Origins and evolution of modern biochemistry: Insights from genomes and molecular structure

Frontiers in Bioscience

Volumn 13, Issue 14, 2008, Pages 5212-5240

  Caetano Anolles, Gustavo ^a   Sun, Feng Jie ^a   Wang, Minglei ^a   Yafremava, Liudmila S ^a   Harish, Ajith ^a   Kim, Hee Shin ^a   Knudsen, Vegeir ^a   Caetano Anolles, Derek ^a   Mittenthal, Jay E ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Archaea; Evolution; Metabolism; Proteins; Proteome; Review; RNA; rRNA; Structure; tRNA

Indexed keywords

ARCHAEA;

RNA;

AUDIOVISUAL EQUIPMENT; BIOCHEMISTRY; CHEMICAL STRUCTURE; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; GENETICS; GENOME; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; REVIEW;

BIOCHEMISTRY; DIRECTED MOLECULAR EVOLUTION; EVOLUTION, MOLECULAR; GENOME; GENOMICS; MODELS, MOLECULAR; MODELS, STRUCTURAL; RNA;

EID: 52049125699     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/3077     Document Type: Article

References (239)

1. Burley, S.K. and J.B. Bonanno: Structuring the universe of proteins. Annu Rev Genomics Hum Genet 3, 243-262 (2002) (Pubitemid 35217437)
2. Zhang, C. and S.H. Kim: Overview of structural genomics: from structure to function. Curr Opin Chem Biol 7, 28-32 (2003) (Pubitemid 36126489)
3. Grant, A., D. Lee, and C. Orengo: Progress towards mapping the universe of protein folds. Genome Biol 5, 107 (2004)
4. Mindell, D.P. and A. Meyer: Homology evolving. Trends Ecol Evol 16, 434-440 (2001) (Pubitemid 32772594)
5. Holder, M. and P.O. Lewis: Phylogeny estimation: traditional and Bayesian approaches. Nature Rev 4, 275-284 (2003) (Pubitemid 36389532)
6. Savva, G., J. Dicks, and I.N. Roberts: Current approaches to whole genome phylogenetic analysis. Brief Bioinform 4, 63-74 (2003)
7. Albert, V.A.: Parsimony, phylogeny and genomics. Oxford University Press, NY (2005)
8. Baldauf, S.L., A.J. Rogers, I. Wenk-Siefert, and W.F. Doolittle: A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972-977 (2000)
9. Brown, J.R., C.J. Douady, M.J. Italia, W.E. Marshall, and M.J. Stanhope: Universal trees based on large combined protein sequence data sets. Nature Genet 28, 281-285 (2001) (Pubitemid 32626033)
10. Ciccarelli, F.D., T. Doerks, C.V. Mering, C.J. Creevey, B. Snel, and P. Bork: Towards automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287 (2006) (Pubitemid 43334717)
11. Gerstein, M.: Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins: Struct Funct Genet 33, 518-534 (1998) (Pubitemid 28565735)
12. Tekaia, F., A. Lazcano, and B. Dujon: The genomic tree as revealed from whole proteome comparisons. Genome Res 9, 550-557 (1999) (Pubitemid 29361271)
13. Wolf, Y.I., S.E. Brenner, P.A. Bash, and E.V. Koonin: Distribution of protein folds in the three superkingdoms of life. Genome Res 9, 17-26 (1999) (Pubitemid 29095145)
14. House, C.H. and S.T. Fitz-Gibbons: Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54, 539-547 (2002) (Pubitemid 34271134)
15. Lin, J. and M. Gerstein: Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10, 808-818 (2000) (Pubitemid 30433354)
16. Wolf, Y.I., I.B. Rogozin, N.V. Grishin, R.L. Tatusov, and E.V. Koonin: Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1, 8 (2001)
17. Snel, B., P. Bork, and M. Huynen: Genome evolution: gene fusion versus gene fission. Trends Genet 16, 9-11 (2000) (Pubitemid 30062226)
18. Caetano-Anollés, G. and D. Caetano-Anollés: An evolutionarily structured universe of protein architecture. Genome Res 13, 1563-1571 (2003) (Pubitemid 36874472)
19. Dutilh, B.E., M.A. Huynen, W.J. Bruno, and B. Snel: The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 58, 527-539 (2004) (Pubitemid 38609888)
20. Yang, S., R.F. Doolittle, and P.E. Bourne: Phylogeny determined by protein domain content. Proc Natl Acad Sci USA 102, 373-378 (2005) (Pubitemid 40116774)
21. Wang, M., S.M. Boca, R. Kalelkar, J.E. Mittenthal, and G. Caetano-Anollés: A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture. Complexity 12, 27-40 (2006) (Pubitemid 44720446)
22. Wang, M., L.S. Yafremava, D. Caetano-Anollés, J.E. Mittenthal, and G. Caetano-Anollés: Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res 17, 1572-1585 (2007) (Pubitemid 350074853)
23. Dadenkar, T., B. Snel, M. Huynen, and P. Bork: Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23, 324-328 (1998) (Pubitemid 28461862)
24. Wolf, Y.I., I.B. Rogozin, and E.V. Koonin: Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res 14, 29-36 (2004) (Pubitemid 38088522)
