Emergence of life: From functional RNA selection to natural selection and beyond

Frontiers in Bioscience - Landmark

Volumn 19, Issue 7, 2014, Pages 1117-1150

  Wong, Jeffrey Tze Fei ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Coevolution theory; Last universal common ancestor; Metabolic expansion law; Peptidated RNA world; RNA World; Synthetic life

Indexed keywords

RNA; TRANSFER RNA;

ANIMAL; BIOGENESIS; CLASSIFICATION; EVOLUTION; GENETIC CODE; GENETIC SELECTION; GENETICS; HUMAN; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY;

ANIMALS; BIOGENESIS; BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; GENETIC CODE; HUMANS; PHYLOGENY; RNA; RNA, TRANSFER; SELECTION, GENETIC;

EID: 84904582489     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/4271     Document Type: Article

References (208)

1. Jacques Monod. Chance and Necessity. Vintage Books, New York p. 138-148 (1972)
2. Michael Polanyi: Life's irreducible structure. Science 160, 1308-12 (1968)
3. Howard H. Pattee: On the origin of macromolecular sequences. Biophys J 1, 683-710 (1961)
4. David L. Abel: The capabilities of chaos and complexity. Int J Mol Sci 10, 247-291 (2009)
5. David L. Abel: The biosemiosis of prescriptive information. Semiotica 174, 1-19 (2009)
6. David L. Abel: The 'cybernetic cut': progressing from description to prescription in systems theory. Open Cybernetics Systematics J 2, 252-262 (2008).
7. Gyula Palyi, Claudia Zucchi, Luciano Caglioti: Short definitions of life. In: Fundamentals of Life. Eds: Palyi G, Zucchi C, Caglioti L. Elsevier, Paris p. 15-55 (2002)
8. J Tze-Fei Wong: Introduction. In: Prebiotic Evolution and Astrobiology. Eds: J Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin 1-9 (2009)
9. J Tze-Fei Wong, Hong Xue: Self-perfecting evolution of heteropolymer building blocks and sequences as the basis of life. In: Fundamentals of Life. Eds: Palyi G, Zucchi C, Caglioti L. Elsevier, Paris p. 473-494 (2002).
10. Gerald F. Joyce, Leslie E. Orgel: Prospects for understanding the origin of the RNA World. In: The RNA world 2nd ed. Eds: Gesteland RF, Cech TR, Atkins JF. Cold Spring Harbor Laboratory Press, p. 49-77 (1999)
11. Tracey A Lincoln, Gerald F Joyce: Self-sustained replication of an RNA enzyme. Science 323, 1229-32 (2009)
12. Jack W Szostak: The eightfold path to non-enzymatic RNA replication, J Systems Chem 3, 2 (2012)
13. Gunter Wachtershauser: Before enzymes and templates: theory of surface metabolism. Microbiol Rev 52, 452-484 (1988)
14. Harold J Morowitz, Jennifer D Kostelnik, Jeremy Yang, George D. Cody: The origin of intermediary metabolism. Proc Natl Acad Sci USA 97, 7704-7708 (2000) (Pubitemid 30460711)
15. Stuart A. Kauffman: Autocatalytic sets of proteins. J Theor Biol 119, 1-24 (1986) (Pubitemid 16104859)
16. Frank AL Anet: The place of metabolism in the origin of life. Curr Opinion Chem Biol 8, 654-659 (2004)
17. Leslie E. Orgel: The implausibility of metabolic cycles on the prebiotic Earth. PLoS Biol 6, e18 (2008)
18. James M. Carothers, Stephanie C. Oestreich, Jonathan H. Davis, Jack W. Szostak: Informational complexity and functional activity of RNA structures. J Am Chem Soc 126, 5130-5137 (2004) (Pubitemid 38509469)
19. Malcolm M. Anderson: Hybridization strategy in gene probes 2, Eds: B. D. Hames and S. J. Higgins, Oxford Univ. Press, p. 8 (1995)
20. Veena Vijayanathan, Thresia Thomas, Leonard H Sigal, T. J. Thomas: Direct measurement of the association constant of HER2/neu antisense oligonucleotide to its target RNA sequence using a molecular beacon. Antisense Nucl Scid Drug Develop 12, 225-233 (2002)
21. H Thomou, NK Katsanos: The theory of DNA-RNA hybridization reaction Biochem J 153, 241-247 (1976)
22. Jack W Szostak: Molecular messages. Nature 423, 689 (2003) (Pubitemid 36735677)
23. Markus Pech, Knud H. Nierhaus. The minimal cell. In: Prebiotic Evolution and Astrobiology. Eds J. Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin p. 10-17 (2009)
