev. Ecol. Evol. Syst. 38 (2007) 361-379
9. Becerra A., and Lazcano A. The role of gene duplication in the evolution of purine nucleotide salvage pathways. Origins Life Evol. Biosphere 28 (1998) 539-553
10. Benner S.A. Enzyme kinetics and molecular evolution. Chem. Rev. 89 (1989) 789-806
11. Benner S.A., Ellington A.D., and Tauer A. Modern metabolism as a palimpsest of the RNA world. Proc. Natl. Acad. Sci. USA 86 (1989) 7054-7058
12. Bernstein M.P., Dworkin J.P., Sandford S.A., Cooper G.W., and Allamandola L.J. Racemic amino acids from the ultraviolet photolysis of interstellar ice analogues. Nature 416 (2002) 401-403
13. Blackmond D.G. Asymmetric autocatalysis and its implications for the origin of homochirality. Proc. Natl. Acad. Sci. USA 101 (2004) 5732-5736
14. Bonner W.A. Chirality and life. Origins Life Evol. Biosphere 25 (1995) 175-190
15. Booth I.R. Regulation of cytoplasmic pH in bacteria. Microbiol. Rev. 49 (1985) 359-378
16. Botta O., and Bada J.L. Extraterrestrial organic compounds in meteorites. Surv. Geophys. 23 (2002) 411-467
17. Brack A., and Spach G. Beta-structures of polypeptides with l and d residues (parts I and II). J. Mol. Evol. 13 (1979) 35-46
18. Canuto V.M., Levine J.S., Augustsson T.R., Imhoff C.L., and Giampapa M.S. The young sun and the atmosphere and photochemistry of the early earth. Nature 305 (1983) 281-286
19. Chang, S., 1993. Prebiotic synthesis in planetary environments. In: The Chemistry of Life's Origins, NATO ASI Series C Mathematical and Physical Sciences, p. 416.
20. Cheng R.P., Gellman S.H., and DeGrado W.H. β-peptides: from structure to function. Chem. Rev. 101 (2001) 3219-3232
21. Chyba C., and Sagan C. Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: an inventory for the origins of life. Nature 355 (1992) 125-132
22. Cleaves H.J., and Miller S.L. Oceanic protection of prebiotic organic compounds from UV radiation. Proc. Natl. Acad. Sci. USA 95 (1998) 7260-7263
23. Cleaves H.J., Chalmers J.H., Lazcano A., Miller S.L., and Bada J.L. A reassessment of prebiotic organic synthesis in neutral planetary atmospheres. Origins Life Evol. Biosphere 38 (2008) 105-115
24. Cockell C.S., and Airo A. On the plausibility of a UV transparent biochemistry. Origins Life Evol. Biosphere 32 (2002) 255-274
25. Cooper G.W., Onwo W.M., and Cronin J.R. Alkyl phosphonic acids and sulfonic acids in the Murchison meteorite. Geochim. Cosmochim. Acta 56 (1992) 4109-4115
26. Crick F.H.C. Origin of the genetic code. J. Mol. Biol. 38 (1968) 367-379
27. Cronin J.R. Origin of organic compounds in carbonaceous chondrites. Adv. Space Res. 9 (1989) 59-64
28. Dagley S. Degradation of synthetic organic molecules in the biosphere (1975), National Academy of Sciences, Washington, USA
29. Dworkin J.P., Lazcano A., and Miller S.L. The roads to and from the RNA world. J. Theor. Biol. 222 (2003) 127-134
30. Eigen M., and Schuster P. The hyper cycle. A principle of natural self organization. Part C. The realistic hyper cycle. Naturwissenschaften 65 (1978) 341-369
31. Engel M.H., and Macko S.A. Isotopic evidence for extraterrestrial non-racemic amino acids in the Murchison meteorite. Nature 389 (1997) 265-268
32. Ferris J.F., Joshi P.C., Edelson E.H., and Lawless JG. HCN: a plausible source of purines, pyrimidines and amino acids on the primitive Earth. J. Mol. Evol. 11 (1978) 293-311
33. Finking R., and Marahiel M.A. Biosynthesis of nonribosomal peptides. Ann. Rev. Microbiol. 58 (2004) 453-488