25. Korbel, J.O., B. Snel, M.A. Huynen, and P. Bork: SHOT: a web server for the construction of genome phylogenies. Trends Genet 18, 158-162 (2002) (Pubitemid 34164642)
26. Wang, M. and G. Caetano-Anollés: Global phylogeny determined by the combination of protein domains in proteomes. Mol Biol Evol 23, 2444-2454 (2006) (Pubitemid 44737138)
27. Wang, M. and G. Caetano-Anollés: The evolutionary mechanics of protein domain organization in proteomes. Ms. submitted (2008)
28. Wolf, Y.I., I.B. Rogozin, N.V. Grishin, and E.V. Koonin: Genome trees and the tree of life. Trends Genet 18, 472-479 (2002)
29. Delsuc, F., H. Brinkmann, and H. Philippe: Phylogenomics and the reconstruction of the tree of life. Nature Rev Genet 6, 361-375 (2005) (Pubitemid 40577180)
30. Doolittle, R.F.: Evolutionary aspects of whole-genome biology. Curr Opin Struct Biol 15, 248-253 (2005) (Pubitemid 40826442)
31. Deeds, E.J., H. Hennessey, and E.I. Shakhnovich: Prokaryotic phylogenies inferred from protein structural domains. Genome Res 15, 393-402 (2005) (Pubitemid 40467781)
32. Woese, C.R., O. Kandler, and M.L. Wheelis: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc Natl Acad Sci USA 87, 4576-4579 (1990)
33. Assembling the Tree of Life (ATOL). http://atol.sdsc.edu
34. Bryant, H.N.: The polarization of character transformations in phylogenetic systematics-Role of axiomatic and auxiliary assumptions. Syst Zool 40, 433-445 (1991)
35. Bryant, H.N.: Hypothetical ancestors and rooting in cladistic analysis. Cladistics 13, 337-348 (1997) (Pubitemid 127434865)
36. Morowitz, J.H.: Beginning of cellular life. Yale University Press, CT (1992)
37. Benner, S.A., A.D. Ellington, and A. Tauer: Modern metabolism as a palimpsest of the RNA world. Proc Natl Acad Sci USA 86, 7054-7058 (1989) (Pubitemid 19240865)
38. Bajaj, M. and T. Blundell: Evolution and the tertiary structure of proteins. Annu Rev Biophys Bioeng 13, 453-492 (1984)
39. Vukmirovic, O.G. and S.M. Tilghman: Exploring genome space. Nature 405, 820-822 (2000) (Pubitemid 30407859)
40. Rokas, A. and P.W.K. Holland: Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15, 454-459 (2000)
41. Sober, E. and M. Steel: Testing the hypothesis of common ancestry. J Theor Biol 218, 395-408 (2002) (Pubitemid 35291132)
42. Penny, D., M.D. Hendy, and A.M. Poole: Testing fundamental evolutionary hypotheses. J Theor Biol 223, 377-385 (2003) (Pubitemid 36808932)
43. Mossell, E.: On the impossibility of reconstructing ancestral data and phylogenies. J Comp Biol 10, 669-678 (2003)
44. Philippe, H. and J. Laurent: How good are deep phylogenetic trees? Curr Opin Genet Dev 8, 6161-623 (1998)
45. Schuster, P., W. Fontana, P. Stadler, and I. Hofacker: From sequences to shapes and back: a case study in RNA secondary structures. Proc R Soc Lond B 255, 279-284 (1994) (Pubitemid 24102288)
46. de Visser, J.A.G.M., J. Hermisson, G.P. Wagner, L. Ancel Meyers, et al.: Perspective: Evolution and detection of genetic robustness. Evolution 57, 1959-1972 (2003) (Pubitemid 37207656)
47. Schuster, P. and P.F. Stadler: Networks in molecular evolution. Complexity 8, 34-42 (2003) (Pubitemid 36218598)
48. Fontana, W.: Modelling 'evo-devo' with RNA. BioEssays 24, 1164-1177 (2002) (Pubitemid 35464946)
49. Schultes, E.A. and D.P. Bartel: One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289, 448-452 (2000) (Pubitemid 30490456)
50. Babajilde, A., R. Farber, I.L. Hofacker, J. Inman, A.S. Lapedes, and P.F. Stadler: Exploring protein sequence space using knowledge based potentials. J Theor Biol 212, 35-46 (2001) (Pubitemid 32844236)
51. Keefe, A.D. and J.W. Szostak: Functional proteins from a random-sequence library. Nature 410, 715-718 (2001) (Pubitemid 32290361)
52. Bornberg-Bauer, E. and H. S. Chang: Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space. Proc Natl Acad Sci USA 96, 10689-10694 (1999) (Pubitemid 29442205)
53. Taverna, D.M. and R.A Goldstein: Why are proteins so robust to site mutations? J Mol Biol 315, 479-484 (2002) (Pubitemid 34729355)
54. Wroe, R., E. Bornberg-Bauer, and H.S. Chan: Comparing folding codes in simple heteropolymer models of protein evolutionary landscapes: robustness of the superfunnel paradigm. Biophys J 88, 118-131 (2005) (Pubitemid 40070663)
55. Huynen, M., R. Gutell, and D. Konings: Assessing the reliability of RNA folding using statistical mechanics. J Mol Biol 267, 1104-1112 (1997) (Pubitemid 27192625)