24. Eun Jeong Cho, Andrew D. Ellington: Optimization of the biological component of a bioelectrochemical cell. Bioelectrochemistry 70, 165-72 (2007) (Pubitemid 44960201)
25. David M. Brackett□, Thorsten Dieckmann: Aptamer to ribozyme: the intrinsic catalytic potential of a small RNA. Chembiochem 7, 839-43 (2006) (Pubitemid 43764195)
26. Gerald F Joyce: Evolution in an RNA World. Cold Spring Harbor Symp Quant Biol 74, 17-23 (2009)
27. Stanley L. Miller: The formation of organic compounds on the primitive Earth. Annals NY Acad Sci 69, 260-275 (1957)
28. S Yuasa, D Flory, B Basile, J. Oro: Abiotic synthesis of purines and other heterocyclic compounds by the action of electric discharges. J Mol Evol 21, 76-80 (1984) (Pubitemid 15172246)
29. David W Deamer. Prebiotic amphiphilic compounds. In: Origins Genesis, Evolution and Diversity of Life. Ed: Joseph Seckbach. Kluwer p. 77-89 (2004)
30. Ahmed I Rushdi, Bernd R T Simoneit: Lipid formation by aqueous Fischer-Tropsch-Type synthesis over a temperature range of 100 to 400 °C. Orig Life Evol Biosph 31, 103-118 (2001) (Pubitemid 32219177)
31. C Cheng, C Fan, R Wan, C Tong, Z Miao, J Chen, Y Zhao: Phosphorylation of adenosine with trimetaphosphate under simulated prebiotic conditions. Orig Life Evol Biosph 32, 219-224 (2002)
32. J Tze-Fei Wong: Biomolecules. In: Prebiotic Evolution and Astrobiology. Eds J Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin p. 65-75 (2009)
33. Leslie E Orgel: Prebiotic chemistry and the origin of the RNA World. Critical Review Biochem Mol Biol 39, 99-123 (2006)
34. James P Ferris: Montmorillonite-catalyzed formation of RNA oligomers: the possible role of catalysis in the origin of life. Phil Tran R Soc B 361, 1777-1786 (2006) (Pubitemid 44580380)
35. Pierre-Alain Monnard, Anastassia Kanavarioti, David W. Deamer: Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucelobases. J Am Chem Soc 125, 13734-13740 (2003) (Pubitemid 37386048)
36. S Rajamani, A Vlassov, S Benner, A Coombs, F Olasagasti, D Deamer: Lipid-assisted synthesis of RNAlike polymers from mononucleotides. Orig. Life Evol Biosph 38, 57-74 (2007)
37. Pierre-Alain Monnard: The dawn of the RNA world. In: Prebiotic Evolution and Astrobiology. Eds J. Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin p. 76-86 (2009)
38. Andre Brack: The chemistry of life's origins. In: Origins, Genesis, Evolution and Diversity of Life. Ed: Seckbach J. Kluwer. Academic Publishers, p. 61-73 (2004)
39. Eugene V Koonin, William Martin: On the origin of genomes and cells within inorganic compartments. Trends Genet 21, 647-54 (2005) (Pubitemid 41608687)
40. Christian De Duve: Blueprint for a Cell. Neil Patterson Publishers. p. 113-116 (1991)
41. Pasquale Stano, Pier Luigi Luisi: Precellular evolution. In: Prebiotic Evolution and Astrobiology. Eds J Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin p. 94-105 (2009)
42. Humberto R Maturana, Francisco J Varela: Autopoiesis and cognition: the realization of the living. Springer. (1980)
43. Stephen J Mojzsis, Ramanarayanan Krishnamurthy, Gustaf Arrhenius. Before RNA and after: geophysical and geochemical constraints on molecular evolution. In: The RNA World, 2nd ed, Eds: R. F. Gesteland, T. R. Cech, J. F. Atkins. Cold Spring Harbor Laboratory Press 1-47 (1999)
44. Atsushi Nakabachi, Atsushi Yamashita, Hidehiro Toh, Hajime Ishikawa, Helen E Dunbar, Nancy A Moran, Masahira Hattori: The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314, 267 (2006) (Pubitemid 44571965)
45. Carole Lartigue, John I Glass, Nina Alperovich, Rembert Pieper, Prashanth P Parmer, Clyde A Hutchison III, Hamilton O Smith, J Craig Venter: Genome transplantation in bacteria: changing one species to another. Science 317, 632-638 (2007) (Pubitemid 47229957)