34. Fox S.W., and Windsor C.R. Synthesis of amino acids by the heating of formaldehyde and ammonia. Science 170 (1970) 984-986
35. Friedmann N., Haverland W.J., and Miller S.L. Prebiotic synthesis of the aromatic and other amino acids. In: Buvet R., and Ponnamperuma C. (Eds). Chemical Evolution and the Origin of Life (1971), North-Holland, Amsterdam
36. Friedmann N., and Miller S.L. Phenylalanine and tyrosine synthesis under primitive earth conditions. Science 166 (1969) 766-767
37. Gilbert W. Origin of life: the RNA world. Nature 319 (1986) 618
38. Haldane J.B.S. The origin of life. Rationalist Annual (1929) 1-11
39. Harada K. Formation of amino-acids by thermal decomposition of formamide-oligomerization of hydrogen cyanide. Nature 214 (1967) 479-480
40. Hazen R.M., Filley T.R., and Goodfriend G.A. Selective adsorption of l- and d-amino acids on calcite: implications for biochemical homochirality. Proc. Natl. Acad. Sci. USA 98 (2001) 5487-5490
41. Higgs P.G., and Pudritz R.E. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9 (2009) 483-490
42. Hitz T., and Luisi P.L. Chiral amplification of oligopeptides in the polymerization of l-α-amino acid N-carboxyanhydrides in water. Helv. Chim. Acta 86 (2003) 1423-1434
43. Horowitz N.H. On the evolution of biochemical syntheses. Proc. Natl. Acad. Sci. USA 31 (1945) 153-157
44. Ikutani Y., Okuda T., Sato M., and Akabori S. The reaction of glycine cobalt complex with acetaldehyde. Bull. Chem. Soc. Jpn. 32 (1959) 203-204
45. Illangasekare M., Sanchez G., Nickles T., and Yarus M. Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267 (1995) 643-647
46. Ingraham, J.L., Frederick C. Neidhardt, F.C. (Eds.), 1987. Escherichia coli & Salmonella typhimurium: Cellular & Molecular Biology, vols. 1-2, ASM Press.
47. Iriarte A., Kagan H.M., and Martinez-Carrion M. Biochemistry and Molecular Biology of Vitamin B6 and PQQ-Dependent Proteins (2000), Birkhäuser, Basel
48. Ivanov Ch.P., Ivanov O.Ch., Simeonova R.A., and Mirkova G.D. A study of the interaction of glycine and its oligohomopeptides with formaldehyde and acetaldehyde under possible primitive Earth conditions. Origins Life 13 (1983) 97-108
49. Joyce G.F., Schwartz A.W., Miller S.L., and Orgel L.E. The case for an ancestral genetic system involving simple analogues of the nucleotides. Proc. Natl. Acad. Sci. USA 84 (1987) 4398-4402
50. Joyce, G.F., Orgel, L.E., 2005. Prospects for understanding the origin of the RNA World. In: Gesteland R.F., Atkins J.F. (Eds.), The RNA World, second ed. Cold Spring Harbor Monograph Series, vol. 37.
51. Kauffman S.A. Autocatalytic sets of proteins. J. Theor. Biol. 119 (1986) 1-24
52. Klavecz R.R. Rapid protein catabolism in mammalian cells is obscured by reutilization of amino acids. Biochem. Biophys. Res. Commun. 43 (1971) 76-81
53. Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 (1982) 105-132
54. Lacey J.C., Weber A.L., and White Jr. W.E. A model for the coevolution of the genetic code and the process of protein synthesis: review and assessment. Origins. Life 6 (1975) 273-283
55. Lacey Jr. J.C., and Mullins Jr. D.W. Experimental studies related to the origin of the genetic code and the process of protein synthesis - a review. Origins. Life 13 (1983) 3-42
56. Lauretta, D., McSween Jr, H.Y., Leshin, L. (Eds.), 2006. Meteorites and the Early Solar System II, Arizona University Press.
