On the origin of genomes and cells within inorganic compartments

Trends in Genetics

Volumn 21, Issue 12, 2005, Pages 647-654

  Koonin, Eugene V ^a   Martin, William ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; DNA PRIMASE; DOUBLE STRANDED DNA; FERROUS SULFIDE; HELICASE; RNA; RNA DIRECTED RNA POLYMERASE;

ARCHAEBACTERIUM; BACTERIAL CELL; BACTERIUM; BIOSYNTHESIS; CELL WALL; DNA REPLICATION; EUKARYOTE; GENE REPLICATION; GENETIC VARIABILITY; GENOME; MODEL; MOLECULAR EVOLUTION; NONHUMAN; OPERON; PRIORITY JOURNAL; REVIEW;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 27744591844     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2005.09.006     Document Type: Article

References (84)

1. J.E. Darnell, and W.F. Doolittle Speculations on the early course of evolution Proc. Natl. Acad. Sci. U. S. A. 83 1986 1271 1275
2. P. Forterre The nature of the last universal ancestor and the root of the tree of life, still open questions BioSystems 28 1992 15 32
3. A.L. Koch Development and diversification of the Last Universal Ancestor J. Theor. Biol. 168 1994 269 280
4. W.F. Doolittle, and J.R. Brown Tempo, mode, the progenote, and the universal root Proc. Natl. Acad. Sci. U. S. A. 91 1994 6721 6728
5. C. Woese The universal ancestor Proc. Natl. Acad. Sci. U. S. A. 95 1998 6854 6859
6. C.R. Woese On the evolution of cells Proc. Natl. Acad. Sci. U. S. A. 99 2002 8742 8747
7. A. Lazcano, and P. Forterre The molecular search for the last common ancestor J. Mol. Evol. 49 1999 411 412
8. D. Penny, and A. Poole The nature of the last universal common ancestor Curr. Opin. Genet. Dev. 9 1999 672 677
9. R.F. Doolittle Searching for the common ancestor Res. Microbiol. 151 2000 85 89
10. T. Cavalier-Smith The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification Int. J. Syst. Evol. Microbiol. 52 2002 7 76
11. C. de Duve A research proposal on the origin of life Orig. Life Evol. Biosph. 33 2003 559 574
12. E.V. Koonin Comparative genomics, minimal gene-sets and the last universal common ancestor Nat. Rev. Microbiol. 1 2003 127 136
13. Penny, D. An interpretative review of the origin of life research. Biol. Philos. (in press)
14. E.V. Koonin How many genes can make a cell: the minimal-gene-set concept Annu. Rev. Genomics Hum. Genet. 1 2000 99 116
15. J.K. Harris The genetic core of the universal ancestor Genome Res. 13 2003 407 412
16. R.L. Charlebois, and W.F. Doolittle Computing prokaryotic gene ubiquity: rescuing the core from extinction Genome Res. 14 2004 2469 2477
17. M.J. Russell, and A.J. Hall The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front J. Geol. Soc. (London) 154 1997 377 402
18. C. de Duve The onset of selection Nature 433 2005 581 582
19. M.J. Russell A hydrothermally precipitated catalytic iron sulphide membrane as a first step toward life J. Mol. Evol. 39 1994 231 243
20. M.J. Russell In vitro growth of iron sulphide chimneys: possible culture chambers for origin-of-life experiments Terra Nova 1 1989 238 241
21. Y. Boucher Origins and evolution of isoprenoid lipid biosynthesis in archaea Mol. Microbiol. 52 2004 515 527
22. O. Kandler, and H. Konig Cell wall polymers in Archaea (Archaebacteria) Cell. Mol. Life Sci. 54 1998 305 308
23. M.J. Russell Submarine hot springs and the origin of life Nature 336 1988 117
24. W. Martin, and M.J. Russell On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 2003 59 83
25. G. Wächtershäuser From pre-cells to Eukarya - a tale of two lipids Mol. Microbiol. 47 2003 13 22
26. J. Pereto Ancestral lipid biosynthesis and early membrane evolution Trends Biochem. Sci. 29 2004 469 477
