Primal eukaryogenesis: On the communal nature of precellular states, ancestral to modern life

Life

Volumn 2, Issue 1, 2012, Pages 170-212

  Egel, Richard ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Cellular escape; Hierarchical clonality; K selection; Karyogenic Proto Coenocyte Hypothesis; Molecular ecosystems; Origin of life; Pre cell theory; Protoeukaryote early concept; R selection

Indexed keywords

EID: 84866487357     PISSN: None     EISSN: 20751729     Source Type: Journal    
DOI: 10.3390/life2010170     Document Type: Article

References (279)

1. Follmann, H.; Brownson, C. Darwin's warm little pond revisited: from molecules to the origin of life. Naturwissenschaften 2009, 96, 1265-1292.
2. Peretó, J. Controversies on the origin of life. Int. Microbiol. 2005, 8, 23-31.
3. Pascal, R.; Boiteau, L.; Forterre, P.; Gargaud, M.; Lazcano, A.; Lopez-Garcia, P.; Maurel, M.C.; Moreira, D.; Peretó, J.; Prieur, D.; Reisse, J. Prebiotic chemistry-biochemistry-emergence of life (4.4-2 Ga). Earth Moon Planets 2006, 98, 153-203.
4. Egel, R. Integrative perspectives: In quest of a coherent framework for origins of life on earth. In Origins of Life: The Primal Self-Organization; Egel, R., Lankenau, D.-H., Mulkidjanian, A.Y., Eds.; Springer-Verlag: Heidelberg, Germany, 2011; pp. 289-360.
5. Mulkidjanian, A.Y. Origin of life in the Zinc World: 1. Photosynthetic, porous edifices built of hydrothermally precipitated zinc sulfide (ZnS) as cradles of life on Earth. Biol. Direct 2009, 4, 26-39.
6. Mulkidjanian, A.Y.; Galperin, M.Y. On the origin of life in the Zinc World: 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biol. Direct 2009, 4, 27-37.
7. Zhang, X.V.; Ellery, S.P.; Friend, C.M.; Holland, H.D.; Michel, F.M.; Schoonen, M.A.A.; Martin, S.T. Photodriven reduction and oxidation reactions on colloidal semiconductor particles: Implications for prebiotic synthesis. J. Photochem. Photobiol. A Chem. 2007, 185, 301-311.
8. Guzman, M.I.; Martin, S.T. Oxaloacetate-to-malate conversion by mineral photoelectrochemistry: Implications for the viability of the reductive tricarboxylic acid cycle in prebiotic chemistry. Int. J. Astrobiol. 2008, 7, 271-278.
9. Guzman, M.I.; Martin, S.T. Prebiotic metabolism: Production by mineral photoelectrochemistry of alpha-ketocarboxylic acids in the reductive tricarboxylic acid cycle. Astrobiology 2009, 9, 833-842.
10. Guzman, M.I.; Martin, S.T. Photo-production of lactate from glyoxylate: How minerals can facilitate energy storage in a prebiotic world. Chem. Commun. 2010, 46, 2265-2267.
11. Morowitz, H.J.; Kostelnik, J.D.; Yang, J.; Cody, G.D. The origin of intermediary metabolism. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 7704-7708.
12. Smith, E.; Morowitz, H.J. Universality in intermediary metabolism. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 13168-13173.
13. Morowitz, H.J.; Smith, E. Energy flow and the organization of life. Complexity 2007, 13, 51-59.
14. Shapiro, R. Small molecule interactions were central to the origin of life. Q. Rev. Biol. 2006, 81, 105-125.
15. Shapiro, R. A simpler origin for life. Scient. Amer. 2007, 296, 46-53.
16. Hunding, A.; Kepes, F.; Lancet, D.; Minsky, A.; Norris, V.; Raine, D.; Sriram, K.; Root-Bernstein, R. Compositional complementarity and prebiotic ecology in the origin of life. BioEssays 2006, 28, 399-412.
17. Kurakin, A. The self-organizing fractal theory as a universal discovery method: the phenomenon of life. Theor. Biol. Med. Model. 2011, 8, 4:1-4:66.
18. Haldane, J.B.S. The origin of life. The Rationalist Annual 1929;-Reproduced in: Haldane, J.B.S. Science and Life: Essays of a Rationalist. Pemberton Publishing in association with Barrie & Rockliff: London, UK, 1968; pp. 1-11.
19. 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.
20. Martin, W.; Russell, M.J. 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. 2003, 358, 59-85.
21. Martin, W.; Baross, J.; Kelley, D.; Russell, M.J. Hydrothermal vents and the origin of life. Nat. Rev. Microbiol. 2008, 6, 805-814.
22. Koonin, E.V. On the origin of cells and viruses: primordial virus world scenario. Ann. N.Y. Acad. Sci. 2009, 1178, 47-64.
23. Blair, N.E.; Bonner, W.A. A model for the enantiomeric enrichment of polypeptides on the primitive earth. Orig. Life Evol. Biosph. 1981, 11, 331-335.
24. Cheng, C.M.; Fan, C.; Wan, R.; Tong, C.Y.; Miao, Z.W.; Chen, J.; Zhao, Y.F. Phosphorylation of adenosine with trimetaphosphate under simulated prebiotic conditions. Orig. Life. Evol. Biosph. 2002, 32, 219-224.
25. Commeyras, A.; Collet, H.; Boiteau, L.; Taillades, J.; Vandenabeele-Trambouze, O.; Cottet, H.; Biron, J.-P.; Plasson, R.; Mion, L.; Lagrille, O.; et al. Prebiotic synthesis of sequential peptides on the Hadean beach by a molecular engine working with nitrogen oxides as energy sources. Polym. Int. 2002, 51, 661-665.
26. Lathe, R. Fast tidal cycling and the origin of life. Icarus 2004, 168, 18-22.
27. Bywater, R.P.; Conde-Frieboes, K. Did life begin on the beach? Astrobiology 2005, 5, 568-574.
28. Plankensteiner, K.; Reiner H.; Rode, B.M. Prebiotic chemistry: The amino acid and peptide world. Curr. Org. Chem. 2005, 9, 1107-1114.
29. Brack, A. From interstellar amino acids to prebiotic catalytic peptides: A review. Chem. Biodiv. 2007, 4, 665-679.
30. Deamer, D.; Weber, A.L. Bioenergetics and life's origins. Cold Spring Harb. Perspect. Biol. 2010, 2, a004929:1-a004929:16.
