The hypothesis that the genetic code originated in coupled synthesis of proteins and the evolutionary predecessors of nucleic acids in primitive cells

Life

Volumn 5, Issue 1, 2015, Pages 467-505

  Francis, Brian R ^a  

^a UNIVERSITY OF WYOMING   (United States)

Author keywords

Coupled protein nucleic acid synthesis; Origin genetic code; Primitive cell

Indexed keywords

EID: 84922785133     PISSN: None     EISSN: 20751729     Source Type: Journal    
DOI: 10.3390/life5010467     Document Type: Article

References (181)

1. Neveu, M.; Kim, H.-J.; Benner, S.A. The “strong” RNA world hypothesis: Fifty years old.Astrobiology 2013, 13, 391–403.
2. Joyce, G.F. The antiquity of RNA-based evolution. Nature 2002, 418, 214–221
3. Kurland, C.G. The RNA dreamtime. Bioessays 2010, 32, 866–871.
4. Bernhardt, H.S. The RNA world hypothesis: The worst theory of the early evolution of life (except for all the others). Biol. Direct 2012, 7, doi:10.1186/1745-6150-7-23.
5. Francis, B.R. An alternative to the RNA world hypothesis. Trends Evol. Biol. 2011, 3, doi:10.4081/eb.2011.e2.
6. Li, L.; Francklyn, C.; Carter, C.W. Aminoacylating urzymes challenge the RNA world hypothesis. J. Biol. Chem. 2013, 288, 26856–26863.
7. Caetano-Anollés, G.; Seufferheld, M.J. The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm. J. Mol. Microbiol. Biotechnol. 2013, 23, 152–177
8. Francis, B.R. A hypothesis that ribosomal protein synthesis evolved from coupled protein and nucleic acid synthesis. Chemtracts Biochem. Mol. Biol. 2000, 13, 153–191.
9. Lipmann, F. Attempts to map a process evolution of peptide biosynthesis. Science 1971, 173, 875–885.
10. Wächtershäuser, G. Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA 1990, 87, 200–204.
11. Morowitz, H.J.; Kostelnik, J.D.; Yang, J.; Cody, G.D. The origin of intermediary metabolism. Proc. Natl. Acad. Sci. USA 2000, 97, 7704–7798.
12. Smith, E.; Morowitz, H.J. Universality in intermediary metabolism. Proc. Natl. Acad. Sci. USA 2004, 101, 13168–13173.
13. Russell, M.J.; Martin, W. The rocky roots of the acetyl-CoA pathway. Trends Biochem. Sci. 2004, 29, 358–363.
14. Hazen, R.; Sverjensky, D.A. Mineral surfaces, geochemical complexities, and the origins of life. Cold Spring Harb. Perspect. Biol. 2010, 2, doi:10.1101/cshperspect.a002162.
15. Trefil, J.; Morowitz, H.; Smith, E. The Origin of Life. Am. Sci. 2009, 97, doi:10.1511/2009.78.206.
16. Nitschke, W.; Russell, M.J. Beating the acetyl coenzyme A-pathway to the origin of life. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2013, 368, doi:10.1098/rstb.2012.0258.
17. Sousa, F.L.; Thiergart, T.; Landan, G.; Nelson-Sathi, S.; Pereira, I.A.; Allen, J.F.; Lane, N.; Martin, W.F. Early bioenergetic evolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2013, 368, doi:10.1098/rstb.2013.0088.
18. Weber, A.L. Nonenzymatic formation of “energy rich” lactoyl and glyceroyl thioesters from glyceraldehyde and a thiol. J. Mol. Evol. 1984, 20, 157–166.
19. Weber, A.L. Prebiotic amino acid thioester synthesis: Thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycoaldehyde) and ammonia. Orig. Life Evol. Biosph. 1998, 28, 259–270.
20. De Duve, C. Blueprint for a Cell: The Nature and Origin of Life; Neil Patterson Publishers: Burlington, NC, USA, 1991.
21. Wächtershäuser, G. Groundworks for an evolutionary biology: The iron-sulphur world. Prog. Biophys. Mol. Biol. 1992, 58, 85–201.
22. Heinen, W.; Lauwers, A.-M. Organic sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic environment. Orig. Life Evol. Biosph. 1996, 26, 131–150.
23. Baltscheffsky, H.; Schultz, A.; Baltscheffsky, M. Energy for the origin of life. In Exobiology: Matter, Energy, and Information in the Origin and Evolution of Life in the Universe; Chela-Flores, J., Raulin, F., Eds.; Kluwer Academic Publishers: South Holland, The Netherlands, 1998; pp. 95–102.
24. Deamer, D.W.; Weber, A.L. Bioenergetics and life’s origins. Cold Spring Harb. Perspect. Biol. 2010, 2, doi:10.1101/cshperspect.a004929.