46. Stephen J Freeland, Robin D Knight, Laura F Landweber: Do proteins predate DNA? Science 286, 690-692. (1999)
47. Albert Eschenmoser: Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 50, 12412-72 (2011)
48. J Tze-Fei Wong. Genetic code. In: Prebiotic Evolution and Astrobiology. Eds J Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin, p. 110-119 (2009)
49. Thomas R Cech: The RNA Worlds in context. Cold Spring Harb Perspective Biol 4(7):a006742 (2012)
50. J Tze-Fei Wong: Origin of genetically encoded protein synthesis: a model based on selection for RNA peptidation. Orig Life Evol Biosph 21, 165-76 (1991)
51. Mali Illangasekare, Michael Yarus: Small moleculesubstrate interactions with a self-aminoacylating ribozyme. J Mol Biol 268, 631-639 (1997) (Pubitemid 27208080)
52. B Zhang, TR Cech: Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features. Chem Biol 5, 539-553 (1998) (Pubitemid 29000115)
53. N Lee, Y Bessho, K Wei, JW Szostak, H Suga: Ribozyme-catalyzed tRNA aminoacylation. Nat Struct Biol 7, 28-33 (2000) (Pubitemid 30043244)
54. Charles G Kurland: The RNA dreamtime: modern cells feature proteins that might have supported a prebiotic polypeptide world but nothing indicates that RNA world ever was. Bioessays 32, 866-871 (2010)
55. Harry F Noller: The driving force for molecular evolution of translation. RNA 10, 1833-1837 (2004) (Pubitemid 39557819)
56. Massimo Di Giulio: On the RNA world: evidence in favor of an early ribonucleopeptide world. J Mol Evol 45, 571-578 (1997) (Pubitemid 28052934)
57. Ajith Harish, Gustavo Caetano-Anolles: Ribosomal history reveals origins of modern protein synthesis. PLoS ONE 7, e32776 (2012)
58. Gustavo Caetano-Anolles, Kyung Mo Kim, Derek Caetano-Anolles: The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein synthesis. J Mol Evol 74, 1-34 (2012)
59. Steven A. Benner, Petra Burgstaller, Thomas R. Battersby, Simona Jurczyk. Did the RNA World exploit an expanded genetic alphabet? In: The RNA World 2nd ed. Eds: R. F. Gesteland, T. R. Cech, J. F. Atkins. Cold Spring Harbor Laboratory Press; 163-181 (1999)
60. Gonzalo L Vilas, Maria M. Corvi, Greg J Plummer, Andrea M. Seime, Gareth R. Lambkin, Luc G. Berthiaume: Posttranslational myristoylation of caspaseactivated p21-activated protein kinase 2 (PAK2) potentiates late apoptotic events. Proc Natl Acad Sci USA 103, 6542-6547 (2006)
61. Randall A. Hughes and Andrew D. Ellington. Ribozymes and the evolution of metabolism. In: Prebiotic Evolution and Astrobiology. Eds: J. Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin (2009)
62. J Tze-Fei Wong: Evolution of the genetic code. Microbiol Sci 5, 174-181 (1988)
63. J Tze-Fei Wong: A coevolution theory of the genetic code. Proc Natl Acad Sci USA 72, 1909-1912 (1975)
64. J Tze-Fei Wong: Question 6: Coevolution theory of the genetic code: a proven theory. Orig Life Evol Biosph 37, 403-408 (2007)
65. J Tze-Fei Wong: Coevolution of the genetic code and amino acid biosynthesis. Trends in Biochem Sci 6, 33-35 (1981)
66. J Tze-Fei Wong: Coevolution theory of the genetic code at age thirty. BioEssays 27, 416-425 (2005) (Pubitemid 40592598)
67. Kensei Kobayashi, Masahiko Tsuchiya, Tairo Oshima, Hiroshi Yanagawa: Abiotic synthesis of amino acids and imidazole by proton irradiation of simulated primitive earth atmosphere. Orig Life Evol Biosph 20, 99-109 (1990)
68. Kensei Kobayashi, Takeo Kaneko, Takeshi Saito, Tairo Oshima: Amino acid formation in gas mixtures by high energy particle irradiation. Orig Life Evol Biosph 28, 155-165 (1998) (Pubitemid 128513028)
69. Sandra Pizzarello: Meteorites and the chemistry that preceded life's origin. In: Prebiotic Evolution and Astrobiology. Eds: J. Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin, p. 46-51. (2009)
70. Massimo Di Giulio, Umberto Amato: The close relationship between the biosynthetic families of amino acids and the organization of the genetic code. Gene 435, 9-12 (2009).