31. Trinks, H.; Schröder, W.; Biebricher, C.K. Ice and the origin of life. Orig. Life Evol. Biosph. 2005, 35, 429-445.
32. Price, P.B. Microbial life in glacial ice and implications for a cold origin of life. FEMS Microbiol. Ecol. 2007, 59, 217-231.
33. Gilbert, W. Origin of life: The RNA world. Nature 1986, 319, 618.
34. The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA World; Gesteland, R.F., Cech, T.R., Atkins, J.F., Eds.; Cold Spring Harbor Lab Press: Cold Spring Harbor, NY, USA, 2006.
35. Robertson, M.P.; Joyce, G.F. The origins of the RNA World. Cold Spring Harb. Perspect. Biol. 2010, 2, a003608:1-a003608:22.
36. Lankenau, D.-H. Two RNA Worlds: toward the origin of replication, genes, recombination, and repair. In Origins of Life: The Primal Self-Organization; Egel, R., Lankenau, D.-H., Mulkidjanian, A.Y., Eds.; Springer-Verlag: Heidelberg, Germany, 2011; pp. 225-286.
37. Kurland, C.G. The RNA dreamtime. BioEssays 2010, 32, 866-871.
38. Moulton, V.; Gardner, P.; Pointon, R.; Creamer, L.; Jameson, G.; Penny, D. RNA folding argues against a hot-start origin of life. J. Mol. Evol. 2000, 51, 416-421.
39. Kritsky, M.; Telegina, T. Role of nucleotide-like coenzymes in primitive evolution. In Origins: Cellular Origin, Life in Extreme Habitats and Astrobiology; Seckbach, J., Ed.; Kluver Academic Publishers: Dordrecht, NL, 2005; pp. 215-231.
40. Sharov, A.A. Coenzyme autocatalytic network on the surface of oil microspheres as a model for the origin of life. Int J. Mol. Sci. 2009, 10, 1838-1852.
41. Raffaelli, N. Nicotinamide coenzyme synthesis: A case of ribonucleotide emergence or a byproduct of the RNA world? In Origins of Life: The Primal Self-Organization; Egel, R., Lankenau, D.-H., Mulkidjanian, A.Y., Eds.; Springer-Verlag: Heidelberg, Germany, 2011; pp. 185-208.
42. Rode, B.M. Peptides and the origin of life. Peptides 1999, 20, 773-786.
43. Milner-White, E.J.; Russell, M.J. Sites for phosphates and iron-sulfur thiolates in the first membranes: 3 to 6 residue anion-binding motifs (nests). Orig. Life Evol. Biosph. 2005, 35, 19-27.
44. van der Gulik, P.; Massar, S.; Gilis, D.; Buhrman, H.; Rooman, M. The first peptides: The evolutionary transition between prebiotic amino acids and early proteins. J. Theor. Biol. 2009, 261, 531-539.
45. Vauthey, S.; Santoso, S.; Gong, H.; Watson, N.; Zhang, S. Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 5355-5360.
46. Fishkis, M. Steps towards the formation of a protocell: the possible role of short peptides. Orig. Life Evol. Biosph. 2007, 37, 537-553.
47. Zhang, S. Plausible lipid-like peptides: prebiotic molecular self-assembly in water. In Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning; Barrow, J.D., Morris, S.C., Freeland, S.J., Harper, C.L., Jr., Eds.; Cambridge University Press: Cambridge, UK, 2008; pp. 440-455.
48. Egel, R. Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy. BioEssays 2009, 31, 1100-1109.
49. Fishkis, M. Emergence of self-reproduction in cooperative chemical evolution of prebiological molecules. Orig. Life Evol. Biosph. 2011, 41, 261-275.
50. Dyson, F.J. A model for the origin of life. J. Mol. Evol. 1982, 18, 344-350.
51. Kauffman, S.A. The Origins of Order; Oxford University Press: Oxford, UK, 1993.
52. Hordijk, W.; Kauffman, S.A.; Steel, M. Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems. Int. J. Mol. Sci. 2011, 12, 3085-3101.
53. de Duve, C. Selection by differential molecular survival: A possible mechanism of early chemical evolution. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 8253-8256.
54. Davidovich, C.; Belousoff, M.; Bashan, A.; Yonath, A. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery. Res. Microbiol. 2009, 160, 487-492.
55. Belousoff, M.J.; Davidovich, C.; Zimmerman, E.; Caspi, Y.; Wekselman, I.; Rozenszajn, L.; Shapira, T.; Sade-Falk, O.; Taha, L.; Bashan, A.; et al. Ancient machinery embedded in the contemporary ribosome. Biochem. Soc. Trans. 2010, 38, 422-427.
56. Weinger, J.S.; Parnell, K.M.; Dorner, S.; Green, R.; Strobel, S.A. Substrate-assisted catalysis of peptide bond formation by the ribosome, Nat. Struct. Mol. Biol. 2004, 11, 1101-1106.
57. Steitz, T.A. A structural understanding of the dynamic ribosome machine. Nat. Rev. Mol. Cell Biol. 2008, 9, 242-253.
58. Woese, C. Molecular mechanics of translation: A reciprocating ratchet mechanism. Nature 1970, 226, 817-820.
59. Zhang W.; Dunkle J.A.; Cate J.H.D. Structures of the ribosome in intermediate states of ratcheting. Science 2009, 325, 1014-1017.
60. Schmeing, T.M.; Huang, K.S.; Strobel, S.A.; Steitz, T.A. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 2005, 438, 520-524.
61. Agmon, I.; Bashan, A.; Zarivach, R.; Yonath, A. Symmetry at the active site of the ribosome: structural and functional implications. Biol. Chem. 2005, 386, 833-844.
62. Luisi, P.L.; Walde, P.; Oberholzer, T. Lipid vesicles as possible intermediates in the origin of life. Curr. Opin. Colloid Interface Sci. 1999, 4, 33-39.
63. Segré, D.; Ben-Eli, D.; Deamer, D.W.; Lancet, D. The Lipid World. Orig. Life Evol. Biosph. 2001, 31, 119-145.
64. Budin, I.; Szostak, J.W. Expanding roles for diverse physical phenomena during the origin of life. Annu. Rev. Biophys. 2010, 39, 245-263.