56. Wagner, A.: Robustness and evolvability: a paradox resolved. Proc R Soc Lond B 275, 91-100 (2008) (Pubitemid 350146738)
57. Albert, R., H. Jeong, and A.L. Barabási: Error and attack of complex networks. Nature 406, 378-382 (2000)
58. Giaever, G., A.M. Chu, L. Ni, C. Connelly, R. Riles et al.: Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391 (2002) (Pubitemid 34826834)
59. Bowie, J.U., J.F. Reidhaar-Olson, W.A. Lim, and R.T. Sauer: Deciphering the message in protein sequences: tolerance to amino acid substitution. Science 247, 1306-1310 (1990)
60. Borenstein, E. and E. Ruppin: Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci USA 103, 6593-6598 (2006)
61. Sanjuán, R., J. Forment, and S.F. Elena: In silico redicted robustness of viroids RNA secondary structures. I. The effect of single mutations. Mol Biol Evol 23, 1427-1436 (2006) (Pubitemid 43992344)
62. Ancel, L.W. and W. Fontana: Plasticity, evolvability, and modularity in RNA. J Exp Zool (Mol Dev Evol) 288, 242-283 (2000)
63. Ancel Meyers, L., J.F. Lee, M. Cowperthwaite, and A.D. Ellington: The robustness of naturally and artificially selected nucleic acid secondary structures. J Mol Evol 58, 681-691 (2004) (Pubitemid 38781701)
64. van Nimwegen, E., J. Crutchfield, and M. Huynen: Neutral evolution of mutational robustness. Proc Natl Acad Sci USA 96, 9716-9720 (1999) (Pubitemid 29398798)
65. Bussemaker, H.J., D. Thirumalai, and J.K. Bhattacharjee: Thermodynamic stability of folded proteins against mutations. Phys Rev Lett 79, 3530-3533 (1997) (Pubitemid 127624823)
66. Vendruscolo, M., A. Maritan, and J.R. Banavar: Stability threshold as a selection principle for protein design. Phys Rev Lett 78, 3967-3970 (1997) (Pubitemid 127655408)
67. Wagner, A. and P. Stadler: Viral RNA and evolved mutational robustness. J Exp Zool (Mol Dev Evol) 285, 119-127 (1999) (Pubitemid 29375322)
68. Rutherford, S.L. and S. Lindquist: Hsp90 as a capacitor for morphological evolution. Nature 396, 336-342 (1998) (Pubitemid 28557387)
69. Queitsch, C., T. Sangster, and S. Lindquist: Hsp90 as a capacitor of phenotypic variation. Nature 417, 618-624 (2002) (Pubitemid 34614814)
70. Schrödinger, E.: What is life? John Wiley and Sons, NY (1944)
71. Gladyshev, G.P.: On the thermodynamics of biological evolution. J Theor Biol 75, 425-441 (1978) (Pubitemid 9105410)
72. Black, S.: On the thermodynamics of evolution. Persp Biol Med 21, 348-356 (1978)
73. Wicken, J.S.: A thermodynamic theory of evolution. J Theor Biol 87, 9-23 (1980) (Pubitemid 11162512)
74. Gladyshev, G.P. and Y.A. Ershov: Principles of the thermodynamics of biological systems. J Theor Biol 94, 301-343 (1982) (Pubitemid 12142867)
75. Nicolis, G. and I. Prigogine: Exploring complexity. W.M. Freeman, NY (1989)
76. Schneider, E.D. and J.J. Kay: Complexity and thermodynamics: towards a new ecology. Futures 26, 626-647 (1994)
77. Schneider, E.D. and J.J. Kay: Life as a manifestation of the second law of thermodynamics. Math Comp Modelling 19, 25-48 (1994)
78. Caetano-Anollés, G.: Grass evolution inferred from chromosomal rearrangements and geometrical and statistical features in RNA structure. J Mol Evol 60, 635-652 (2005) (Pubitemid 40896562)
79. Stegger, G., H. Hofman, J. Fortsch, H.J. Gross, J.W. Randles, H.L. Sanger, and D. Riesner: Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data. J Biomol Struct Dynam 2, 543-571 (1984)
80. Higgs, P.G.: RNA secondary structure: a comparison of real and random sequences. J Phys I France 3, 43-59 (1993)
81. Higgs, P.G.: Thermodynamic properties of transfer RNA: a computational study. J Chem Soc Faraday Trans 91, 2531-2540 (1995)
82. Schultes, E.A., P.T. Hraber, and T.H. LaBean: Estimating the contributions of selection and selforganization in RNA secondary structure. J Mol Evol 49, 76-83 (1999) (Pubitemid 29293416)
83. Steffens, W. and D. Digby: mRNA have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27, 1578-1584 (1999) (Pubitemid 29209532)
84. Gultyaev, P.A., F.H.D. van Batenburg, and C.W.A. Pleij: Selective pressures on RNA hairpins in vivo and in vitro. J Mol Evol 54, 1-8 (2002) (Pubitemid 33131998)
85. Higgs, P.G.: RNA secondary structure: physical and computational aspects. Quaterly Rev Biophys 33, 199-253 (2000) (Pubitemid 32059803)
86. Kierzek, E., E. Biala, and R. Kierzek: Elements of thermodynamics in RNA evolution. Acta Biochim Polonica 48, 485-493 (2001) (Pubitemid 33638631)
87. Billoud, B., M.A. Guerrucci, M. Masselot, and J.S. Deutsch: Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol 17, 1435-1445 (2000)