71. Edward N Trifonov, Idan Gabdank, Danny Barash, Yehoshua Sobolevsky: Primordia Vita. Deconvolution from modern sequences. Orig Life Evol Biosph 36, 559-565 (2006) (Pubitemid 46141439)
72. J Tze-Fei Wong, Patricia M. Bronskill: Inadequacy of prebiotic synthesis as origin of proteinous amino acids. J Mol Evol 13, 115-125 (1979)
73. J Tze-Fei Wong. Evolution and mutation of the amino acid code. In: Dynamics of Biochemical Systems. Eds: Ricard J, Cornish-Bowden A. Plenum New York, 247-257 (1984)
74. Patrick O'Donoghue, Anurag Sethi, Carl R. Woese, Zaida A. Luthey-Schulten: The evolutionary history of Cys-tRNACys formation. Proc Natl Acad Sci USA 102, 19003-19008 (2005)
75. Hong-Yu Zhang, Tao Qin, Ying-Ying Jiang, Gustavo Caetano-Anolles: Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis ansd iron-sulfur proteins. J Biol Struct Dynamics 30, 542-545 (2012)
76. Herve Roy, Hubert Dominique Becker, Joseph Reinbolt, Daniel Kern: When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism. Proc Nalt Acad Sci USA 100, 9837-42 (2003) (Pubitemid 37087028)
77. Christopher Francklyn: tRNA synthetase paralogs: Evolutionary links in the transition from tRNA-dependent amino acid biosynthesis to de novo biosynthesis. Proc Nalt Acad Sci USA 100, 9650-52 (2003) (Pubitemid 37086993)
78. Stephane Commans, August Böck: Selenocysteine inserting tRNAs: an overview. FEMS Microb Rev 23, 335-351 (1999) (Pubitemid 29236182)
79. Gayathri Srinivasan, Carey M. James, Joseph A. Krzycki: Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296, 1459-1462 (2002) (Pubitemid 34553089)
80. Paul G Higgs: A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biology Direct 4, doi:10.1186/1745-6150-4-16 (2009)
81. Massimo Di Giulio: An extension of the coevolution theory of the genetic code. Biology Direct 3:37, doi:10.1186/1745-6150-3-37 (2008)
82. Hong Xue, Wenyan Shen, Giege R. J Tze-Fei Wong: Identity elements of tRNA (Trp). Identification and evolutionary conservation. J Biol Chem 268, 9316-22 (1993) (Pubitemid 23145977)
83. Qing Guo, Qingguo Gong, Ka-Lok Tong, Bente Vestergaard, Annie Costa, Jean Desgres, Mansim Wong, Henri Grosjean, Guang Zhu, J Tze-Fei Wong, Hong Xue: Recognition by tryptophanyl-tRNA synthetases of discriminator base on tRNATrp from three biological domains. J Biol Chem 277, 14343-9 (2002) (Pubitemid 34968052)
84. Richard Giege, Marie Sissler, Catherine Florentz: Universal rules and idiosyncratic features in tRNA identity. Nucleic Acid Res 26, 5017-5035 (1998)
85. J Tze-Fei Wong: The evolution of a universal genetic code. Proc Natl Acad Sci USA 73, 2336-2340 (1976)
86. J Tze-Fei Wong. Kinetics of Enzyme Mechanisms. Academic Press p. 200-201 (1975)
87. J Tze-Fei Wong: Role of minimization of chemical distances between amino acids in the evolution of the genetic code. Proc Natl Acad Sci USA 77, 1083-1086 (1980)
88. Stephen J Freeland, Laurence D Hurst: The genetic code is one in a million. J Mol Evol 47, 238-248 (1998) (Pubitemid 28455140)
89. Massimo Di Giulio, Mario Medugno: The level and landscape of optimization in the origin of the genetic code. J Mol Evol 52, 372-382 (2001) (Pubitemid 32368247)
90. Massimo Di Giulio: The origin of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analysis tautologous. J Theo Biol 208, 141-144 (2001) (Pubitemid 32099416)
91. David Morgens, Andre Cavalcanti: An alternative look at code evolution: using non-canonical codes to evaluate adaptive and historical models for the origin of the genetic code. J Mol Evol, 76:71-80 (2013).
92. Rob Knight, Laura Landweber, and Michael Yarus: Tests of a stereochemical genetic code. In: Translation Mechanisms. Eds. J. Lapointe, L. Brakier-Gingras. Landes Bioscence 115-12 (2003)
93. Antonio Lazcano, Stanley L. Miller: On the origin of metabolic pathways. J Mol Evol 49, 424-431 (1999) (Pubitemid 29463385)
94. Carl Zimmer. How and where did life on Earth arise? Science 309, 89 (2005) (Pubitemid 40934969)
95. Jeffrey L Bada, Bruce Fegley Jr, Stanley L Miller, Antonio Lazcano, H. James Cleaves, Robert M. Hazen, John Chalmers. Debating evidence for the origin of life on Earth. Science 315, 937-938 (2007) (Pubitemid 46281165)
96. Günter Wächtershäuser, Claudia Huber: Response to "Debating evidence for the origin of life on Earth". Science 315, 938-939 (2007)
97. David S Ross: A quantitative evaluation of the ironsulfur world and its relevance to life's origins. Astrobiology 8, 267-272 (2008) (Pubitemid 351518433)