65. Koch, A.L.; Silver, S. The first cell. Adv. Microb. Physiol. 2005, 50, 227-259.
66. Cairns-Smith, A.G. Genetic Takeover and the Mineral Origins of Life; Cambridge University Press: Cambridge, UK, 1982.
67. Baaske, P.; Weinert, F.M.; Duhr, S.; Lemke, K.H.; Russell, M.J.; Braun, D. Extreme accumulation of nucleotides in simulated hydrothermal pore systems. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 9346-9351.
68. Branciamore, S.; Gallori, E.; Szathmary, E.; Czaran, T. The origin of life: Chemical evolution of a metabolic system in a mineral honeycomb? J. Mol. Evol. 2009, 69, 458-469.
69. Hansma, H.G. Possible origin of life between mica sheets. J. Theor. Biol. 2010, 266, 175-188.
70. Maynard Smith, J.; Szathmáry, E. The Major Transitions in Evolution; Freeman: Oxford, UK, 1995.
71. Trevors, J.T.; Pollack, G.H. Hypothesis: The origin of life in a hydrogel environment. Prog. Biophys. Mol. Biol. 2005, 89, 1-8.
72. Spitzer, J.; Poolman, B. The role of biomacromolecular crowding, ionic strength, and physicochemical gradients in the complexities of life's emergence. Microbiol. Mol. Biol. Rev. 2009, 73, 371-388.
73. Trevors, J.T. Hypothesized origin of microbial life in a prebiotic gel and the transition to a living biofilm and microbial mats. C. R. Biologies 2011, 334, 269-272.
74. Pollack, G.H.; Figueroa, X.; Zhao, Q. The minimal cell and life's origin: Role of water and aqueous interfaces. In The Minimal Cell: The Biophysics of Cell Compartment and the Origin of Cell Functionality; Luisi, P.L., Stano, P., Eds.; Springer: Dordrecht, The Netherlands, 2011.
75. Griffiths, G. Cell evolution and the problem of membrane topology. Nat. Rev. Mol. Cell Biol. 2007, 8, 1018-1024.
76. Sobolewski, A.L.; Domcke, W. On the mechanism of rapid non-radiative decay in intramolecularly hydrogen-bonded-systems. Chem. Phys. Lett. 1999, 300, 533-539.
77. Sobolewski, A.L.; Domcke, W. The chemical physics of the photostability of life. Europhys. News 2006, 37, 20-23.
78. Shemesh, D.; Hattig, C.; Domcke, W. Photophysics of the Trp-Gly dipeptide: Role of electron and proton transfer processes for efficient excited-state deactivation. Chem. Phys. Lett. 2009, 482, 38-43.
79. Mulkidjanian, A.Y.; Cherepanov, D.A.; Galperin, M.Y. Survival of the fittest before the beginning of life: Selection of the first oligonucleotide-like polymers by UV light. BMC Evol. Biol. 2003, 3, 12:1-12:7.
80. Brack, A.; Barbier, B. Chemical activity of simple basic peptides. Orig. Life. Evol. Biosph. 1990, 20, 139-144.
81. Braun, S.; Humphreys, C.; Fraser, E.; Brancale, A.; Bochtler, M.; Dale, T.C. Amyloid-associated nucleic acid hybridisation. PLoS One 2011, 6, e19125:1-e19125:11.
82. Hoffmann, M.R.; Martin, S.T.; Choi, W.; Bahnemann, D.W. Environmental applications of semiconductor photocatalysis. Chem. Rev. 1995, 95, 69-96.
83. Mulkidjanian, A.Y.; Galperin, M.Y. Evolutionary origins of membrane proteins. In Structural Bioinformatics of Membrane Proteins; Frishman, D. Ed.; Springer: Wien, Austria, 2010; pp. 1-28.
84. Takagi, M.; Goto, S.; Matsuda, T. Photo-reaction of lipoic acid and related organic disulphides: reductive acylation with aldehydes. J. Chem. Soc. Chem. Commun. 1976, 1976, 92-93.
85. Weber, A.L. Formation of the thioester, N, S-diacetylcysteine, from acetaldehyde and N, N'-diacetylcystine in aqueous solution with ultraviolet light. J. Mol. Evol. 1981, 17, 103-107.
86. Di Sabato, G.; Jencks, W.P. Mechanism and catalysis of acyl phosphates II. Hydrolysis. J. Am. Chem. Soc. 1961, 83, 4400-4405.
87. Weber, A.L. Formation of pyrophosphate, tripolyphosphate, and phosphorylimidazole with the thioester, N, S-diacetylcysteamine, as the condensing agent. J. Mol. Evol. 1981, 18, 24-29.
88. Weber, A.L. Formation of pyrophosphate on hydroxyapatite with thioesters as condensing agents. BioSystems 1982, 15, 183-189.
89. Wächtershäuser, G. Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. U. S. A. 1990, 87, 200-204.
90. de Duve, C. Clues from present-day biology: the thioester world. In The Molecular Origins of Life; Brack A., Ed.; Cambridge Univ Press: Cambridge, UK, 1998; pp. 219-236.
91. Maheen, G.; Tian, G.; Wang, Y.; He, C.; Shi, Z.; Yuan, H.; Feng, S. Resolving the enigma of prebiotic C-O-P bond formation: Prebiotic hydrothermal synthesis of important biological phosphate esters. Heteroatom Chem. 2010, 21, 161-167.
92. Maheen, G.; Wang, Y.; Wang, Y.; Shi, Z.; Tian, G.; Feng, S. Mimicking the prebiotic acidic hydrothermal environment: One-pot prebiotic hydrothermal synthesis of glucose phosphates. Heteroatom Chem. 2011, 22, 186-191.
93. Powner, M.W.; Gerland, B.; Sutherland, J.D. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 2009, 459, 239-242.
94. Szostak, J.W. Origins of life: systems chemistry on early Earth. Nature 2009, 459, 171-172.
95. Hagan, W.J., Jr. Uracil-catalyzed synthesis of acetyl phosphate: a photochemical driver for protometabolism. ChemBioChem 2010, 11, 383-387.