88. Collins, L.J., V. Moulton, and D. Penny: Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. J Mol Evol 51, 194-2004 (2000)
89. Caetano-Anollés, G.: Novel strategies to study the role of mutation and nucleic acid structure in evolution. Plant Cell Tissue Org Culture 67, 115-132 (2001) (Pubitemid 32974412)
90. Caetano-Anollés, G.: Evolved RNA secondary structure and the rooting of the universal tree of life. J Mol Evol 54, 333-345 (2002) (Pubitemid 34165418)
91. Caetano-Anollés, G.: Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res 30, 2527-2587 (2002)
92. Swain, T.D. and D.J. Taylor: Structural rRNA characters support monophyly of raptorial limbs and paraphyly of limb specialization in water fleas. Proc R Soc Lond B 270, 887-896 (2003) (Pubitemid 36561023)
93. Sun, F.-J., S. Fleurdépine, C. Bousquet-Antonelli, G. Caetano-Anollés, and J.-M. Deragon: Common evolutionary trends for tRNA-derived SINE RNA structures. Trends Genet 23, 26-33 (2007) (Pubitemid 44960531)
94. Sun, F.-J. and G. Caetano-Anollés: The origin and evolution of tRNA inferred from phylogenetic analysis of structure. J Mol Evol 66, 21-23 (2008)
95. Hartwell, L.H., J.J. Hopfield, S. Leibler, and A.W. Murray: From molecular to modular cell biology. Nature 401, C47-C52 (1999)
96. Krakauer, D.C. and J.B. Plotkin: Redundancy, antiredundancy, and the robustness of genomes. Proc Natl Acad Sci USA 99, 1405-1409 (2002) (Pubitemid 34136505)
97. Berezovsky, I.N., A.Y. Grosberg, and E.N. Trifonov: Closed loops of nearly standard size: common basic elements of protein structure. FEBS Lett 446, 283-286 (2000). (Pubitemid 30069842)
98. Sobolevsky, Y., Z.M. Frenkel, and E.N. Trifonov: Combinations of ancestral modules in proteins. J Mol Evol doi 10.1007/s00239-007-9032-x (2007)
99. Söding, J. and A.N. Lupas: More than the sum of their parts: on the evolution of proteins from peptides. BioEssays 25, 837-846 (2003) (Pubitemid 37081749)
100. Vogel, C., M. Bashton, N.D. Kerrison, C. Chothia, and S.A. Teichmann: Structure, function and evolution of multidomain proteins. Curr Opin Struc Biol 14, 208-216 (2004) (Pubitemid 38490788)
101. Pereira-Leal, J.B., E.D. Levy, C. Kamp, and S.A. Teichmann: Evolution of protein complexes by duplication of homomeric interactions. Genome Biol 8, R51 (2007)
102. Ravasz, E., A.L. Somera, D.A. Mongru, Z.N. Oltvai, and A.L. Barabási: Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555 (2002) (Pubitemid 34971002)
103. Spirin, V. and L.A. Mirny: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100, 12123-12128 (2003) (Pubitemid 37271525)
104. Gilbert, W.: The RNA world. Nature 319, 618 (1986)
105. Woese, C.R.: The genetic code: The molecular basis for genetic expression. Harper & Row, NY (1967)
106. Crick, F.H.C.: The origin of the genetic code. J Mol Biol 38, 367-379 (1968)
107. Orgel, L.E.: Evolution of the genetic apparatus. J Mol Biol 38, 381-393 (1968)
108. Cech, T.R., A.J. Zaug, and P.J. Grabowski: In vitro splicing of the ribosomal RNA precursor of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27, 487-496 (1981) (Pubitemid 12200785)
109. Guerrier-Takada, C., K. Gardiner, T. Marsh, N. Pace, and S. Altman: The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857 (1983) (Pubitemid 14168384)
110. Jeffares, D.C., A.M. Poole, and D. Penny: Relics from the RNA World. J Mol Evol 46, 18-36 (1998) (Pubitemid 28047236)
111. Yusupov, M.M., G.Z. Yusupova, A. Baucom, K. Lieberman, T.N. Earnest, J.H.D. Cate, and H.F. Noller: Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883-896 (2001) (Pubitemid 32422479)
112. Nissen, P., J. Hansen, N. Ban, P.B. Moore, and T.A. Steitz: The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930 (2000) (Pubitemid 30659940)
113. Ogle, J.M., A.P. Carter, and V. Ramakrishnan: Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 28, 259-266 (2003) (Pubitemid 36588668)
114. Schuwirth, B.S., M.A. Borovinskaya, C.W. Hau, W. Zhang, A. Vila-Sanjurjo, J.M. Holton, and J.H.D. Cate: Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827-834 (2005) (Pubitemid 41567336)
115. Noller, H., V. Hoffarth, and L. Zimniak: Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416-1419 (1992)
116. Steitz, T.A. and P.B. Moore: RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci 28, 411-418 (2003) (Pubitemid 36976743)
117. Eddy, S.R.: Non-coding RNA genes and the modern RNA world. Nature Rev Genet 2, 919-929 (2001) (Pubitemid 33691089)