25. Koonin, E.V. The origins of cellular life. Antonie Van Leeuwenhoek 2014, 106, 27–41.
26. Janssen, M.J. Thiolo, thiono, and dithio acids and esters. In The Chemistry of Carboxylic Acids and Esters; Patai, S., Ed.; Interscience: London, UK, 1969; pp. 705–764.
27. Wieland, T.; Schäfer, W. Synthese von oligopeptiden unter zellmoglichen bedingungen. Angew. Chem. 1951, 63, 146–147.
28. Wieland, T.; Pfleiderer, G. Activation of amino acids. Adv. Enzymol. Relat. Subj. Biochem. 1957, 19, 235–266.
29. Maurel, M.C.; Orgel, L.E. Oligomerization of α-thioglutamic acid. Orig. Life Evol. Biosph. 2000, 30, 423–430.
30. Zepik, H.H.; Rajamani, S.; Maurel, M.C.; Deamer, D. Oligomerization of thioglutamic acid: Encapsulated reactions and lipid catalysis. Orig. Life Evol. Biosph. 2007, 37, 495–505.
31. Weber, A.L. Oligoglyceric acid synthesis by autocondensation of glyceroyl thioester. J. Mol. Evol. 1987, 25, 191–196.
32. Dawes, E.A.; Senior, P.J. The role and regulation of energy reserve polymers in micro-organisms. Adv. Microbiol. Physiol. 1973, 10, 135–266.
33. Castresana, J.; Saraste, M. Evolution of energetic metabolism: The respiration-early hypothesis. Trends Biochem. Sci. 1995, 20, 443–448.
34. Martin, W.; Russell, M.J. On the origin of biochemistry at an alkaline hydrothermal vent. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2007, 362, 1887–1925.
35. Liu, Y.; Beer, L.L.; Whitman, W.B. Sulfur metabolism in archaea reveals novel processes. Environ. Microbiol. 2012, 14, 2632–2644.
36. Khare, B.N.; Thompson, W.R.; Chyba, C.F.; Arakawa, E.T.; Sagan, C. Organic solids produced from simple C/H/O/N ices by charged particles: Applications to the outer solar system. Adv. Space Res. 1989, 9, 41–53.
37. Cody, G.D.; Boctor, N.Z.; Filley, T.R.; Hazen, R.M.; Scott, J.H.; Yoder, H.S., Jr. Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science 2000, 289, 1337–1340.
38. Yin, S.; Wang, Z.; Bernstein, E.R. Formaldehyde and methanol formation from reaction of carbon monoxide and hydrogen on neutral Fe2S2 clusters in the gas phase. Phys. Chem. Chem. Phys. 2013, 15, 4699–4706.
39. Fuchs, G. Alternative pathways of carbon dioxide fixation: Insights into the early evolution of life? Ann. Rev. Microbiol. 2011, 65, 631–658.
40. O’Connell, C.; Hommeltoft, S.I.; Eisenberg, R. Electrochemical approaches to the reduction of carbon dioxide. In Carbon Dioxide as a Source of Carbon; Aresta, M., Forti, G., Eds.; D. Reidel Publishing Co.: Dordrecht, The Netherlands, 1987; pp. 33–54.
41. Tezuka, M.; Yajima, T.; Tsuchiya, A.; Matsumoto, Y.; Uchida, Y.; Hidai, M. Electroreduction of carbon dioxide catalyzed by iron-sulfur cluster compounds [Fe4S4(SR)4]2−. J. Am. Chem. Soc. 1982, 104, 6834–6836.
42. Lucas, B.H.; Ritcey, G.M. Reduction of ferric iron by SO2 with heat or SO2 with activated carbon. In Department of Energy, Mines and Resources, Technical Bulletin TB 107; Queen’s Printer and Controller of Stationary: Ottawa, ON, Canada, 1969.
43. Cremlyn, R.J. An Introduction to Organosulfur Chemistry; John Wiley & Sons: Chichester, UK, 1996.
44. Ducluzeau, A.L.; van Lis, R.; Duval, S.; Schoepp-Cothenet, B.; Russell, M.J.; Nitschke, W. Was nitric oxide the first deep electron sink? Trends Biochem. Sci. 2009, 34, 9–15.
45. Mancinelli, R.L.; McKay, C.P. The evolution of nitrogen cycling. Orig. Life Evol. Biosph. 1988, 18, 311–325.
46. Summers, D.P.; Chang, S. Prebiotic ammonia from reduction of nitrite by iron(II) on the early Earth. Nature 1993, 365, 630–633.
47. Summers, D.P. Ammonia formation by the reduction of nitrite/nitrate by FeS: Ammonia formation under acidic conditions. Orig. Life Evol. Biosph. 2005, 35, 299–312.
48. Summers, D.P.; Basa, R.C.; Khare, B.; Rodoni, D. Abiotic nitrogen fixation on terrestrial planets: Reduction of NO to ammonia by FeS. Astrobiology 2012, 12, 107–114.