96. Conrad, M. The geometry of evolution. BioSystems 1990, 24, 61-81.
97. Woese, C.R. Evolution of the genetic code. Proc. Natl. Acad. Sci. U. S. A. 1973, 54, 1546-1552.
98. Wong, J.T.-F. Evolution of the genetic code. Microbiol. Sci. 1988, 5, 164-181.
99. Davis, B.K. Evolution of the genetic code. Progr. Biophys. Mol. Biol. 1999, 72, 157-243.
100. Koonin, E.V.; Novozhilov, A.S. Origin and evolution of the genetic code: the universal enigma. IUBMB Life 2009, 61, 99-111.
101. Rodin, A.S.; Szathmáry, E.; Rodin, S.N. One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation. Biol. Direct 2009, 4, 4:1-4:30.
102. Johnson, D.B.F.; Wang, L. Imprints of the genetic code in the ribosome. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 8298-8303.
103. Freeland, S.J.; Knight, R.D.; Landweber, L.F.; Hurst, L.D. Early fixation of an optimal genetic code. Mol. Biol. Evol. 2000, 17, 511-518.
104. Itzkovitz, S.; Alon, U. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 2007, 17, 405-412.
105. Butler, T.; Goldenfeld, N.; Mathew, D.; Luthey-Schulten, Z. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys. Rev. E 2009, 79, 060901:1-060901:4.
106. Vetsigian, K.; Woese, C.R.; Goldenfeld, N. Collective evolution and the genetic code. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 10696-10701.
107. Woese, C. The universal ancestor. Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 6854-6859.
108. Calabretta, R.; Nolfi, S.; Parisi, D.; Wagner, P. A case study of the evolution of modularity: towards a bridge between evolutionary biology, artificial life, neuro-and cognitive science. In Artificial Life VI: Proceedings of the Sixth International Conference on Artificial Life; Adami, C., Belew, R.K., Kitano, H., Taylor C.E., Eds.; MIT Press: Cambridge, MA, USA, 1998; pp. 275-284.
109. Dauscher, P.; Uthmann, T. Self-organized modularization in evolutionary algorithms. Evolut. Comput. 2005, 13, 303-328.
110. Polani, D.; Dauscher, P.; Uthmann, T. On a quantitative measure for modularity based on information theory. In Advances in Artificial Life. ECAL 2005; Capcarrère, M.S., Freitas, A.A., Bentley, P.J., Johnson, C.G., Timmis, J., Eds.; Springer-Verlag: Heidelberg, Germany, 2005; pp. 393-402.
111. Schimmel, P. Origin of genetic code: A needle in the haystack of tRNA sequences. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 4521-4522.
112. Rodin, A.S.; Szathmáry, E.; Rodin, S.N. On origin of genetic code and tRNA before translation. Biol. Direct 2011, 6, 14-24.
113. Callebaut, W.; Rasskin-Gutman, D., Eds. Modularity: Understanding the Development and Evolution of Natural Complex Systems; MIT Press: Cambridge, MA, USA, 2005.
114. Pereira-Leal, J.B.; Levy, E.D.; Teichmann, S.A. The origins and evolution of functional modules: lessons from protein complexes. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2006, 361, 507-517.
115. Bonabeau, E.; Dorigo, M.; Theraulaz, G. Swarm intelligence: From natural to artificial systems; Oxford University Press: Oxford, UK, 1999.
116. Chen, H.; Zhu, Y.; Hu, K.; He, X. Hierarchical swarm model: A new approach to optimization. Discrete Dyn. Nat. Soc. 2010, 2010, 379649:1-379649:30.
117. Sun, J.; Deem, M. Spontaneous emergence of modularity in a model of evolving individuals. Phys. Rev. Lett. 2007, 99, 228107:1-228107:4.
118. Goldenfeld, N.; Woese C. Biology's next revolution. Nature 2007, 445, 369.
119. Cohen, E.; Kessler, D.A.; Levine, H. Recombination dramatically speeds up evolution of finite populations. Phys. Rev. Lett. 2005, 94, 098102:1-098102:5.
120. Reanney, D.C. Genetic error and genome design. Trends Genet. 1986, 2, 41-46.
121. Lehman, N. A case for the extreme antiquity of recombination. J. Mol. Evol. 2003, 56, 770-777.
122. Vogan, A.A.; Higgs, P.G. The advantages and disadvantages of horizontal gene transfer and the emergence of the first species. Biology Direct 2011, 6, 1-14.
123. Lehman, N.; Unrau, P.J. Recombination during in vitro evolution J. Mol. Evol. 2005, 61, 245-252.
124. Lehman, N. A recombination-based model for the origin and early evolution of genetic information. Chem. Biodivers. 2008, 5, 1707-1717.
125. Lankenau, D.H. The legacy of the germ line-maintaining sex and life in metazoans: Cognitive roots of the concept of hierarchical selection. In Recombination and Meiosis-Models, Means and Evolution; Egel, R., Lankenau, D.H., Eds.; Springer-Verlag: Heidelberg, Germany; Genome Dyn. Stab. 2007, 3, 289-339.
126. Fedorov, A.; Fedorova, L. Introns: mighty elements from the RNA world. J. Mol. Evol. 2004, 59, 718-721.
127. Jeffares, D.C.; Poole, A.M.; Penny, D. Relics from the RNA world. J. Mol. Evol. 1998, 46, 18-36.
128. Penny, D.; Hoeppner, M.P.; Poole, A.M.; Jeffares, D.C. An overview of the introns-first theory. J. Mol. Evol. 2009, 69, 527-540.
129. Kooter, J.M.; de Lange, T.; Borst, P. Discontinuous synthesis of mRNA in trypanosomes. EMBO J. 1984, 3, 2387-2392.
130. Günzl, A. The pre-mRNA splicing machinery of trypanosomes: complex or simplified? Eukaryot. Cell 2010, 9, 1159-1170.
131. Dorit, R.L.; Schoenbacher, L.; Gilbert, W. How big is the universe of exons? Science 1990, 250, 1377-1382.
132. Gilbert, W.; de Souza, S.J.; Long, M. Origin of genes. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 7698-7703.
133. Patthy, L. Genome evolution and the evolution of exon-shuffling-a review. Gene 1999, 238, 103-114.
134. Roy, S.W.; Gilbert, W. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat. Rev. Genet. 2006, 7, 211-221.
135. Siefert, J.L.; Martin, K.A.; Abdi, F.; Widger, WR.; Fox, G.E. Conserved gene clusters in bacterial genomes provide further support for the primacy of RNA. J. Mol. Evol. 1997, 45, 467-472.