98. Frederick A Kundell: A suggested pioneer organism for the Wachtershauser origin of life hypothesis. Orig Life Evol Biosph 41, 175-198 (2011)
99. Carl R Woese, Otto Kandler, Mark L Wheelis: Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87, 4576-79 (1990)
100. N Iwabe, K Kuma, M Hasegawa, S Osawa, T Miyata: Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86, 9355-59 (1989) (Pubitemid 20010424)
101. James R Brown, W Ford Doolittle: Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92, 2441-45 (1995)
102. Carl R Woese: Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97, 8392-96 (2000) (Pubitemid 30639683)
103. E Pennisi: Is it time to uproot the tree of life? Science 284, 1305-07 (1999)
104. Yuri I Wolf, Igor B Rogozin, Nick V Grishin, Eugene V Koonin: Genome trees and the tree of life. Trends Genetics 18, 472-479 (2002)
105. J Tze-Fei Wong, Jianhuan Chen, Wai-Kin Mat, Siu-Kin Ng, Hong Xue: Polyphasic evidence delineating the root of life and roots of biological domains. Gene 403, 39-52. (2007) (Pubitemid 47488703)
106. Hong Xue, Ka-Lok Tong, Christian Marck, Henri Grosjean, J Tze-Fei Wong: Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life. Gene 310, 59-66 (2003) (Pubitemid 36703300)
107. Hong Xue, Siu-Kin Ng, Ka-Lok Tong, J Tze-Fei Wong: Congruence of evidence for a Methanopyrusproximal root of life based on transfer RNA and aminoacyl-tRNA synthetase genes. Gene 360, 120-130 (2005) (Pubitemid 41446886)
108. Feng-Jie Sun, Gustavo Caetano-Anollés: Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses. PLoS Computational Biol 4:e1000018. (2008)
109. Jason Raymond, Daniel Segrè: The effect of oxygen on biochemical networks and the evolution of complex life. Science 311, 1764-67 (2006)
110. Ka-Lok Tong, J Tze-Fei Wong: Anticodon and wobble evolution. Gene 333, 169-177 (2004) (Pubitemid 38737363)
111. Wai-Kin Mat, Hong Xue, J Tze-Fei Wong: The genomics of LUCA. Frontiers Biosc 13, 5605-5613 (2008)
112. J Tze-Fei Wong. Root of life. In: Prebiotic Evolution and Astrobiology. Eds J. Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin, p. 120-144 (2009)
113. Eugene V Koonin: Comparative genomics, minimum gene sets and the last universal common ancestor. Nat Rev Microbiol 1, 127-136 (2003)
114. A Mushegian: Gene content of LUCA, the last universal common ancestor. Frontiers Biosc 13, 4657-66 (2008) (Pubitemid 351589190)
115. Massimo Di Giulio: The evidence that the tree of life is not rooted within the archaea is unreliable: a reply to Skophammer et al. Gene 194, 105-106 (2007).
116. John B. Corliss, John A. Baross, Sarah E. Hoffman: A hypothesis concerning the relationship between submarine hot springs and the origin of life on Earth. Oceanol Acta 4, 59-69 (1981)
117. Everett L. Shock: Chemical environment in submarine hydrothermal systems. Orig Life Evol Biosphere (suppl.) 22, 67-107 (1992)
118. James F. Kasting, Janet L. Siefert: Life and the evolution of Earth's atmosphere. Science 296, 1066-1068 (2002) (Pubitemid 34517114)
119. James Kasting: The primitive earth. In: Prebiotic Evolution and Astrobiology. Eds J. Tze-Fei Wong, Antonio Lazcano. Landes Bioscience, Austin, p. 57-64 (2009)
120. A Lazcano, R Guerrero, L Margulis, J. Oro: The evolutionary transition from RNA to DNA in early cells. J Mol Evol 27, 283-290. (1988)
121. Patrick Forterre: The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie 87, 793-803 (2005) (Pubitemid 41297805)
122. Patrick Forterre: Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domains. Proc Natl Acad Sci USA 103, 3669-3674 (2006) (Pubitemid 43376613)
123. Norman H. Sleep, Kevin J Zahnle, James F Kasting, Harold J Morowitz: Annihilation of ecosystems by large asteroid impacts on the early Earth. Nature 342, 139-142. (1989) (Pubitemid 20409866)
124. Norman H Sleep: The Hadean-Archaean environment. Cold Spring Harb Perspective Biol 2, a002527 (2010)
125. J Tze-Fei Wong: Membership mutation of the genetic code: loss of fitness by tryptophan. Proc Natl Acad Sci USA 80, 6303-6306 (1983)
126. Wai-Kin Mat, Hong Xue, J Tze-Fei Wong: Genetic code mutations: the breaking of a three billion year invariance. PLoS ONE 5(8):e12206 (2010)
127. Patricia M. Bronskill, J Tze-Fei Wong: Suppression of fluorescence of tryptophan residues in proteins by replacement with 4-fluorotryptophan. Biochem J 249, 305-308. (1988)