49. Saville, B. A scheme for colorimetric determination of microgram amounts of thiol. Analyst 1958, 83, 670–672.
50. Broniowska, K.A.; Diers, A.R.; Hogg, N. S-nitrosoglutathione. Biochim. Biophys. Acta. 2013, 1830, 3173–3181.
51. Chyba, C.E.; Sagan, C. Endogenous production, exogenous delivery, and impact-shock synthesis of organic molecules: An inventory for the origin of life. Nature 1992, 355, 125–132.
52. Deamer, D.W. Origins of life: How leaky were primitive cells. Nature 2008, 454, 37–38.
53. Mansy, S.S. Model protocells from single-chain lipids. Int. J. Mol. Sci. 2009, 10, 835–843.
54. Chen, I.A.; Walde, P. From self-assembled vesicles to protocells. Cold Spring Harb. Perspect. Biol. 2010, 2, doi:10.1101/cshperspect.a002170.
55. Pizzarello, S.; Shock, E. The organic composition of carbonaceous meteorites: The evolutionary story ahead of biochemistry. Cold Spring Harb. Perspect. Biol. 2010, 2, doi:10.1101/ cshperspect.a002105.
56. Allamandola, L.J.; Sandford, S.A.; Wpoenka, B. Interstellar polycyclic aromatic hydrocarbons and carbon in interplanetary dust particles and meteorites. Science 1987, 237, 56–59.
57. Parker, E.T.; Zhou, M.; Burton, A.S.; Glavin, D.P.; Dworkin, J.P.; Krishnamurthy, R.; Fernandez, F.M.; Bada, J.L. A plausible simultaneous synthesis of amino acids and simple peptides on the primordial Earth. Angew. Chem. Int. Ed. Engl. 2014, 53, 8132–8136.
58. Mulkidjanian, A.Y.; Bychkov, A.Y.; Dibrova, D.V.; Galperin, M.Y.; Koonin, E.V. Origin of first cells at terrestrial, anoxic geothermal fields. Proc. Natl. Acad. Sci. USA 2012, 109, E821–E830.
59. Mulkidjanian, A.Y.; Bychkov, A.Y.; Dibrova, D.V.; Galperin, M.Y.; Koonin, E.V. Open questions on the origin of life at anoxic geothermal fields. Orig. Life Evol. Biosph. 2012, 42, 507–516.
60. Parker, E.T.; Cleaves, H.J.; Dworkin, J.P.; Glavin, D.P.; Callahan, M.; Aubrey, A.; Lazcano, A.; Bada, J.L. Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. Proc. Natl. Acad. Sci. USA 2011, 108, 5526–5531.
61. Sagan, C.; Khare, B.N. Tholins: Organic chemistry of interstellar grains and gas. Nature 1979, 277, 102–107.
62. McCord, T.B.; Carlson, R.W.; Smythe, W.D.; Hansen, G.B.; Clark, R.N.; Hibbitts, C.A.; Fanale, F.P.; Granahan, J.C.; Segura, M.; Matson, D.L.; et al. Organics and other molecules in the surfaces of Callisto and Ganymede. Science 1997, 278, 271–275.
63. Khare, B.N.; Bakes, E.L.; Cruikshank, D.; McKay, C.P. Solid organic matter in the atmosphere and on the surface of outer Solar System bodies. Adv. Space Res. 2001, 27, 299–307.
64. Waite, J.H., Jr.; Young, D.T.; Cravens, T.E.; Coates, A.J.; Crary, F.J.; Magee, B.; Westlake, J. The process of tholin formation in Titan’s upper atmosphere. Science 2007, 316, 870–875.
65. Gu, X.; Kim, Y.S.; Kaiser, R.I.; Mebel, A.M.; Liang, M.C.; Yung, Y.L. Chemical dynamics of triacetylene formation and implications to the synthesis of polyynes in Titan’s atmosphere. Proc. Natl. Acad. Sci. USA 2009, 106, 16078–16083.
66. Folsom, C.E. The Origin of Life; W.H. Freeman & Co.: San Francisco, CA, USA, 1979
67. McDonald, G.D.; Khare, B.N.; Thompson, W.R.; Sagan, C. CH4/NH3/H2O spark tholin: Chemical analysis and interaction with Jovian aqueous clouds. Icarus 1991, 94, 354–367.
68. Khare, B.N.; Sagan, C. Synthesis of cystine in simulated primitive conditions. Nature 1971, 232, 577–579.
69. Van Trump, J.E.; Miller, S.L. Prebiotic synthesis of methionine. Science 1972, 178, 859–860
70. Raulin, F.; Toupance, G. Effect of H2S on the formation of organic compounds from C, N, H, S model atmospheres submitted to a glow discharge. Orig. Life 1975, 6, 507–512.