136. Dandekar, T.; Snel, B.; Huynen, M.; Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 1998, 23, 324-328.
137. Glansdorff, N. On the origin of operons and their possible role in evolution toward thermophily. J. Mol. Evol. 1999, 49, 432-438.
138. Fondi, M.; Emiliani, G.; Fani, R. Origin and evolution of operons and metabolic pathways. Res. Microbiol. 2009, 160, 502-512.
139. Emiliani, G.; Fondi, M.; Liò, P.; Fani, R. Evolution of metabolic pathways and evolution of genomes. In Geomicrobiology, Molecular and Environmental Perspective.; Barton, L.L., Mandl, M., Loy, A., Eds.; Springer: Dordrecht, NL, 2010; pp. 37-68.
140. Møller-Jensen, J.; Jensen, R.B.; Gerdes, K. Plasmid and chromosome segregation in prokaryotes. Trends Microbiol. 2000, 8, 313-320.
141. Yanagida, M. Basic mechanism of eukaryotic chromosome segregation. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2005, 360, 609-621.
142. Dye, N.A.; Shapiro, L. The push and pull of the bacterial cytoskeleton. Trends Cell Biol. 2007, 17, 239-245.
143. Blackburn, E.H. Telomeres and telomerase: their mechanisms of action and the effects of altering their functions. FEBS Lett. 2005, 579, 859-862.
144. Blackburn, E.H.; Collins, K. Telomerase: an RNP enzyme synthesizes DNA. Cold Spring Harb. Perspect. Biol. 2010, 2, a003558:1-a003558:9.
145. Khan, S.A. Rolling-circle replication of bacterial plasmids. Microbiol. Mol. Biol. Rev. 1997, 61, 442-455.
146. Fiore-Donno, A.-M.; Berney, C.; Pawlowski, J.; Baldauf, S.L. Higher-order phylogeny of plasmodial slime molds (Myxogastria) based on elongation factor-1 a and small subunit rRNA gene sequences. J. Eukaryot. Microbiol. 2005, 52, 1-10.
147. Hoppe, T.; Kutschera, U. In the shadow of Darwin: Anton deBary's origin of myxomycetology and a molecular phylogeny of the plasmodial slime molds. Theory Biosci. 2010, 129, 15-23.
148. Egel, R.; Penny, D. On the origin of meiosis in eukaryotic evolution: Coevolution of meiosis and mitosis from feeble beginnings. In Recombination and Meiosis-Models, Means and Evolution; Egel, R., Lankenau, D.H., Eds.; Springer-Verlag: Heidelberg, Germany; Genome Dyn. Stab. 2007, 3, 249-388.
149. Woese, C.R.; Fox, G. The concept of cellular evolution. J. Mol. Evol. 1977, 10, 1-6.
150. Kandler, O. The early diversification of life. In Early Life on Earth: Nobel Symposium 84; Bengtson, S., Ed.; Columbia University Press: New York, NY, USA, 1994; pp. 152-160.
151. Kandler, O. Cell wall biochemistry in Archaea and its phylogenetic implications. J. Biol. Phys. 1994, 20, 165-169.
152. Kandler, O. Cell wall biochemistry and three-domain concept of life. System. Appl. Microbiol. 1994, 16, 501-509.
153. Moreira, D.; López-García, P. The last common ancestor of modern cells. In Lectures in astrobiology, Vol II; Gargaud, M., Martin, H., Claeys, P., Eds.; Springer-Verlag: Berlin, Germany, 2007; Adv. Astrobiol. Biogeophys., pp. 305-317.
154. Blobel, G. Intracellular protein topogenesis. Proc. Natl. Acad. Sci. U. S. A. 1980, 77, 1496-1500.
155. Cavalier-Smith, T. Obcells as proto-organisms: Membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J. Mol. Evol. 2001, 53, 555-595.
156. Collins, O.R.; Haskins, E.F. Genetics of somatic fusion in Physarum polycephalum: the PpII strain. Genetics 1972, 71, 63-71.
157. Woldringh, C.L.; Nanninga, N. Structural and physical aspects of bacterial chromosome segregation. J. Struct. Biol. 2006, 156, 273-283.
158. Iborra, F.J. Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organisation? Theor. Biol. Med. Model. 2007, 12, 4-15.
159. Rippe, K. Dynamic organization of the cell nucleus. Curr. Opin. Genet. Dev. 2007, 17, 373-380.
160. Lake, J.A.; Rivera, M.C. Was the nucleus the first endosymbiont? Proc. Natl. Acad. Sci. U. S. A. 1994, 91, 2880-2881.
161. Güttinger, S.; Laurell, E.; Kutay, U. Orchestrating nuclear envelope disassembly and reassembly during mitosis. Nat. Rev. Mol. Cell Biol. 2009, 10, 178-191.
162. de Roos, A.D.G. The origin of the eukaryotic cell based on conservation of existing interfaces. Artif. Life 2006, 12, 513-523.
163. Martin, W. Archaebacteria (Archaea) and the origin of the eukaryotic nucleus. Curr. Opin. Microbiol. 2005, 8, 630-637.
164. Sanders, I.R.; Croll D. Arbuscular mycorrhiza: The challenge to understand the genetics of the fungal partner. Annu. Rev. Genet. 2010, 44, 271-292.
165. Jany, J.L.; Pawlowska, T.E. Multinucleate spores contribute to evolutionary longevity of asexual Glomeromycota. Amer. Naturalist 2010, 175, 424-435.
166. Koonin, E.; Martin, W. On the origin of genomes and cells within inorganic compartments. Trends Genet. 2005, 21, 647-654.
167. Lane, N.; Allen, J.F.; Martin, W. How did LUCA make a living? Chemiosmosis in the origin of life. BioEssays, 2010, 32, 271-280.
168. Fischer, H.M. Genetic regulation of nitrogen fixation in rhizobia. Microbiol. Rev. 1994, 58, 352-386.
169. Poole, A.M.; Jeffares, D.C.; Penny, D. Prokaryotes, the new kids on the block. BioEssays 1999, 21, 880-889.
170. Bapteste, E.; O'Malley, M.A.; Beiko, R.G.; Ereshefsky, M.; Gogarten, J.P.; Franklin-Hall, L.; Lapointe, F.J.; Dupré, J.; Dagan, T.; Boucher, Y.; Martin, W. Prokaryotic evolution and the tree of life are two different things. Biol. Direct 2009, 4, 34:1-34:20.