128. Chi-Shing Yu, Aldrin Kay-Yuen Yim, Wai-Kin Mat, Amy Hin-Yan Tong, Si Lok, Hong Xue, Stephen Kwok-Wing Tsui, J Tze-Fei Wong, Ting-Fung Chan: Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code. Genome Biol Evol doi:10.1093/gbe/evu044 (2014)
129. Tina Hesman: Code breakers. Scientists are altering bacteria in a most fundamental way. Science News 157, 360-362 (2000)
130. J Tze-Fei Wong, Hong Xue: Synthetic genetic codes as the basis of synthetic life. In: Chemical Synthetic Biology. Eds: Pier Luigi Luisi, Cristano Chiarabelli. Wiley, p. 178-199 (2010)
131. Jamie M Bacher, Andrew D. Ellington: Selection and characterization of Escherichia coli variants capable of growth on otherwise toxic tryptophan analogues. J Bacteriol 183:5414-5425 (2001) (Pubitemid 32802615)
132. Jamie M Bacher, Randall A Hughes, J Tze-Fei Wong, Andrew D Ellington: Evolving new genetic codes. Trends Ecol Evol 19, 69-75 (2004) (Pubitemid 38105890)
133. JM Bacher, JJ Bull, AD Ellington: Evolution of phage with chemically ambiguous proteomes. BMC Evol Biol 3, 24 (2003)
134. Beatrice Lemeignan, Pierre Sonigo, Philippe Marliere: Phenotypic suppression by incorporation of an alien amino acid. J Mol Biol 231, 161-166 (1993) (Pubitemid 23188240)
135. Yau Kwok, J Tze-Fei Wong: Evolutionary relationships between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes. Can J Biochem 58, 213-218 (1980) (Pubitemid 10047605)
136. Stephen W Santoro, J Christopher Anderson, Vishva Lakshman, Peter G Schultz: An archaealbacteria-derived glutamyl-tRNA synthetase and RNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. Nucleic Acid Res 31, 6700-6709 (2003) (Pubitemid 37508777)
137. Chang C Liu, Peter G Schultz: Adding new chemistries to the genetic code. Annu Rev Biochem 79, 413-44 (2010)
138. Michael Georg Hoesl, Nediljko Budisa: Recent advances in genetic code engineering in Escherichia coli. Curr Opinion Biotech 23, 751-757 (2012)
139. RA Mehl, JC Anderson, SW Santoro, L Wang, AB Martin, DS King, DM Horn, PG Schultz: Generation of a bacterium with a 21 amino acid genetic code. J Am Chem Soc 125, 935-939 (2003) (Pubitemid 36152644)
140. Hong Tian, Danni Deng, Jie Huang, Dongning Yao, Xiaowei Xu, Xiangdong Gao: Screening system for orthogonal suppressor tRNAs based on the species-specific toxicity of suppressor tRNAs. Biochimie doi: 10.1016/j. biochip. 2012.12.010 (2012)
141. Chang C Liu, Lei Qi, Charles Yanofsky, Adam P Arkin: Regulation of transcription by unnatural amino acids. Nat Biotechnol 29, 164-168 (2011)
142. Jiangyun Wang, Wei Zhang, Wenjiao Song, Yizhong Wang, Zhipeng Yu, Jiasong Li, Minhao Wu, Lin Wang, Jianye Zang, Qing Lin: A biosynthetic route to photoclick chemistry on proteins. J Am Chem Soc 132, 14812-18 (2010)
143. Kaihang Wang, Wolfgang H. Schmied, Jason W Chin: Reprogramming the genetic code: from triplet to quadruplet codes. Angew Chem Int Ed Engl 51, 2288-2297 (2012)
144. S Lepthien, L Merkel, N Budisa: In vivo double and triple labeling of proteins using synthetic amino acids. Angew Chem Int Ed Engl 49, 5446-50 (2010)
145. Lars Merkel, Melina Schauer, Garabed Antranikian, Nediljko Budisa: Parallel incorporation of different fluorinated amino acids: on the way to "Teflon" proteins. Chembiochem 11, 1505-07 (2010)
146. Susan M Hancock, Rajendra Uprety, Alexander Deiters, Jason W Chin: Expanding the genetic code of yeast for incorporartion of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair. J Am Chem Soc 132, 14819-24 (2010)
147. Sebastian Nehring, Nediljko Budisa, Birgit Wiltschi: Performance analysis of orthogonal pairs designed for an expanded eukaryotic genetic code. PLoS One 7(4):e31992 (2012)
148. Shixin Ye, Morgane Riou, Stephanie Carvalho, Pierre Paoletti: Expanding the genetic code in Xenopus laevis oocytes. Chembiochem 14, 230-235 (2013)
149. Bin Shen, Zheng Xiang, Barbara Miller, Gordon Louie, Wenyuan Wang, Joseph P Noel, Fred H Gage, Lei Wang: Genetically encoding unnatural amino acids in neural stem cells and optically reporting voltage-sensitive domain changes in differentiated neurons. Stem Cells 29, 1231-40 (2011)
150. Gabrielle Nina Thibodeaux, Xiang Liang, Kathryn Moncivais, Aiko Umeda, Oded Singer, Lital Alfonta, Zhiwen Jonathan Zhang: Transforming a pair of orthogonal tRNAaminoacyltRNA synthetase from Archaea to function in mammalian cells. PLoS One 5(6):e11263 (2010)
151. Sebastian Greiss, Jason W Chin: Expanding the genetic code of an animal. J Am Chem Soc 133, 14196-14199 (2011)