118. Storz, G.: An expanding universe of noncoding RNAs. Science 296, 1260-1263 (2002) (Pubitemid 34522771)
119. Bartel, D.P.: MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
120. Hutvágner, G. and P.D. Zamore: RNAi: nature abhors a double-strand. Curr Opin Genet Develop 12, 225-232 (2002) (Pubitemid 34219496)
121. Baulcombe, D.: RNA silencing in plants. Nature 431, 356-363 (2004) (Pubitemid 39265676)
122. Frank, D.N. and N.R. Pace: Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67, 153-180 (1998) (Pubitemid 28411127)
123. Eliceiri, G.L.: Small nucleolar RNAs. Cell Mol Life Sci 56, 22-31 9 (1999) (Pubitemid 29471922)
124. Keenan, R.J., D.M. Freymann, R.M. Stroud, and P. Walter: The signal recognition particle. Annu Rev Biochem 70, 755-775 (2001) (Pubitemid 32662224)
125. Washietl, S., I.L. Hofacker, M. Lukasser, A. Hüttenhofer, and P.F. Stadler: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 23, 1383-1389 (2005)
126. Leontis, N.B., R.B. Altman, H.M. Berman, S.E. Brenner, D.R. Engelke, et al: The RNA Ontology Consortium: an open invitation to the RNA community. Nucleic Acids Res 12, 533-541 (2006)
127. Klosterman, P.S., M. Tamura, S.R. Holbrook, and S.E. Brenner: SCOR: a structural classification of RNA database. Nucleic Acids Res 30, 392-394 (2002) (Pubitemid 34679594)
128. Gan, H.H., S. Pasquali, and T. Schlick: Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res 31, 2926-2943 (2003) (Pubitemid 37442136)
129. Zorn, J., H.H. Gan, N. Schiffeldrim, and T. Schlick: Structural motifs in ribosomal RNAs: implications for RNA design and genomics. Biopolymers 73, 340-347 (2004) (Pubitemid 38222209)
130. Kim, N., N. Schiffeldrim, H.H. Gan, and T. Schlick: Candidates for novel RNA topologies. J Mol Biol 341, 1129-1144 (2004) (Pubitemid 39092306)
131. Hermann, T. and D.J. Patel: Stitching together RNA tertiary structures. J Mol Biol 294, 829-849 (1999) (Pubitemid 30000378)
132. Leontis, N.B. and E. Westhof: Analysis of RNA motifs. Curr Opin Struct Biol 13, 300-308 (2003) (Pubitemid 36782455)
133. Pollock, D.D.: The Zuckerkandl Prize: structure and evolution. J Mol Evol 56, 375-376 (2003) (Pubitemid 36390768)
134. Fontana, W., D.A. Konings, P.F. Stadler, and P. Schuster: Statistics of RNA secondary structures. Biopolymers 33, 1389-1404 (1993) (Pubitemid 23249156)
135. Gardner, P.P., B.R. Holland, V. Moulton, M. Hendy, and D. Penny: Optimal alphabets for an RNA world. Proc R Soc Lond B 270, 1177-1182 (2003) (Pubitemid 36683463)
136. Gultyaev, P.A. and A. Roussis: Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants. Nucleic Acids Res 35, 3144-3152 (2007) (Pubitemid 47073651)
137. Caetano-Anollés, G.: Evolution of genome size in the grasses. Crop Sci 45, 1809-1816 (2005) (Pubitemid 41361432)
138. Sun, F.-J. and G. Caetano-Anollés: The evolutionary significance of the long variable arm in transfer RNA. Ms. submitted (2008)
139. Sun, F.-J. and G. Caetano-Anollés: Evolutionary patterns in the sequence and structure of transfer RNA: early origins of Archaea and viruses. PLoS Comp Biol, in press (2008)
140. Woese, C.R.: Translation: in retrospect and prospect. RNA 7, 1055-1067 (2001) (Pubitemid 32726905)
141. Cochella, L. and R. Green: An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308, 1178-1180 (2005) (Pubitemid 40696436)
142. Himeno, H., T. Hasegawa, T. Ueda, K. Watanabe, and M. Shimizu: Conversion of aminoacylation specificity from tRNATyr to tRNASer in vitro. Nucleic Acids Res 18, 6815-6819 (1990) (Pubitemid 120006062)
143. Biou, V., A. Yaremchuk, M. Tukalo, and S. Cusack: The 2.9 Å crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNASer. Science 263, 1404-1410 (1994)
144. Wu, X.-Q. and H.J. Gross: The long extra arms of human tRNA(Ser)Sec and tRNASer function as major identity elements for serylation in an orientation-dependent, but not sequence-specific manner. Nucleic Acids Res 21, 5589-5594 (1993) (Pubitemid 24003081)
145. Breitschopf, K., T. Achsel, K. Busch, and H.J. Gross: Identity elements of human tRNALeu: structural requirements for converting human tRNASer into a leucine acceptor in vitro. Nucleic Acids Res 23, 3633-3637 (1995)
146. Soma, A., K. Uchiyama, T. Sakamoto, M. Maeda, and H. Himeno: Unique recognition style of tRNALeu by Haloferax volcanii Leucyl-tRNA synthetase. J Mol Biol 293, 1029-1038 (1999)
147. Widmann, J., M. Di Giulio, M. Yarus, and R. Knight: tRNA creation by hairpin duplication. J Mol Evol 61, 524-535 (2005)