171. Cavalier-Smith, T, Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol. Direct 2010, 5, 7-78.
172. Schopf, J.W.; Packer, B.M. Early Archean (3.3 billion to 3.5 billion-year-old) microfossils from Warrawoona group, Australia. Science 1987, 237, 70-73.
173. Forterre, P. Thermoreduction, a hypothesis for the origin of prokaryotes. C. R. Acad. Sci. III. 1995, 318, 415-422.
174. Embley, M.T.; Martin, W. Eukaryotic evolution, changes and challenges. Nature 2006, 440, 623-630.
175. Martin, W.; Dagan, T.; Koonin, E.V.; Dipippo, J.L.; Gogarten, J.P.; Lake J.A. The evolution of eukaryotes. Science 2007, 316, 542-543; author reply 543.
176. Gribaldo, S.; Poole, A.M.; Daubin, V.; Forterre P.; Brochier-Armanet, C. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat. Rev. Microbiol. 2010, 8, 743-752.
177. Dagan, T.; Roettger, M.; Bryant, D.; Martin, W. Genome Networks Root the Tree of Life between Prokaryotic Domains. Genome Biol. Evol. 2010, 2, 379-392.
178. Poole, A.; Penny, D. Eukaryote evolution: engulfed by speculation. Nature 2007, 447, 913.
179. Javaux, E.J.; Marshall, C.P.; Bekker A. Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits. Nature 2010, 463, 934-938.
180. David, L.A.; Alm, E.J. Rapid evolutionary innovation during an Archaean Genetic Expansion. Nature 2010, 469, 93-96.
181. Fuerst, J.A. Intracellular compartmentation in planctomycetes. Annu. Rev. Microbiol. 2005, 59, 299-328.
182. Forterre, P.; Gribaldo, S. Bacteria with a eukaryotic touch: a glimpse of ancient evolution? Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 12739-12740.
183. McInerney, J.O.; Martin, W.F.; Koonin, E.V.; Allen, J.F.; Galperin, M.Y.; Lane, N.; Archibald J.M.; Embley, T.M. Planctomycetes and eukaryotes: A case of analogy not homology. BioEssays 2011, 33, 810-817
184. Fuerst, J.A.; Sagulenko, E. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat. Rev. Microbiol. 2011, 9, 403-413.
185. Pace, N.R. Time for a change. Nature 2006, 441, 289.
186. Harris, J.K.; Kelley, S.T.; Spiegelman, G.B.; Pace N.R. The genetic core of the universal ancestor. Genome Res. 2003, 13, 407-412.
187. Puigbò, P.; Wolf, Y.I.; Koonin E.V. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J. Biol. 2009, 8, 59:1-59:17.
188. Goldman, A.D.; Samudrala, R.; Baross, J.A. The evolution and functional repertoire of translation proteins following the origin of life. Biol. Direct 2010, 5, 15:1-15:12.
189. Dagan, T.; Martin W. The tree of one percent. Genome Biol. 2006, 7, 118:1-118:7.
190. Bapteste, E.; Boucher, Y. Lateral gene transfer challenges principles of microbial systematics. Trends Microbiol. 2008, 16, 200-207.
191. Puigbò, P.; Wolf, Y.I.; Koonin, E.V. The tree and net components of prokaryote evolution. Genome Biol. Evol. 2010, 2, 745-756.
192. Raoult, D. The post-Darwinist rhizome of life. Lancet 2010, 375, 104-105.
193. Beauregard-Racine, J.; Bicep, C.; Schliep, K.; Lopez, P.; Lapointe, F.J.; Bapteste E. Of Woods and Webs: Possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol. Direct 2011, 6, 39:1-39:21.
194. Marcet-Houben, M.; Gabaldon, T. Acquisition of prokaryotic genes by fungal genomes. Trends Genet. 2010, 26, 5-8.
195. Doolittle, W.F. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 1998, 14, 307-311.
196. Martin, W.; Rujan, T.; Richly, E.; Hansen, A.; Cornelsen, S.; Lins, T.; Leister, D.; Stoebe, B.; Hasegawa, M.; Penny, D. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Nat. Acad. Sci. U. S. A. 2002, 99, 12246-12251.
197. Dacks, J.; Roger, A.J. The first sexual lineage and the relevance of facultative sex. J. Mol. Evol. 1999, 48, 779-783.
198. Logsdon, J.M.J. Evolutionary genetics: sex happens in Giardia. Curr. Biol. 2008, 18, R66-68.
199. Wilkins, A.S.; Holliday R. The evolution of meiosis from mitosis. Genetics 2009, 181, 3-12.
200. Carlile, M. Prokaryotes and eukaryotes: strategies and successes. Trends Biochem. Sci. 1982, 7, 128-130.
201. Cavalier-Smith, T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 2002, 52, 297-354.
202. Hartman, H.; Fedorov, A. The origin of the eukaryotic cell: a genomic investigation. Proc. Natl. Acad. Sci. USA 2002, 99, 1420-1425.
203. Poole, A. Eukaryote evolution: the importance of the stem group. In Evolutionary Genomics and Systems Biology. Caetano-Anollés, G., Ed.; Wiley-Blackwell: Hoboken, NJ, USA, 2010; pp 63-80.
204. Poole, A.M.; Neumann, N. Reconciling an archaeal origin of eukaryotes with engulfment: A biologically plausible update of the Eocyte hypothesis. Res. Microbiol. 2011, 162, 71-76.
205. de Nooijer, S.; Holland, B.R.; Penny, D. The emergence of predators in early life: there was no Garden of Eden. PLoS One 2009, 4, e5507:1-e5507:10.
206. Lonhienne, T.G.; Sagulenko, E.; Webb, R.I.; Lee, K.C.; Franke, J.; Devos, D.P.; Nouwens, A.; Carroll, B.J.; Fuerst, J.A. Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 12883-12888.
207. Jékely, G. Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms. Biol. Direct 2007, 2, 3:1-3:15.
208. Gross, J.; Bhattacharya, D. Uniting sex and eukaryote origins in an emerging oxygenic world. Biol. Direct 2010, 5, 53:1-53:20.