71. Khare, B.N.; Sagan, C.; Bandurski, E.L.; Nagy, B. Ultraviolet-photoproduced organic solids synthesized under simulated jovian conditions: Molecular analysis. Science 1978, 199, 1199–1201.
72. Minard, R.D.; Hatcher, P.G.; Gourley, R.C.; Matthews, C.N. Structural investigations of hydrogen cyanide polymers: New insights using TMAH thermochemolysis/GC-MS. Orig. Life Evol. Biosph. 1998, 28, 461–473.
73. He, C.; Lin, G.; Upton, K.T.; Imanaka, H.; Smith, M.A. Structural investigation of Titan tholins by solution-state 1H, 13C, and 15N NMR: One-dimensional and decoupling experiments. J. Phys. Chem. A 2012, 116, 4760–4767.
74. Martin, W.F.; Sousa, F.L.; Lane, N. Evolution. Energy at life’s origin. Science 2014, 344, 1092–1093.
75. Bernstein, M.P.; Sandford, S.A.; Allamandola, L.J.; Gillette, J.S.; Clemett, S.J.; Zare, R.N. UV irradiation of polycyclic aromatic hydrocarbons in ices: Production of alcohols, quinones, and ethers. Science 1999, 283, 1135–1138.
76. Hayashi, T.; Stuchebrukhov, A.A. Electron tunneling in respiratory complex I. Proc. Natl. Acad. Sci. USA 2010, 107, 19157–19162.
77. Schenning, A.P.; Meijer, F.W. Supramolecular electronics; nanowires from self-assembled  π-conjugated systems. Chem. Commun. (Camb.) 2005, doi:10.1039/B501804H.
78. Gray, H.B.; Winkler, J.R. Electron transfer in proteins. Annu. Rev. Biochem. 1996, 65, 537–561.
79. Seyedsayamdost, M.R.; Yee, C.S.; Reece, S.Y.; Nocera, D.G.; Stubbe, J. pH Rate profiles of FnY356-R2s (n = 2, 3, 4) in Escherichia coli ribonucleotide reductase: Evidence that Y356 is a redox-active amino acid along the radical propagation pathway. J. Am. Chem. Soc. 2006, 128, 1562–1568.
80. Koch, A.L.; Schmidt, T.M. The first cellular bioenergetic process: Primitive generation of a proton-motive force. J. Mol. Evol. 1991, 33, 297–304.
81. Wächtershäuser, G. Before enzymes and templates: Theory of surface metabolism. Microbiol. Rev. 1988, 52, 452–484.
82. Huber, C.; Wächtershäuser, G. Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. Science 1997, 276, 245–247.
83. Ragsdale, S.W.; Pierce, E. Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 2008, 1784, 1873–1898.
84. Johnson, D.C.; Dean, D.R.; Smith, A.D.; Johnson, M.K. Structure, function, and formation of biological iron sulfur clusters. Annu. Rev. Biochem. 2005, 74, 247–281.
85. Eck, R.V.; Dayhoff, M.O. Evolution of the structure of ferredoxin based on living relics of primitive amino acid sequences. Science 1966, 152, 363–366.
86. Davis, B.K. Evolution before the origin of species. Prog. Biophys. Mol. Biol. 2002, 79, 77–133.
87. Evans, M.C.; Buchanan, B.B. Photoreduction of ferredoxin and its use in carbon dioxide fixation by a subcellular system from a photosynthetic bacterium. Proc. Natl. Acad. Sci. USA 1965, 53, 1420–1425.
88. Reed, G.H.; Ragsdale, S.W.; Mansoorabadi, S.O. Radical reactions of thiamin pyrophosphate in 2-oxoacid oxidoreductases. Biochim. Biophys. Acta 2012, 1824, 1291–1298.
89. Flint, D.H.; Allen, R.M. Iron-sulfur proteins with nonredox functions Chem. Rev. 1996, 96, 2315–2334.
90. Van Vugt-Lussenburg, B.M.; van der Weel, L.; Hagen, W.R.; Hagedoorn, P.L. Biochemical similarities and differences between the catalytic [4Fe-4S] cluster containing fumarases FumA and FumB from Escherichia coli. PLoS One 2013, 8, e55549.
91. Holm, R.H. Synthetic approaches to the active sites of iron-sulfur proteins. Acc. Chem. Res. 1977, 10, 427–434.
92. Holm, R.H. Electron transfer: Iron-sulfur clusters. In Comprehensive Coordination Chemistry II; McCleverty, J.A., Meyer, T.J., Eds.; Elsevier: New York, NY, USA, 2003; Volume 8, pp. 61–90.
93. Bonomi, F.; Werth, M.T.; Kurtz, D.M. Assembly of FenSn(SR)2− (n = 2, 4) in aqueous media from iron salts, thiols, and sulfur, sulfide, or thiosulfate plus rhodonase. Inorg. Chem. 1985, 24, 4331–4335.