57. Lazcano A., and Miller S.L. On the origin of metabolic pathways. J. Mol. Evol. 49 (1999) 424-431
58. Lazcano A., and Miller S.L. How long did it take for life to begin and evolve to cyanobacteria?. J. Mol. Evol. 39 (1994) 546-554
59. Lu Y., and Freeland S. On the evolution of the standard amino-acid alphabet. Genome Biol. 7 (2006) 102
60. Lu Y., and Freeland S.J. A quantitative investigation of the chemical space surrounding amino acid alphabet formation. J. Theor. Biol. 250 (2008) 349-361
61. Martin W., and Russell M.J. On the origin of biochemistry at an alkaline hydrothermal vent. Philos. Trans. R. Soc. London B Biol. Sci. 362 (2007) 1887-1925
62. McKay, C.P., 2004. What is life-and how do we search for it in other worlds? PLoS Biol. 2: E302.
63. Metzler D.D., and Snell E.E. Deamination of serine. I. Catalytic deamination of serine and cysteine by pyridoxal and metal salts. J. Biol. Chem. 198 (1952) 353-361
64. Miller S.L. A production of amino acids under possible primitive earth conditions. Science 117 (1953) 528-529
65. Miller S.L. The mechanism of synthesis of amino acids by electric discharges. Biochim. Biophys. Acta 23 (1957) 480-489
66. Miller S.L. The prebiotic synthesis of organic compounds on the Early Earth. In: Michael H.E., and Stephen A.M. (Eds). Organic Geochemistry: Principles and Applications (1993), Plenum Press, New York
67. Miller S.L., and Bada J.L. Submarine hot springs and the origin of life. Nature 334 (1988) 609-611
68. Miller S.L., and Orgel L.E. The Origins of Life on the Earth (1974), Prentice-Hall, New Jersey
69. Miller S.L., Urey H.C., and Oró J. Origin of organic compounds on the primitive earth and in meteorites. J. Mol. Evol. 9 (1976) 59-72
70. Miyakawa S., Cleaves H.J., and Miller S.L. The cold origin of life: A. Implications based on the hydrolytic stabilities of hydrogen cyanide and formamide. Origins Life Evol. Biosphere 32 (2002) 195-208
71. Morowitz H.J., Kostelnik J.D., Yang J., and Cody G.D. The origin of intermediary metabolism. Proc. Natl. Acad. Sci. USA 97 (2000) 7704-7708
72. Nanda V., Andrianarijaona A., and Narayanan C. The role of protein homochirality in shaping the energy landscape of folding. Protein Sci. 16 (2007) 1667-1675
73. Neidhardt, F.C., Ingraham, J.L., Schaechter, M., 1990. Physiology of the Bacterial Cell: A Molecular Approach. Sinauer Associates.
74. Oparin, A.I., 1924. The Origin of Life.
75. Orgel L.E. Evolution of the genetic apparatus. J. Mol. Biol. 38 (1968) 381-393
76. Orgel L.E. Evolution of the genetic apparatus: a review. Cold Spring Harbor Symposium on Quantitative Biology 52 (1987) 9-16
77. Orgel L.E. The implausibility of metabolic cycles on the prebiotic Earth. PLoS Biol. 6 (2008) e18
78. Oró J., and Kamat S. Amino-acid synthesis from hydrogen cyanide under possible primitive Earth conditions. Nature 190 (1961) 442-443
79. Oró J., Miller S.L., and Lazcano A. The origin and early evolution of life on Earth. Ann. Rev. Earth Planet. Sci. 18 (1990) 317-356
80. Pace N.R. The universal nature of biochemistry. Proc. Natl. Acad. Sci. USA 98 (2001) 805-808
81. Peltzer E.T., Bada J.L., Schlesinger G., and Miller S.L. The chemical conditions on the parent body of the Murchison meteorite: Some conclusions based on amino, hydroxy and dicarboxylic acids. Adv. Space Res. 4 (1984) 69-74
82. Pizzarello S., Huang Y., and Fuller M. The carbon isotopic distribution of Murchison amino acids. Geochim. Cosmochim. Acta 68 (2004) 4963-4969
83. Pizzarello S. The chemistry of life's origin: a carbonaceous meteorite perspective. Acc. Chem. Res. 39 (2006) 231-237
84. Ring D., Wolman Y., Friedmann N., and Miller S.L. Prebiotic synthesis of hydrophobic and protein amino acids. Proc. Natl. Acad. Sci. USA 69 (1972) 765-768
85. Robinson B.A., and Tester J.W. Kinetics of alkaline hydrolysis of organic esters and amides in neutrally-buffered solution. Int. J. Chem. Kinet. 22 (1990) 431-448
86. Sagan C., and Khare B.N. Long-wavelength ultraviolet photoproduction of amino acids on the primitive Earth. Science 173 (1971) 417-420
87. 2. I. Amino acids. J. Mol. Evol. 19 (1983) 376-382
88. 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. 290, 1347-1351.