209. Poole, A.M.; Phillips, M.J.; Penny, D. Prokaryote and eukaryote evolvability. BioSystems 2003, 69, 163-185.
210. Kurland, C.G.; Collins, L.J.; Penny, D. Genomics and the irreducible nature of eukaryote cells. Science 2006, 312, 1011-1014.
211. Poole, A.M. Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes? Biol. Direct 2006, 1, 36:1-36:6.
212. Martin, W.; Koonin, E.V. Introns and the origin of nucleus-cytosol compartmentation. Nature 2006, 440, 41-45.
213. Koonin, E.V. The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol. 2010, 11, 209:1-209:12.
214. Stetter, K.O. The lesson of archaebacteria. In Early Life on Earth: Nobel Symposium 84; Bengtson, S., Ed.; Columbia University Press: New York, NY, USA, 1994; pp. 143-151.
215. Stetter, K.O. Hyperthermophiles in the history of life. Phil. Trans. R. Soc. Lond. B 2006, 361, 1837-1843.
216. Levy, M.; Miller, S.L. The stability of the RNA bases: implications for the origin of life. Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 7933-7938.
217. Moulton, V.; Gardner, P.P.; Pointon, R.F.: Creamer, L.K.: Jameson, G.B.: Penny, D. RNA folding argues against a hot-start origin of life. J. Mol. Evol. 2000, 51, 416-421.
218. Galtier, N.; Tourasse, N.; Gouy, M. A nonhyperthermophilic common ancestor to extant life forms. Science 1999, 283, 220-221.
219. Forterre, P.; Confalonieri, F.; Charbonnier, F.; Duguet, M. Speculations on the origin of life and thermophily: review of available information on reverse gyrase suggests that hyperthermophilic procaryotes are not so primitive. Orig. Life Evol. Biosph. 1995, 25, 235-249.
220. Forterre, P. A hot topic: the origin of hyperthermophiles. Cell 1996, 85, 789-792.
221. Boussau, B.; Blanquart, S.; Necsulea, A.; Lartillot, N.; Gouy, M. Parallel adaptations to high temperatures in the Archaean eon. Nature 2008, 456, 942-945.
222. Poole, A.M.; Jeffares, D.C.; Penny, D. The path from the RNA world. J. Mol. Evol. 1998, 46, 1-17.
223. Penny, D.; Poole, A. The nature of the last universal common ancestor. Curr. Opin. Genet. Dev. 1999, 9, 672-677.
224. Poole, A.M.; Penny, D. Evaluating hypotheses for the origin of eukaryotes. BioEssays 2007, 29, 74-84.
225. Collins, L.; Penny, D. Complex spliceosomal organization ancestral to extant eukaryotes. Mol. Biol. Evol. 2005, 22, 1053-1066.
226. Collins, L.J.; Penny, D. The RNA infrastructure: dark matter of the eukaryotic cell? Trends Genet. 2009, 25, 120-128.
227. Collins, L.J.; Kurland, C.G.; Biggs, P.; Penny, D. The modern RNP world of eukaryotes. J. Hered. 2009, 100, 597-604.
228. Cech, T.R. The generality of self-splicing RNA: Relationship to nuclear mRNA splicing. Cell 1986, 44, 207-210.
229. Copertino, D.W.; Hallick, R.B. Group II and group III introns of twintrons: potential relationships with nuclear pre-mRNA introns. Trends Biochem. Sci. 1993, 18, 467-471.
230. Bonen, L.; Vogel, J. The ins and outs of group II introns. Trends Genet. 2001, 6, 322-331.
231. Wang, M.; Yafremava, L.S.; Caetano-Anollés, D.; Mittenthal, J.E.; Caetano-Anollés, G. Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res. 2007, 17, 1572-1585.
232. Wang, M.; Caetano-Anollés, G. The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 2009, 17, 66-78.
233. Makarova, K.S.; Yutin, N.; Bell, S.D.; Koonin, E.V. Evolution of diverse cell division and vesicle formation systems in Archaea. Nat. Rev. Microbiol. 2010, 8, 731-741.
234. Wickstead, B.; Gull, K. The evolution of the cytoskeleton. J. Cell Biol. 2011, 194, 513-525.
235. Roberts, E.; Sethi, A.; Montoya, J.; Woese, C.R.; Luthey-Schulten, Z. Molecular signatures of ribosomal evolution. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 13953-13958.
236. Vishwanath, P.; Favaretto, P.; Hartman, H.; Mohr, F.C.; Smith, T.F. Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Mol. Phylogenet. Evol. 2004, 33, 615-625.
237. Kirschvink, J.L.,; Gaidos, E.J.; Bertani, L.E.; Beukes, N.J.; Gutzmer, J.; Maepa, L.N.; Steinberger, R.E. Paleoproterozoic snowball Earth: extreme climatic and geochemical global change and its biological consequences. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 1400-1405.
238. Bengston, S. Origins and early evolution of predation. In The fossil record of predation. Kowalewski, M., Kelley, P.H., Eds.; The Paleontological Society: Boulder, CO, USA, 2002; (Paleontol. Soc. Papers 8), pp. 289-317.
239. Brocks, J.J.; Logan, G.A.; Buick, R.; Summons, R. Archean molecular fossils and the early rise of eukaryotes. Science 1999, 285, 1033-1036.
240. George, S.C.; Volk, H.; Dutkiewicz, A.; Ridley, J.; Buick, R. Preservation of hydrocarbons and biomarkers in oil trapped inside fluid inclusions for <2 billion years. Geochim. Cosmochim. Acta 2008, 72, 844-870.
241. Glansdorff, N. About the last common ancestor, the universal lifetree and lateral gene transfer: a reappraisal. Mol. Microbiol. 2000, 38, 177-185.
242. Glansdorff, N.; Xu, Y.; Labedan, B. The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol. Direct 2008, 3, 29-35.
243. Glansdorff, N.; Xu, Y.; Labedan, B. The origin of life and the last universal common ancestor: do we need a change of perspective? Res. Microbiol. 2009, 160, 522-528.
244. Glansdorff, N.; Xu, Y.; Labedan, B. The conflict between horizontal gene transfer and the safeguard of identity: origin of meiotic sexuality. J. Mol. Evol. 2009, 9, 470-480.