94. Lo, W.; Scott, T.A.; Zhang, P.; Ling, C.C.; Holm, R.H. Stabilities of cubane type [Fe4S4(SR)4]2− clusters in partially aqueous media. J. Inorg. Biochem. 2011, 105, 497–508.
95. Job, R.C.; Bruice, T.C. Iron-sulfur Clusters II: Kinetics of ligand exchange studied on a water-soluble Fe4S4(SR)4n− cluster. Proc. Natl. Acad. Sci. USA 1975, 72, 2478–2482.
96. Dai, S.; Friemann, R.; Glauser, D.A.; Bourquin, F.; Manieri, W.; Schürmann, P.; Eklund, H. Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase. Nature 2007, 448, 92–96.
97. Welte, C.; Deppenmeier, U. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Biochim. Biophys. Acta 2014, 1837, 1130–1147.
98. Duin, E.C.; Madadi-Kahkesh, S.; Hedderich, R.; Clay, M.D.; Johnson, M.K. Heterodisulfide reductase from Methanothermobacter marburgensis contains an active-site [4Fe-4S] cluster that is directly involved in mediating heterodisulfide reduction. FEBS Lett. 2002, 512, 263–268.
99. Shokes, J.E.; Duin, E.C.; Bauer, C.; Jaun, B.; Hedderich, R.; Koch, J.; Scott, R.A. Direct interaction of coenzyme M with the active-site Fe-S cluster of heterodisulfide reductase. FEBS Lett. 2005, 579, 1741–1744.
100. Sakuraba, H.; Oshima, T. Novel energy metabolism in anaerobic hyperthermophilic archaea: A modified Embden-Meyerhof pathway. J. Biosci. Bioeng. 2002, 93, 441–448.
101. Reher, M.; Gebhard, S.; Schonheit, P. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) and nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), key enzymes of the respective modified Embden-Meyerhof pathways in the hyperthermophilic crenarchaeota Pyrobaculum aerophilum and Aeropyrum pernix. FEMS Microbiol. Lett. 2007, 273, 196–205.
102. Leman, L.; Orgel, L.; Ghadiri, M.R. Carbonyl-sulfide-mediated prebiotic formation of peptides. Science 2004, 306, 283–286.
103. Rode, B.M. Peptides and the origin of life. Peptides 1999, 20, 773–786.
104. Mulkidjanian, A.Y.; Galperin, M.Y.; Koonin, E.V. Co-evolution of primordial membranes and membrane proteins. Trends Biochem. Sci. 2009, 34, 206–215.
105. Deamer, D.W. Proton permeation of lipid bilayers. J. Bioenerg. Biomembr. 1987, 19, 457–479.
106. Hofvander, P.; Doan, T.T.; Hamberg, M. A prokaryotic acyl-CoA reductase performing reduction of fatty acyl-CoA to fatty alcohol. FEBS Lett. 2011, 585, 3538–3543.
107. De Duve, C. Clues from present-day biology: The thioester world. In The Molecular Origins of Life; Brach, A., Ed.; Cambridge University Press: Cambridge, UK, 1998; pp. 219–236.
108. Nivikov, Y.; Copley, S.D. Reactivity landscape of pyruvate under simulated hydrothermal vent conditions. Proc. Natl. Acad. Sci. USA 2013, 110, 13283–13288.
109. Wang, W.; Yang, B.; Qu, Y.; Liu, X.; Su, W. FeS/S/FeS2 redox system and its oxidoreductase-like chemistry in the iron-sulfur world. Astrobiology 2011, 11, 471–476.
110. Fukuyama, T.; Lin, S.C.; Li, L. Facile reduction of ethyl thiol esters to aldehydes: Application to a total synthesis of a (+)-neothromycin A methyl ester. J. Am. Chem. Soc. 1990, 112, 7050–7051.
111. Ragsdale, S.W. Pyruvate ferredoxin oxidoreductase and its radical intermediate. Chem. Rev. 2003, 103, 2333–2346.
112. Chabrière, E.; Vernède, X.; Guigliarelli, B.; Charon, M.H.; Hatchikian, E.C.; Fontecilla-Camps, J.C. Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase. Science 2001, 294, 2559–2563.
113. Nakajima, T.; Yabushita, Y.; Tabushi, I. Amino acid synthesis through biogenetic-type CO2 fixation. Nature 1975, 256, 60–61
114. Tanaka, K.; Matsui, T.; Tanaka, T. Catalytic formation of α-keto acids by artifical CO2 fixation. J. Am. Chem. Soc. 1989, 111, 3765–3767.
115. Olsen, R.K.; Currie, J.O. Synthetic uses of thiols. In The Chemistry of the Thiol Group, Part 2; Patai, S., Ed.; John Wiley & Sons: London, UK, 1974; pp. 519–588.