27. M.J. Russell On the dissipation of thermal and chemical energies on the early Earth: The onsets of hydrothermal convection, chemiosmosis, genetically regulated metabolism and oxygenic photosynthesis R. Ikan Natural and Laboratory-Simulated Thermal Geochemical Processes 2003 Kluwer Academic Publishers 325 338
28. D.A. Stone, and R.E. Goldstein Tubular precipitation and redox gradients on a bubbling template Proc. Natl. Acad. Sci. U. S. A. 101 2004 11537 11541
29. D.S. Kelley An off-axis hydrothermal vent field near the Mid-Atlantic Ridge at 30 degrees N Nature 412 2001 145 149
30. D.S. Kelley A serpentinite-hosted ecosystem: the Lost City hydrothermal field Science 307 2005 1428 1434
31. G.L. Fruh-Green 30,000 years of hydrothermal activity at the lost city vent field Science 301 2003 495 498
32. M.J. Russell, and W. Martin The rocky roots of the acetyl-CoA pathway Trends Biochem. Sci. 29 2004 358 363
33. V. Svetlitchnyi A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans Proc. Natl. Acad. Sci. U. S. A. 101 2004 446 451
34. G.D. Cody Transition metal sulfides and the origins of metabolism Annu. Rev. Earth Planet. Sci. 32 2004 569 599
35. E.L. Shock The emergence of metabolism from within hydrothermal systems J. Wiegel M.W.W. Adams Thermophiles: The Keys to Molecular Evolution and the Origin of Life 1998 Taylor and Francis 59 76
36. C. Huber, and G. Wachtershauser Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life Science 281 1998 670 672
37. L. Leman Carbonyl sulfide-mediated prebiotic formation of peptides Science 306 2004 283 286
38. E. Douville The Rainbow vent fluids (36°14′ N, MAR): the influence of ultramafic rocks and phase separation on trace metal content in Mid-Atlantic Ridge hydrothermal fluids Chem. Geol. 184 2002 37 48
39. D.R. Mills An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule Proc. Natl. Acad. Sci. U. S. A. 58 1967 217 224
40. M. Eigen Hypercycles and compartments. Compartments assists-but do not replace-hypercyclic organization of early genetic information J. Theor. Biol. 85 1980 407 411
41. M. Eigen, and P. Schuster The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle Naturwissenschaften 64 1977 541 565
42. W. Hordijk, and M. Steel Detecting autocatalytic, self-sustaining sets in chemical reaction systems J. Theor. Biol. 227 2004 451 461
43. U. Wintersberger, and E. Wintersberger Retroviruses and the origin of life Trends Genet. 3 1987 198 202
44. D.D. Leipe Did DNA replication evolve twice independently? Nucleic Acids Res. 27 1999 3389 3401
45. J. Lawrence Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes Curr. Opin. Genet. Dev. 9 1999 642 648
46. J.G. Lawrence, and J.R. Roth Selfish operons: horizontal transfer may drive the evolution of gene clusters Genetics 143 1996 1843 1860
47. A.R. Mushegian, and E.V. Koonin A minimal gene set for cellular life derived by comparison of complete bacterial genomes Proc. Natl. Acad. Sci. U. S. A. 93 1996 10268 10273
48. D.R. Edgell, and W.F. Doolittle Archaea and the origin(s) of DNA replication proteins Cell 89 1997 995 998
49. D.D. Leipe The bacterial replicative helicase DnaB evolved from a RecA duplication Genome Res. 10 2000 5 16
50. J.L. Keck Structure of the RNA polymerase domain of E. coli primase Science 287 2000 2482 2486
51. B.K. Tye Insights into DNA replication from the third domain of life Proc. Natl. Acad. Sci. U. S. A. 97 2000 2399 2401
52. P. Forterre The origin of DNA genomes and DNA replication proteins Curr. Opin. Microbiol. 5 2002 525 532
53. V. Anantharaman Comparative genomics and evolution of proteins involved in RNA metabolism Nucleic Acids Res. 30 2002 1427 1464
54. A.E. Gorbalenya Big nidovirus genome. When count and order of domains matter Adv. Exp. Med. Biol. 494 2001 1 17