148. Woese, C.R., G.J. Olsen, M. Ibba, and D. Söll: Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64, 202-236 (2000) (Pubitemid 30143846)
149. Schimmel P., R. Giegé, D. Moras, and S. Yokohama: An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci USA 90, 8765-8768 (1993)
150. Maizels, N. and A.M. Weiner: Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA 91, 6729-6734 (1994) (Pubitemid 24226740)
151. Schimmel P. and L. Ribas de Pouplana: Transfer RNA: from minihelix to genetic code. Cell 81, 983-986 (1995)
152. Weiner, A.M. and N. Maizels: tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: implications for the origin of protein synthesis. Proc Natl Acad Sci USA 84, 7383-7387 (1987)
153. Weiner, A.M. and N. Maizels: The genomic tag hypothesis: Modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein synthesis. Biol Bull 196, 327-330 (1999) (Pubitemid 29321640)
154. Tanaka, T. and Y. Kikuchi: Origin of the cloverleaf shape of transfer RNAthe double-hairpin model: implication for the role of tRNA intron and the long extra loop. Viva Origino 29, 134-142 (2001)
155. Weiner, A.M.: SINEs and LINEs: the art of biting the hand that feeds you. Curr Opin Cell Biol 14, 343-350 (2002) (Pubitemid 34626973)
156. Cate, J., M. Yusupov, G. Yusupova, T. Earnest, and H. Noller: X-ray crystal structure of 70S ribosome functional complexes. Science 285, 2095-2104 (1999) (Pubitemid 29451422)
157. Frank, J. and R.K. Agrawal: A ratchet-like intersubunit reorganization of the ribosome during translocation. Nature 406, 318-322 (2000) (Pubitemid 30604411)
158. Mathews, D.W., J. Sabina, M. Zuker, and D, H, Turner: Expanded sequence dependence of thermodynamic parameters providesrobust prediction of RNA seconsdary structure. J Mol Biol 288, 911-940 (1999) (Pubitemid 29248642)
159. Ponting, C.P. and R.R. Russell: The natural history of protein domains. Annu Rev Biophys Biomol Struct 31, 45-71 (2002) (Pubitemid 34666825)
160. Todd, A.E., L.R. Marsden, J.M. Thornton and C.A. Orengo: Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol 348, 1235-1260 (2005)
161. Todd, A.E., C.A. Orengo, and J.M. Thornton: Plasticityof enzyme active sites. Trends Biochem Sci 27, 419-426 (2002)
162. Gutteridge , A. and J.M. Thornton: Understanding nature's catalytic toolkit. Trends Biochem Sci 30, 622-629 (2005) (Pubitemid 41540082)
163. Chothia, C., J. Gough, C. Vogel, and S.A. Teichmann: Evolution of the protein repertoire. Science 300, 1701-1703 (2003) (Pubitemid 36712556)
164. James, L.C. and D.S. Tawfick: Conformational diversity and protein evolution. Trends Biochem Sci 30, 622-629 (2003)
165. Vogel, C., S.A. Teichmann, and J. Pereira-Leal: The relationship between domain duplication and recombination. J Mol Biol 346, 355-365 (2005) (Pubitemid 40128326)
166. Apic, G., J. Gough, and S.A. Teichmann: An insight into domain combinations. Bioinformatics 17, suppl. 1, S83-9 (2001) (Pubitemid 33793497)
167. Apic, G., J. Gough, and S.A. Teichmann: Domain combinations in Archaeal, Eubacterial and Eukaryotic proteomes. J Mol Biol 310, 311-25 (2001) (Pubitemid 32664871)
168. Bornberg-Bauer, E., F. Beausart, S.K. Kummerfeld, S.A. Teichmann, and J. Weiner: The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci 62, 435-445 (2005) (Pubitemid 40379234)
169. Bashton, M. and C. Chothia: The geometry of domain combination in proteins. J Mol Biol 315, 927-39 (2002) (Pubitemid 34729337)
170. Han, J.H., S. Batey, A.A. Nickson, S.A. Teichmann, and J. Clarke: The folding and evolution of multidomain proteins. Nat Rev Mol Cell Biol 8, 319-330 (2007) (Pubitemid 46474660)
171. Vogel, C., C. Berzuini, M. Bashton, J. Gough, and S.A. Teichmann: Supra-domains-Evolutionary units larger than single protein domains. J Mol Biol 336, 809-823 (2004) (Pubitemid 38183030)
172. Richardson, J.S.: The anatomy and taxonomy of protein structure. Adv Protein Chem 34, 167-339 (1981)
173. Murzin, A., S.E. Brenner, T. Hubbard, and C. Clothia: SCOP: a structural classification of proteins for the investigation of sequences and structures. J Mol Biol 247, 536-540 (1995)
174. Andreeva, A., D. Howorth, S.E. Brenner, T.J.P. Hubbard, C. Chothia, and A.G. Murzin: SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res 32, D226-D229 (2004) (Pubitemid 38081644)
175. Orengo, C.A., A.D. Michie, S. Jones, D.J. Jones, M.B. Swindells, and J.M. Thornton: CATH: a hierarchic classification of protein domain structures. Structure 5, 1093-1108 (1997) (Pubitemid 27393093)