116. Stacy, G.W.; Day, R.I.; Morath, R.J. Schiff bases and related substances II. Reactions of thiols with N-benzylidene aniline and N-benzylidene anthranilic acid. J. Am. Chem. Soc. 1955, 77, 3869–3873.
117. Oakes, T.R.; Stacy, G.W. Reactions of thiols with Schiff bases in nonaqueous solvents. Addition equilibria, cleavage, and reduction. J. Am. Chem. Soc. 1972, 94, 1594–1600.
118. Huber, C.; Wächtershäuser, G. Primordial reductive amination revisited. Tetrahedron Lett. 2003 44, 1695–1697.
119. Kochi, H.; Kikuchi, G. Reactions of glycine synthesis and glycine cleavage catalyzed by extracts of Arthrobacter globiformis grown on glycine. Arch. Biochem. Biophys. 1969, 132, 359–369.
120. Van Poelje, P.D.; Snell, E.E. Pyruvoyl-dependent enzymes. Annu. Rev. Biochem. 1990, 59, 29–59.
121. Hess, U.; Theile, R. Electosynthesis of N-substituted DL-arylglycineesters and 1,2-diarylamino- 1,2-diarylethanes by cathodic reduction of azomethines in the presence of carbon dioxide. J. Prakt. Chem. 1982, 324, 385–399.
122. Silvestri, G.; Gambino, S.; Filardo, G. Electrochemical syntheses involving carbon dioxide. In Enzymatic and Model Carboxylation and Reduction Reactions for Carbon Dioxide Utilization; Arresta, M., Schloss, M.V., Eds.; Kluwer Academic Publishers: South Holland, The Netherlands, 1990; pp. 101–127.
123. Nakada, H.I.; Weinhouse, S. Non-enzymatic transamination with glyoxylic acid and various amino acids. J. Biol. Chem. 1953, 204, 831–836.
124. Howard, B.R.; Endrizzi, J.A.; Remington, S.J. Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 Å resolution: Mechanistic implications. Biochemistry 2000, 39, 3156–3168.
125. Hsu, R.Y.; Mildvan, A.; Chang, G.; Fung, C. Mechanism of malic enzyme from pigeon liver. Magnetic resonance and kinetic studies of the role of Mn2+. J. Biol. Chem. 1976, 251, 6574–6583.
126. Aktas, D.F.; Cook, P.F. A lysine-tyrosine pair carries out acid-base chemistry in the metal ion-dependent pyridine dinucleotide-linked β-hydroxyacid oxidative decarboxylases. Biochemistry 2009, 48, 3565–3577.
127. Goward, C.R.; Nicholls, D.J. Malate dehydrogenase: A model for structure, evolution, and catalysis. Protein Sci. 1994, 3, 1883–1888.
128. Mukhopadhyay, B.; Stoddard, S.F.; Wolfe, R.S. Purification, regulation, and molecular and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain ΔH. J. Biol. Chem. 1998, 273, 5155–5166.
129. Flint, D.H. Escherichia coli fumarase A catalyzes the isomerization of enol and keto oxalacetic acid. Biochemistry 1993, 32, 799–805.
130. White, R.H. Intermediates in the biosynthesis of Coenzyme M (2-mercaptoethane sulfonic acid). Biochemistry 1986, 25, 5304–5308.
131. White, R.H. Biosynthesis of the 7-mercaptoheptanoic acid subunit of component B [(7-mercaptoheptanoyl) threonine phosphate] of methanogenic bacteria. Biochemistry 1989, 28, 860–865.
132. Dörr, M.; Käßbohrer, J.; Grunert, R.; Kreisel, G.; Brand, W.A.; Werner, R.A.; Geilmann, H.; Apfel, C.; Robl, C.; Weigand, W.; et al. A possible prebiotic formation of ammonia from dinitrogen on iron sulfide surfaces. Angew. Chem. Int. Ed. 2003, 42, 1540–1543.
133. Robertson, M.P.; Joyce, G.F. The origins of the RNA world. Cold Spring Harb. Perspect. Biol. 2012, 4, doi:10.1101/cshperspect.a003608.
134. Braud, C.; Brunel, C.; Vert, M. Poly(β-malic acid): A new polymeric drug-carrier. Polym. Bull. (Berl.) 1985, 13, 293–299.
135. Karl, M.; Anderson, R.; Holler, E. Injection of poly(β-L-malate) into the plasmodium of Physarum polycephalum shortens the cell cycle and increases the growth rate. Eur. J. Biochem. 2004, 271, 3805–3811.
136. Liu, S.; Steinbüchel, A. Investigation of poly(β-L-malic acid) production by strains of Aureobasidium pullulans. Appl. Microbiol. Biotechnol. 1996, 46, 273–278.