55. Brown, D. and Goddard, N.L. (2003) Exponential DNA replication by laminar convection. Phys. Rev. Lett. 91, 158103-158101-158103-158104
56. A.P. Gmyl Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? RNA 9 2003 1221 1231
57. C.K. Biebricher Kinetics of RNA replication: competition and selection among self-replicating RNA species Biochemistry 24 1985 6550 6560
58. E. Mossel, and M. Steel Random biochemical networks: the probability of self-sustaining autocatalysis J. Theor. Biol. 233 2005 327 336
59. R.H. Symons The intriguing viroids and virusoids: what is their information content and how did they evolve? Mol. Plant Microbe Interact. 4 1991 111 121
60. T.O. Diener The viroid: biological oddity or evolutionary fossil? Adv. Virus Res. 57 2001 137 184
61. N. Nemoto, and Y. Husimi A model of the virus-type strategy in the early stage of encoded molecular evolution J. Theor. Biol. 176 1995 67 77
62. O. Kandler The early diversification of life S. Bengston Early Life on Earth 1994 Columbia Univ. Press 152 160
63. E. Szathmary, and L. Demeter Group selection of early replicators and the origin of life J. Theor. Biol. 128 1987 463 486
64. E. Zintzaras Living under the challenge of information decay: the stochastic corrector model vs. hypercycles J. Theor. Biol. 217 2002 167 181
65. J. Brosius Gene duplication and other evolutionary strategies: from the RNA world to the future J. Struct. Funct. Genomics 3 2003 1 17
66. A.D. Altstein Origin of the genetic system Mol. Biol. 21 1987 309 322
67. A. Poole Early evolution: prokaryotes, the new kids on the block BioEssays 21 1999 880 889
68. W.C. Lathe 3rd Gene context conservation of a higher order than operons Trends Biochem. Sci. 25 2000 474 479
69. Y.I. Wolf Genome alignment, evolution of prokaryotic genome organization and prediction of gene function using genomic context Genome Res. 11 2001 356 372
70. A.M. Poole, and D.T. Logan Modern mRNA proofreading and repair: clues that the Last Universal Common Ancestor (LUCA) possessed an RNA genome? Mol. Biol. Evol. 22 2005 1444 1455
71. P. Forterre The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells Biochimie 87 2005 793 803
72. E.J. Snijder Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage J. Mol. Biol. 331 2003 991 1004
73. P. Forterre Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins Mol. Microbiol. 33 1999 457 465
74. H. Brinkmann, and H. Philippe Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies Mol. Biol. Evol. 16 1999 817 825
75. W. Martin, and M. Muller The hydrogen hypothesis for the first eukaryote Nature 392 1998 37 41
76. P. Lopez-Garcia, and D. Moreira Metabolic symbiosis at the origin of eukaryotes Trends Biochem. Sci. 24 1999 88 93
77. M.C. Rivera, and J.A. Lake The ring of life provides evidence for a genome fusion origin of eukaryotes Nature 431 2004 152 155
78. D.C. Jeffares Relics from the RNA world J. Mol. Evol. 46 1998 18 36
79. E. Hilario, and J.P. Gogarten Horizontal transfer of ATPase genes-the tree of life becomes a net of life Biosystems 31 1993 111 119
80. W. Heinen, and A.M. Lauwers Organic sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic aqueous environment Orig. Life Evol. Biosph. 26 1996 131 150
81. G.D. Cody Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate Science 289 2000 1337 1340
82. G.D. Cody Assaying the catalytic potential of transition metal sulfides for abiotic carbon fixation Geochim. Cosmochim. Acta 68 2004 2185 2196
83. R.S. Gupta Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes Microbiol. Mol. Biol. Rev. 62 1998 1435 1491
84. S.D. Copley A mechanism for the association of amino acids with their codons and the origin of the genetic code Proc. Natl. Acad. Sci. U. S. A. 102 2005 4442 4447