245. Darwin, C. On the origin of species by means of natural selection; Murray: London, UK, 1859.
246. Lake, J.A.; Henderson, E.; Oakes, M.; Clark, M.W. Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 1984, 81, 3786-3790.
247. Cox, C.J.; Foster, P.G.; Hirt, R.P.; Harris, S.R.; Embley, T.M. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U. S. A. 2008, 105, 20356-20361.
248. Ouzounis, C.A.; Kunin, V.; Darzentas, N.; Goldovsky, L. A minimal estimate for the gene content of the last universal common ancestor-exobiology from a terrestrial perspective. Res. Microbiol. 2006, 157, 57-68.
249. Jékely, G. Did the last common ancestor have a biological membrane? Biol. Direct 2006, 1, 35:1-35:4.
250. Mulkidjanian, A.Y.; Galperin, M.Y.; Koonin, E.V. Co-evolution of primordial membranes and membrane proteins. Trends Biochem. Sci. 2009, 34, 206-215.
251. Peretó, J.; López-Garcia, P.; Moreira, D. Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem. Sci. 2004, 29, 469-477.
252. Matsumi, R.; Atomi, H.; Driessen, A.J.M.; van der Oost, J. Isoprenoid biosynthesis in Archaea-Biochemical and evolutionary implications. Res. Microbiol. 2011, 162, 39-52.
253. Boucher, Y.; Kamekura, M.; Doolittle, W.F. Origins and evolution of isoprenoid lipid biosynthesis in archaea. Mol. Microbiol. 2004, 52, 515-527.
254. Koga, Y.; Morii, H. Biosynthesis of ether-type polar lipids in Archaea and evolutionary considerations. Microbiol. Mol. Biol. Rev. 2007, 71, 97-120.
255. Lee, Y.; Chan, S.I. Effect of lysolecithin on the structure and permeability of lecithin bilayer vescicles. Biochemistry 1977, 16, 1303-1309.
256. Stahlberg, H.; Fotiadis, D.; Scheuring, S.; Rémigny, H.; Braun, T.; Mitsuoka, Y.; Fujiyoshi, Y.; Engel, A. Two-dimensional crystals: a powerful approach to assess structure, function and dynamics of membrane proteins. FEBS Lett. 2001, 504, 166-172.
257. Bulik, D.; van Ophem, P.; Manning, J.; Shen, Z.; Newburg, D.; Jarroll, E. UDP-Nacetylglucosamine pyrophosphorylase: a key enzyme in encysting Giardia is allosterically regulated. J. Biol. Chem. 2000, 275, 14722-14728.
258. Berbee, M.L.; Taylor, J.W. Systematics and evolution. In The Mycota; McLaughlin, D.J., McLaughlin, E.G., Lemke, P.A., Eds.; Springer-Verlag: Berlin, Germany, 2001; Volume VIIB, pp. 229-245.
259. Dujon, B. Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet. 2006, 22, 375-387.
260. Carlile, M.J. 1980 From prokaryote to eukaryote: gains and losses. In The Eukaryotic Microbial Cell; Gooday, G.W., Lloyd, D., Trinci, A.P.J., Eds.; Cambridge University Press: Cambridge, UK; pp. 1-40.
261. Pianka, E.R. On r-and K-selection. Am. Nat. 1970, 104, 592-597.
262. Lynch, M. Streamlining and simplification of microbial genome architecture. Annu. Rev. Microbiol. 2006, 60, 327-349.
263. Perkins, T.J.; Swain, P.S. Strategies for cellular decision-making. Mol. Syst. Biol. 2009, 5, 326:1-326:15
264. Forterre, P. The universal tree of life and the last universal cellular ancestor: revolution and counterrevolutions. In Evolutionary Genomics and Systems Biology, Caetano-Anollés, G., Ed.; Wiley-Blackwell: Hoboken, NJ, USA, 2010; pp. 43-62.
265. Wolf, Y.I.; Rogozin, I.B.; Kondrashov, A.S.; Koonin, E.V. Genome alignment, evolution of prokaryotic genome organization and prediction of gene function using genomic context. Genome Res. 2001, 11, 356-372.
266. Martin, W.; Hoffmeister, M.; Rotte, C.; Henze, K. An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle. Biol. Chem. 2001, 382, 1521-1539.
267. Koonin, E.V. Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol. Direct 2006, 1, 39:1-39:18.
268. Koonin, E.V.; Senkevich, T.G.; Dolja, V.V. The ancient Virus World and evolution of cells. Biol. Direct 2006, 1, 29:1-29:27.
269. Claverie, J.M.; Ogata, H.; Audic, S.; Abergel, C.; Suhre, K.; Fournier, P.E. Mimivirus and the emerging concept of "giant" virus. Virus Res. 2006, 117, 133-144.
270. Raoult, D.; Forterre, P. Redefining viruses: Lessons from Mimivirus. Nat. Rev. Microbiol. 2008, 6, 315-319.
271. Boyer, M.; Madoui, M.A.; Gimenez, G.; La Scola, B.; Raoult, D. Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4th Domain of Life including Giant Viruses. PLoS One 2010, 5, e15530:1-e15530:8.
272. This epigraph is paraphrased from Voltaire, "Le doute n'est pas une condition agréable, mais la certitude est absurde", letter to Frederick II of Prussia, 6 April 1767. Available online: http://en.wikiquote.org/wiki/Voltaire (accessed on 13 January 2012).
273. Forterre, P.; Philippe, H. Where is the root of the universal tree of life? BioEssays 1999, 21, 871-879.
274. Reanney, D.C. On the origin of prokaryotes. J. Theor. Biol. 1974, 48, 243-251.
275. Lane, N.; Martin, W. The energetics of genome complexity. Nature 2010, 467, 929-934.
276. Danchin, A. Archives or palimpsests? Bacterial genomes unveil a scenario for the origin of life. Biol. Theory 2007, 2, 52-61.
277. Danchin, A.; Fang, G.; Noria, S. The extant core bacterial proteome is an archive of the origin of life. Proteomics 2007, 7, 875-889.
278. Egel, R., Lankenau, D.-H., Mulkidjanian, A.Y., Eds.; Origins of Life: The Primal Self-Organization; Springer-Verlag: Heidelberg, Germany, 2011.
279. Martin, W. Heinrich-Heine-Universität, Düsseldorf. Personal communication, 17 October 2011.