152. Angela R Parish, Xingyu She, Zheng Xiang, Irene Coin, Zhouxin Shen, Stephen P Briggs, Andrew Dillin, Lei Wang: Expanding the genetic code of Caenorhabditis elegans using bacterial aminoacyl-tRNA synthetase/tRNA pairs. ACS Chem Biol 7, 1292-1302 (2012)
153. Philippe Marliere, Julien Patrouix, Volker Doring, Piet Herdewijn, Sabine Tricot, Stephane Cruveiller, Madeline Bouzon, Rupert Mutzel: Chemical evolution of a bacterium's genome. Angew Chem International 50, 7109-7114 (2011)
154. Philip Cohen: Life the Sequel. New Scientist 30 September, 167, 32-36 (2000)
155. Gene D McDonald, Michael C Storrie-Lombardi: Biochemical constraints in a protobiotic earth devoid of basic amino acids: the "BAA (-) world". Astrobiology 10, 989-1000 (2010)
156. Alan W Schwartz: Phosphorus in prebiotic chemistry. Phil Trans R Soc B 361, 1743-1749 (2006) (Pubitemid 44580376)
157. MW Powner, B Gerland, JD Sutherland: Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239-242 (2009)
158. Ronald R Breaker: Riboswitches and the RNA world. Cold Spring Harb Perspect Biol 4, doi: 10.1101/cshperspect.a003566
159. Rebecca M Turk, Nataliya V Chumachenko, Michael Yarus: Multiple translational products from a five-nucleotide ribozyme. Proc Nat Acad Sci USA 107, 4585-89 (2010)
160. Na Li, Faqing Huang: Ribozyme-catalyzed aminoacylation from CoA thioesters. Biochemistry 44, 4582-90 (2005) (Pubitemid 40404001)
161. H Jakubowski: Amino acid selectivity in the aminoacylation of coenzyme A and RNA minihelices by aminoacyl-tRNA synthetases. J Biol Chem 275, 34845-48 (2000)
162. Gene H Hur, Christopher R Vickery, Michael D Burkart: Explorations of catalytic domains in non-ribosomal peptide synthetase enzymology. Nat Prod Rep 29, 1074-98 (2012)
163. P Bieling, M Beringer, S Adio, MV Rodnina: Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat Struct Mol Biol 13, 423-428 (2006) (Pubitemid 43881582)
164. Antoine Danchin: Homeotropic transformation and the origin of translation. Prog Biophys Mol Biol 54, 81-86 (1989)
165. Michael Ibba, Alan W Curnow, Dieter Soll: AminoacyltRNA synthesis: divergent routes to a common goal. Trends Biochem Sci 22, 39-42 (1997) (Pubitemid 27076803)
166. L Randau, S Schauer, S Ambrogelly, JC Salazar, J Moser, S Sekine, S Yokoyama, D Soll, D Jahn: tRNA recognition by glutamyl-tRNA reductase. J Biol Chem 279, 34931-7 (2004) (Pubitemid 39318129)
167. CS Franklyn, A Minajigi: tRNA as an active chemical scaffold for diverse chemical transformations. FEBS Lett 584, 366-375 (2010)
168. Zhiliang Yu, Ken Takai, Alexei Slesarev, Hong Xue, J Tze-Fei Wong: Search for primitive Methanopyrus based on genetic distance between Val- and Ile-tRNA synthetases. J Mol Evol 69, 386-394 (2009)
169. Robert Pascal, Laurent Boiteau: Enerygy flows, metabolism and translation. Philos Trans R Soc Lond B Biol Sci 366, 2949-58 (2011)
170. I Prigogine, G Nicolis: Biological order, structure and instabilities. Q Rev Biophys 4, 107-48 (1971)
171. Manfred Eigen, Peter Schuster: A principle of natural self-organization. Naturwissenschaften 64, 541-565 (1977)
172. Stuart A Kauffman: The origins of order: Self-organization and selection in evolution. Oxford University Press, Oxford (1993)
173. Helmut H Zepik, Eveline Blochliger, Pier Luigi Luisi: A chemical model of homeostasis. Angew Chem Int Ed 40, 199-202 (2001)
174. Zehavit Dadon, Nathaniel Wagner, Gonon Ashkenasy: The road to non-enzymatic molecular networks. Angew Chem Int Ed 47, 6128-36 (2008)
175. Jacques Ricard: Are biochemical networks possible ancestors of living systems? C R Biol 333, 769-778 (2010)
176. Nilesh Vaidya, Michael L Manapat, Irene A Chen, Ramon Xulvi-Brunet, Eric J Hayden, Niles Lehman: Spontaneous network formation among cooperative RNA replicators. Nature 491, 72-77 (2012)
177. Omer Markovitch, Doron Lancet: Excess mutual catalysis is required for effective evolvability. Artif Life 18, 243-266 (2012)
178. Addy Pross: How does biology emerge from chemistry? Orig Life Evol Biosph 42, 433-435 (2012)
179. Yan Qin, Norbert Polacek, Oliver Vesper, Eike Staub, Edda Einfeldt, Daniel N. Wilson, Knud H. Nierhaus: The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 127, 721-733 (2006) (Pubitemid 44716253)
180. Marcelo Rogalski, Daniel Karcher, Ralph Bock: Superwobbling facilitates translation with reduced tRNA sets. Nature Struct Mol Biol 15, 192-198 (2008) (Pubitemid 351207507)