176. Harrison, A., F. Pearl, R. Mott, J. Thornton, and C. Orengo: Quantifying the similarities within fold space. J Mol Biol 323, 909-926 (2002) (Pubitemid 35341064)
177. Kunin, V., I. Cases, A.J. Enright, V. de Lorenzo, and C.A. Ouzounis: Myriads of protein families, and still counting. Genome Biol 4, 401 (2003)
178. Koonin, E.V., L. Aravind, and A.S. Kondrashov: The impact of comparative genomics on our understanding of evolution. Cell 101, 573-576 (2000)
179. Gough, J., K. Karplus, R. Hughey, and C. Chothia: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 31, 903-919 (2001) (Pubitemid 33063435)
180. Efimov, A.V.: Structural trees for protein superfamilies. Proteins 28, 241-260 (1997) (Pubitemid 27276310)
181. Zhang, C. and S.H. Kim: A comprehensive analysis of the Greek key motifs in protein beta-barrels and betasandwiches. Proteins 40, 409-419 (2000) (Pubitemid 30624448)
182. Przytycka, T., R. Aurora, and G.D. Rose: A protein taxonomy based on secondary structure. Nature Struct Biol 6, 672-682 (1999) (Pubitemid 29318959)
183. Hou, J., G.E. Sims, C. Zhang, S.-H. Kim: A global representation of the protein fold space. Proc Natl Acad Sci USA 100, 2386-2390 (2003) (Pubitemid 36297508)
184. Dokholyan, N.V., B. Shakhnovich, and E.I. Shakhnovich: Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci USA 99, 14132-14136 (2002) (Pubitemid 35257637)
185. Shakhnovich, B.E.: Improving the precision of the structure-function relationship by considering phylogenetic context. PLoS Comp Biol 1, e9 (2005)
186. Taylor, W.R.: A 'periodic table' for protein structures. Nature 416, 657-660 (2002)
187. Taylor, W.R.: Evolutionary transitions in protein fold space. Curr Opin Struct Biol 17, 354-361 (2007). (Pubitemid 47021367)
188. Caetano-Anollés, G. and D. Caetano-Anollés: Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol 60, 484-498 (2005) (Pubitemid 40754789)
189. Fukami-Kobayashi, K., Y. Minezaki, Y. Tateno, and K. Nishikawa: A tree of life based on protein domain organizations. Mol Biol Evol 24, 1181-1189 (2007). (Pubitemid 47343640)
190. Cavalier-Smith, T.: Only six kingdoms of life. Proc Biol Sci 271, 1251-1262 (2004) (Pubitemid 38789317)
191. Gough, J.: Convergent evolution of domain architectures (is rare). Bioinformatics 21, 1464-1471 (2005) (Pubitemid 40552751)
192. White, S.H.: Global statistics of protein sequences: implications for the origin, evolution, and prediction of structure. Annu Rev Biophys Biomol Struct 23, 407-439 (1994) (Pubitemid 24217374)
193. Winstanley, H, F, S. Abeln, and C.M. Deane: How old is your fold? Bioinformatics 21, i449-i458 (2005) (Pubitemid 41794519)
194. Murzin, A.: How far divergent evolution goes in proteins. Curr Opin Struct Biol 8, 380-387 (1998) (Pubitemid 28321367)
195. Grishin, N.V.: Fold change in evolution of protein structures. J Struct Biol 134, 167-185 (2001)
196. Pagel, M., C. Venditti, and A. Meade: Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 314, 119-121 (2006) (Pubitemid 44547754)
197. Caetano-Anollés, G., H.S. Kim, and J.E. Mittenthal: The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci USA 104, 9358-9363 (2007) (Pubitemid 47185784)
198. Kacser, H. and R. Beeby: On the origin of enzyme species by means of natural selection. J Mol Evol 20, 38-51 (1984)
199. Ji, H.-F., D.-X Kong, L. Shen, L.-L. Chen, B.-G. Ma, and H.-Y. Zhang: Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biol 8, R176 (2007)
200. Dupont, C.L., S. Yang, B. Palenik, and P.E. Bourne: Modern proteomes contain putative imprints of of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci USA 103, 17822-17827 (2006) (Pubitemid 44852244)
201. Danchin, A., G. Fang, and S. Noria: The extant core bacterial proteome is an archive of the origin of life. Proteomics 7, 875-889 (2007). (Pubitemid 46506735)
202. Barabási, A.L. and Z.N. Oltvai: Network biology: understanding the cell's functional organization. Nature Rev 5, 101-113 (2004) (Pubitemid 38160277)
203. Rives, A.W. and T. Galitski: Modular organization of cellular networks. Proc Natl Acad Sci USA 100, 1128-1133 (2003) (Pubitemid 36183967)
204. Pfeiffer, T., O.S. Soyer, S. Bonhoeffer: The evolution of connectivity in metabolic networks. PLoS Biology 3, 1269-1275 (2005) (Pubitemid 41032193)
205. Peregrin-Alves, J., S. Tsoka, and C.A. Ouzounis: The phylogenetic extnt of metabolic enzymes in pathways. Genome Res 13, 422-427 (2003) (Pubitemid 36395400)
206. Huynen, M.A., T. dadenkar, and P. Bork: variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol 7, 281-291 (1999) (Pubitemid 29304564)