137. Goodman, I. Polyesters, Volume I: Saturated Polymers; Elsevier: New York, NY, USA, 1965
138. Kasting, J.F. Earth’s earliest atmosphere. Science 1993, 259, 920–926.
139. Portilla-Arias, J.A.; García-Alvarez, M.; Martínez de Ilarduya, A.; Holler, E.; Muñoz-Guerra, S. Thermal decomposition of fungal poly(β-L-malic acid) and poly(β-L-malate)s. Biomacromolecules 2006, 7, 3283–3290.
140. Van der Sluis, P.; Kroon, J. The structure of (+/−) malic acid, (+/−)-C4H6O5. Acta Crystallogr. 1985, C41, 956–959.
141. Gavezzotti, A. Hydrogen bond strength and bond geometry in cyclic dimers of crystalline carboxylic acids. Acta Crystallogr. B 2008, 864, 401–403.
142. Heisler, I.A.; Mazur, K.; Yamaguchi, S.; Tominaga, K.; Meech, S.R. Measuring acetic acid dimer modes by ultra fast time-domain Raman spectroscopy. Phys. Chem. Chem. Phys. 2011, 13, 15573–15579.
143. Losada, M.; Tran, H.; Xu, Y. Lactic acid in solution: Investigations of lactic acid self-aggregation and hydrogen bonding interactions with water and methanol using vibrational absorption and vibrational circular dichroism spectroscopies. J. Chem. Phys. 2008, 128, doi:10.1063/1.2806192.
144. Nakamura, A.; Yao, M.; Chimnaronk, S.; Sakai, N.; Tanaka, I. Ammonia channel couples glutaminase with transamidase reactions in GatCAB. Science 2006, 312, 1954–1958.
145. Beccera-Figueroa, L.; Ojeda-Porras, A.; Gamba-Sánchez, D. Transamidation of carboxamides catalyzed by Fe(III) and water. J. Org. Chem. 2014, 79, 4544–4552.
146. Levy, M.; Silberman, D.E. The reactions of amino and imino acids with formaldehyde. J. Biol. Chem. 1937, 118, 723–734.
147. Kitamoto, Y.; Maeda, H. Reevaluation of the reaction of formaldehyde at low concentrations with amino acids. J. Biochem. 1980, 87, 1519–1530.
148. Argyrou, A.; Washabaugh, M.W.; Pickart, C.M. Dihydroorotate dehydrogenase from Clostridium oroticum is a class 1B enzyme and utilizes a concerted mechanism of catalysis. Biochemistry 2000, 39, 10373–10384.
149. Wise, E.; Yew, W.S.; Babbitt, P.C.; Gerlt, J.A.; Rayment, I. Homologous (β/α)8-barrel enzymes that catalyze unrelated reactions: Orotidine-5'-monophosphate decarboxylase and 3-keto-L-gulonate-6-phosphate decarboxylase. Biochemistry 2002, 41, 3861–3869.
150. Mittapalli, G.K.; Osornio, Y.M.; Guerrero, M.A.; Reddy, K.R.; Krishnamurthy, R.; Eschenmoser, A. Mapping the landscape of potentially primordial informational oligomers: Oligodipeptides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Angew. Chem. Int. Ed. 2007, 46, 2478–2484.
151. Stuecker, T.N.; Hodge, K.M.; Escalante-Semerena, J.C. The missing link in coenzyme A biosynthesis: PanM (formerly YhhK), a yeast GCN5 acetyltransferase homologue triggers aspartate decarboxylase (PanD) maturation in Salmonella enterica. Mol. Microbiol. 2012, 84, 608–619.
152. Chladek, S. The synthesis, reactions and properties of the 2'(3')-O-aminoacyl and peptidyl nucleosides and nucleotides. In Chemistry of Nucleosides and Nucleotides; Townsend, L.B., Ed.; Springer Science & Business Media: New York, NY, USA, 1994; Volume 3, pp. 107–143.
153. Gavrilova, L.P.; Kostiashkina, O.E.; Koteliansky, V.E.; Rutkevitch, N.M.; Spirin, A.S. Factor-free (“non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J. Mol. Biol. 1976, 101, 537–552.
154. Southworth, D.R.; Brunelle, J.L.; Green, R. EFG-independent translocation of the mRNA:tRNA complex is promoted by modification of the ribosome with thiol-specific reagents. J. Mol. Biol. 2002, 324, 611–623.
155. Rich, A. On the problems of evolution and biochemical information transfer. In Horizons in Biochemistry; Kasha, M., Pullman, B., Eds.; Academic Press: New York, NY, USA, 1962; pp. 103–126.
156. Weber, A.L.; Orgel, L.E. Poly(U)-directed peptide bond formation from the 2'(3')-glycyl esters of adenosine derivatives. J. Mol. Evol. 1980, 16, 1–10.