181. AJ Macario, E Conway de Macario: The molecular chaperon system and other anti-stress mechanisms in archaea. Frontiers Biosc 6, d263-283 (2001)
182. Stamatina Giannouli, Athanasios Kyritsis, Nikolaos Malissovas, Hubert Dominique Becker, Constantinos Stathopoulos: On the role of an unusual tRNAGly isoacceptor in Staphylococcus aureus. Biochime 91, 344-351 (2008)
183. Utz Kohlrausch, Joachim-Volker Höltje: One-step purification procedure for UDP-N-acetylmuramyl-peptide murein precursor from Bacillus cereus. FEMS Microbiol Lett 62, 253-257 (1991)
184. DW Smith, AL McNamara, M Rice, DL Hatfield: The effects of a post-transcriptional modification on the function of tRNALys isoaccepting species in translation. J Biol Chem 256, 10033-36 (1981)
185. Mark Odell, Verl Sriskanda, Stewart Shuman, Dimitar B Nikolov: Crystal structure of eukaryotic DNA ligaseadenylate illuminates the mechanism of nick sensing and strand joining. Mol Cell 6, 1183-93 (2000)
186. SM Hengel, DR Goodlett: A review of tandem mass spectrometry characterization of adenosine diphosphateribosylated proteins. Int J Mass Spectrom 312, 114-121 (2012)
187. James B Flanegan, Ralf F Pettersson, Victor Ambros, Martinez J. Hewlett, David Baltimore: Covalent linkage of a protein to a defined nucleotide sequence at the 5'-terminus of virion and replicative intermediate RNAs of poliovirus. Proc Natl Acad Sci USA 74, 961-965 (1977) (Pubitemid 8068723)
188. James J Champoux: DNA is linked to the rat liver DNA nicking-closing enzyme by a phosphodiester bond to tyrosine. J Biol Chem 256, 4805-9 (1981)
189. Monica J Roth, David R Brown, Jerard Hurwitz: Analysis of bacteriophage phi X174 gene A proteinmediated termination and reinitiation of phi X DNA synthesis. II. Structural characterization of the covalent phi X A protein-DNA complex. J Biol Chem 259, 10556-68 (1984) (Pubitemid 14064158)
190. Akhtar Samad, Robert B Carroll: The tumor suppressor p53 is bound to RNA by a stable covalent linkage. Mol Cell Biol 11, 1598-1606 (1991) (Pubitemid 21895517)
191. Alexei I Slesarev et al: The complete genome of hyperthermophilic Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci USA 99, 4644-49 (2002) (Pubitemid 34286038)
192. Fabia U Battistuzzi, Andreia Feijao, S Blair Hedges: A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 4, 44-57 (2004)
193. Massimo Di Giulio: A methanogen hosted the origin of the genetic code. J Theoret Biol 260, 77-82 (2009)
194. Marco Archetti, Massimo Di Giulio: The evolution of the genetic code took place in an anaerobic environment. J Theoret Biol 245, 169-174 (2007) (Pubitemid 46215679)
195. Karl O Stetter: Hyperthermophilic prokaryotes. FEMS Microbiol Rev 18, 149-158 (1996)
196. Massimo Di Giulio: The universal ancestor and the ancestor of bacteria were hyperthermophiles. J Mol Evol 57, 721-730 (2003) (Pubitemid 37543986)
197. Eric A Gaucher, Sridhar Govindarajan and Omjoy K. Ganesh: Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451, 704-708 (2008)
198. Mathieu Groussin, Manolo Gouy: Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea. Mol Biol Evol 28, 2661-74 (2011)
199. Massimo Di Giulio: A comparison of proteins of Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code. Gene 346, 1-6 (2005) (Pubitemid 40332618)
200. Massimo Di Giulio: Structuring of the genetic code took place at acidic pH. J Theoret Biol 237, 219-226 (2005) (Pubitemid 41406407)
201. Harold S Bernhardt, Warren P Tate: Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? Biol Direct 10.1186/1745-6150-7-4 (2012)
202. John A Leigh: Evolution of energy metabolism. In: Biodiversity of Microbial Life, eds. Staley JT & Reysenbach A-L. Wiley-Liss p. 103-120 (2001)
203. Paul G Falkowski: Tracing oxygen's imprint on Earth's metabolic evolution. Science 2006;311, 1724-1725 (2006)
204. E. L. Shock: High-temperature life without photosynthesis as a model for Mars. J Geophys Res 102, 23687-94 (1997)
205. Ken Takai, Kentaro Nakamura: Archaeal diversity and community development in deep-sea hydrothermal vents. Curr Opin Microbiol 14, 282-291 (2011)
206. Feng-Jie Sun, Gustavo Caetano-Anollés: The evolutionary history of the structure of 5S ribosomal RNA. J Mol Evol 69, 430-443 (2009)
207. Feng-Jie Sun, Gustavo Caetano-Anollés: The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics 11, 153 (2010)
208. Kyung Mo Kim, Gustavo Caetano-Anollés: The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other kingdoms. BMC Bioinformatics 12, 13 (2012)