207. Maden, B.E.H.: No soup for starters? Autotrophy and the origins of metabolism. Trends Biochem Sci 20, 337-341 (1995)
208. Orgel, L.E.: Self-organizing biochemical cycles. Proc Natl Acad Sci USA 97, 12503-12507 (2000)
209. Orgel, L.E.: Some consequences of the RNA world hypothesis. Orig Life Evol Biosphere 33, 211-218 (2003) (Pubitemid 37007890)
210. Lazcano, A. and S.L. Miller: On the origin of metabolic pathways. J Mol Evol 49, 424-431 (1999) (Pubitemid 29463385)
211. Schmidt, S., S. Sunyaev, P. Bork, and T. Dandekar: Metabolites: a helping hand for pathway evolution? Trends Biochem Sci 28, 336-341 (2003) (Pubitemid 36776297)
212. Horowitz, N.H.: On the evolution of biochemical syntheses. Proc Natl Acad Sci USA 31, 153-157 (1945)
213. Cordón, F. : Tratado Evolucionista de Biologia, Aguilar, Madrid, Spain (1990)
214. Jensen, R.A.: Enzyme recruitment in evolution of new function. Ann Rev Microbiol 30, 409-425 (1976)
215. Copley, R.R. and P. Bork: Homology among (ba)8 barrels: Implications for the evolution of metabolic pathways. J Mol Biol 303, 627-41 (2000)
216. Teichmann, S.A., S.C.G. Rison, J.M. Thornton, M. Riley, J. Gough, and C. Chothia: Small-molecule metabolism: an enzyme mosaic. Trends Biotech 19, 482-486 (2001) (Pubitemid 33063603)
217. Teichmann, S.A., S.C.G. Rison, J.M. Thornton, M. Riley, J. Gough, and C. Chothia: The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol 311, 693-708 (2001) (Pubitemid 32803729)
218. Kim, H.S., J. Mittenthal, and G. Caetano-Anollés: MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics 7, 351 (2006)
219. Ogata, H., S. Goto, K. Sato, W. Fujibuchi, H. Bono, and M. Kanehisa: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acid Res 27, 29-34 (1999) (Pubitemid 29209394)
220. Ma, H. and A.-P. Zeng: Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19, 270-277 (2003) (Pubitemid 36181913)
221. Alves, R., R.A.G. Chaleil, and M.J.E. Sternberg: Evolution of enzymes in metabolism: A network perspective. J Mol Biol 320, 751-770 (2002) (Pubitemid 34729403)
222. Light, S., and P. Kraulis: Network analysis of metabolic enzyme evolution in Escherichia coli. BMC Bioinformatics 5, 15 (2004)
223. Lazcano, A. and S.L. Miller: The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85, 793-798 (1996) (Pubitemid 26192133)
224. Kurland, C.G., B. Canbäck, and O.G. Berg: The origins of modern proteomes. Biochimie 89, 1454-1463 (2007) (Pubitemid 350122859)
225. Poole, A. D.C. Jeffares, and D. Penny: The path from the RNA world. J Mol Evol 46, 1-17 (1998) (Pubitemid 28047235)
226. Kurland, C.G., L.J. Collins, and D. Penny: Genomics and the irreducible nature of eukaryote cells. Science 312, 1011-1014 (2006)
227. Woese, C.R.: The universal ancestor. Proc Natl Acad Sci USA 95, 6854-6859 (2000)
228. Ouzounis, C.A., V. Kunin, N. Darzentas, and L. Goldovsky: A minimal estimate for the gene content of the lst universal common ancestor-exobiology from a terrestrial perspective. Res Microbiol 157, 57-68 (2006) (Pubitemid 43202118)
229. Berezovsky, I.N. and E.I. Shakhnovich: Physics and evolution of thermophylic adaptation. Proc Natl Acad Sci USA 102, 12742-12747 (2005)
230. Penny, D. and A. Poole: The nature of the last universal common ancestor. Curr Opin Genet Dev 9, 672-677 (1999)
231. Bamford, D.H.: Do viruses form lineages across different domains of life? Res Microbiol 154, 231-236 (2003) (Pubitemid 36645268)
232. Daubin, V. and H. Ochman: Start-up entities in the evolution of new genes. Curr Opin Genet Devel 14, 616-619 (2004) (Pubitemid 39505365)
233. Forterre, P.: The origin of DNA genomes and DNA replication proteins. Curr Opin Microbiol 5, 525-532 (2002)
234. Forterre, P., J. Filé, and H. Myllykallio: Origin and evolution of DNA and DNA replication machineries. In: The Genetic Code and the Origin of Life. Ed: Ribas de Pouplana L, Springer, NY (2004)
235. Forterre, P.: 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)
236. Forterre, P.: Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain. Proc Natl Acad Sci USA 103, 3669-3674 (2006) (Pubitemid 43376613)
237. Prangishvili, D., P. Forterre, and R. A. Garrett: Viruses of the Archaea: a unifying view. Nature Rev Microbiol 4, 837-848 (2006) (Pubitemid 44593950)
238. Wächtershäuser, G.: On the chemistry and evolution of the pioneer organism. Chem Biodiversity 4, 584-602 (2007) (Pubitemid 46930026)
239. Carson, M.: Ribbons. Meth Enzymol 277, 493-505 (1997) (Pubitemid 27392859)