89. Seita T., Yamauchi K., Kinoshita M., and Imoto M. Condensation polymerization of nucleotide analogues. Makromol. Chem. 154 (1972) 255-261
90. Seligmann H. Cost-minimization of amino acid usage. J. Mol. Evol. 56 (2003) 151-161
91. Sephton M.A. Organic compounds in carbonaceous meteorites. Nat. Prod. Rep. 19 (2002) 292-311
92. Shen C., Yang L., Miller S.L., and Oró J. Prebiotic synthesis of histidine. J. Mol. Evol. 31 (1990) 167-174
93. Shibata T., Yamamoto J., Matsumoto N., Yonekubo S., Osanai S., and Soai K. Amplification of a slight enantiomeric imbalance in molecules based on asymmetric autocatalysis: the first correlation between high enantiomeric enrichment in a chiral molecule and circularly polarized light. J. Am. Chem. Soc. 120 (1998) 12157-12158
94. Shock E.L., Amend J.P., and Zolotov M.Y. The early Earth vs the origin of life. In: Canup R.M., and Righter K. (Eds). Origin of the Earth and Moon (2000), University of Arizona Press, Tuscon
95. Swire J. Selection on synthesis cost affects interprotein amino acid usage in all three domains of life. J. Mol. Evol. 64 (2007) 558-571
96. Taillades J., Beuzelin I., Garrel L., Tabacik V., Bied C., and Commeyras A. N-carbamoyl-alpha-amino acids rather than free alpha-amino acids formation in the primitive hydrosphere: a novel proposal for the emergence of prebiotic peptides. Origins Life Evol. Biosphere 28 (1998) 61-77
97. Thomas, P.J., Chyba, C.F., McKay, C.P. (Eds), 1996. Comets and the Origin and Evolution of Life. Springer, Berlin.
98. Trifonov E.N. The triplet code from first principles. J. Biomol. Struct. Dyn. 22 (2004) 1-11
99. Van Trump J.E., and Miller S.L. Prebiotic synthesis of methionine. Science 178 (1972) 859-860
100. Wächtershäuser G. Before enzymes and templates: theory of surface metabolism. Microbiol. Rev. 52 (1988) 452-484
101. Walker J. Formaldehyde. third ed. (1964), Rheinhold, New York
102. Weber A.L., and Lacey Jr. J.C. Aminoacyl transfer from an adenylate anhydride to polyribonucleotides. J. Mol. Evol. 6 (1975) 309-320
103. Weber A.L., and Miller S.L. Reasons for the occurrence of the twenty coded protein amino acids. J. Mol. Evol. 17 (1981) 273-284
104. White R.H. Hydrolytic stability of biomolecules at high temperatures and its implication for life at 250 °C. Nature 310 (1984) 430-432
105. Woese C.R. The Origins of the Genetic Code (1967), Harper & Row, New York
106. Wolfenden R. Degrees of difficulty of water-consuming reactions in the absence of enzymes. Chem. Rev. 106 (2006) 3379-3396
107. Wolman Y., Haverland W.J., and Miller S.L. Nonprotein amino acids from spark discharges and their comparison with the murchison meteorite amino acids. Proc. Natl. Acad. Sci. USA 69 (1972) 809-811
108. Wong J.T. The evolution of a universal genetic code. Proc. Natl. Acad. Sci. USA 73 (1976) 2336-2340
109. Zhang L., Peritz A., and Meggers E. A simple glycol nucleic acid. J. Am. Chem. Soc. 127 (2005) 4174-4175