157. Reusch, R.N. Physiological importance of poly-(R)-3-hydroxybutyrates. Chem. Biodivers. 2012, 9, 2343–2366.
158. Brooks, D.J.; Fresco, J.R. Increased frequency of cysteine, tyrosine, and phenylalanine residues since the last universal ancestor. Mol. Cell. Proteomics 2002, 1, 125–131.
159. Francis, B.R. Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J. Mol. Evol. 2013, 77, 134–158.
160. Eigen, M.; Winkler-Oswatitsch, R. Transfer-RNA, an early gene? Naturwissenschaften 1981, 68, 217–228.
161. Ikehara, K.; Omori, Y.; Arai, R.; Hirose, A. A novel theory on the origin of the genetic code: A GNC-SNS hypothesis. J. Mol. Evol. 2002, 54, 530–538.
162. Higgs, P.G. A four-column theory for the origin of the genetic code: Tracing the evolutionary pathways that gave rise to an optimized code. Biol. Direct 2009, 4, doi:10.1186/1745-6150-4-16.
163. Van der Gulik, P.; Massar, S.; Gilis, D.; Burhman, H.; Rooman, M. The first peptides: The evolutionary transition between prebiotic amino acids and early proteins. J. Theor. Biol. 2009, 261, 531–539.
164. Fujihashi, M.; Numoto, N.; Kobayashi, Y.; Mizushima, A.; Tsujimura, M.; Nakamura, A.; Kawarabayasi, Y.; Miki, K. Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor. J. Mol. Biol. 2007, 365, 903–910.
165. Deamer, D.W.; Dworkin, J.P.; Sandford, S.A.; Bernstein, M.P.; Allamandola, L.J. The first cell membranes. Astrobiology 2002, 2, 371–381.
166. Segré, D.; Ben-Eli, D.; Deamer, D.W.; Lancet, D. The Lipid World. Orig. Life Evol. Biosph. 2001, 31, 119–145.
167. Russell, M.J.; Hall, A.J. The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. J. Geol. Soc. Lond. 1997, 154, 377–402.
168. Alpermann, T.; Rüdel, K.; Rüger, R.; Steiniger, F.; Nietzsche, S.; Filiz, V.; Förster, S.; Fahr, A.; Weigand, W. Polymersomes containing iron sulfide (FeS) as primordial cell model: For the investigation of energy providing redox reactions. Orig. Life Evol. Biosph. 2010, 41, 103–119.
169. Menzel, K.; Menzel, K.; Apfel, U.P.; Wolter, N.; Rüger, R.; Alpermann, T.; Steiniger, F.; Gabel, D.; Förster, S.; Weigand, W.; et al. [FeFe]-hydrogenase models assembled into vesicular structures. J. Liposome Res. 2014, 24, 59–68.
170. Summers, D.P.; Noveron, J.; Basa, R.C. Energy transduction inside of amphiphilic vesicles: Encapsulation of photochemically active semiconducting particles. Orig. Life Evol. Biosph. 2009, 39, 127–140.
171. Emiliozzi, R.; Pichat, L.; Herbert, M. Preparation of cysteine-S35 hydrochloride. Bull. Soc. Chem. Fr. 1959, 1544–1545.
172. Orgel, L.E. Some consequences of the RNA world hypothesis. Orig. Life Evol. Biosph. 2003, 33, 211–218.
173. Ross, D.S. The viability of a nonenzymatic reductive citric acid cycle—Kinetics and thermochemistry. Orig. Life Evol. Biosph. 2007, 37, 61–65.
174. Orgel, L.E. The implausibility of metabolic cycles on the prebiotic Earth. PLoS Biol. 2008, 6, doi:10.1371/journal.pbio.0060018.
175. Copley, S.D.; Smith, E.; Morowitz, H.J. The emergence of sparse metabolic networks. J. Cosmol. 2010, 10, 3345–3361.
176. Engelhart, A.E.; Hud, N.V. Primitive genetic polymers. Cold Spring Harb. Perspect. Biol. 2010, 2, doi:10.1101/cshperspect.a002196.
177. Szathmáry, E. Why are there four letters in the genetic alphabet? Nat. Rev. Genet. 2003, 4, 995–1001.
178. Calvin, M. Chemical Evolution: Molecular Evolution towards the Origin of Living Systems on the Earth and Elsewhere; Clarendon Press: London, UK, 1969.
179. Rauchfuss, H. Chemical Evolution and the Origin of Life; Springer-Verlag: Berlin/Heidelberg, Germany, 2008.
180. Schrum, J.P.; Zhu, T.F.; Szostak, J.W. The origins of cellular life. Cold Spring Harb. Perspect. Biol. 2010, 2, doi:10.1101/cshperspect.a002212.
181. Mansy, S.S.; Schrum, J.P.; Krishnamurthy, M.; Tobé, S.; Treco, D.A.; Szostak, J.W. Template-directed synthesis of a genetic polymer in a model protocell. Nature 2008, 454, 122–125.