Causes and consequences of eukaryotization through mutualistic endosymbiosis and compartmentalization

Acta Biotheoretica

Volumn 52, Issue 2, 2004, Pages 105-154

  Hengeveld, R ^a   Fedonkin, M A ^b  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARTMENTALIZATION; ENDOSYMBIONT; EVOLUTIONARY BIOLOGY; EVOLUTIONARY THEORY; ORIGIN OF LIFE;

EUKARYOTIC CELL; REVIEW; SYMBIOSIS; THERMODYNAMICS;

EUKARYOTIC CELLS; SYMBIOSIS; THERMODYNAMICS;

EUKARYOTA;

EID: 5444253939     PISSN: 00015342     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:ACBI.0000043439.34470.29     Document Type: Review

References (128)

1. Altman, S. (1984). Aspects of biochemical catalysis. Cell 36: 237-239.
2. Anbar, A.D. and A.H. Knoll (2002). Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297: 1137-1142.
3. Arnon, D.I. (1988). The discovery of ferredoxin: the photosynthetic path. Trends in Biochemical Sciences 13: 30-33.
4. Bada, J.L. and A. Lazcano (2002). Some like it hot, but not the first biomolecules. Science 296: 1982-1983.
5. Baltscheffsky, H. and M. Baltscheffsky (1994). Molecular origin and evolution of early biological energy conversion. In: Bengtson, S. (Ed.). Early Life on Earth. p. 81-90. Columbia University Press, New York.
6. Barbieri, M. (2003). The Organic Codes. An Introduction to Semantic Biology. Cambridge University Press, Cambridge.
7. Baymann, F., E. Lebrun, M. Brugna, B. Schoepp-Cothenet, M.-T Giudici-Orticoni and W. Nitschke (2003). The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes. Philosophical Transactions of the Royal Society of London B 358: 267-274.
8. 2 decline in the Late Palaeozoic Era. Nature 410: 352-354.
9. Benner, S.A., A.D. Ellington and A. Tauer (1989). Modern metabolism as a palimpsest of the RNA world. Proceedings of the National Academy of Sciences USA 86: 7054-7058.
10. Bernstein, C. and H. Bernstein (1997). Ageing, sex and DNA repair. Academic Press, New York.
11. Bjerrum, C.J. and D.E. Canfield (2002). Ocean productivity before about 1.9 Gyr ago limited by phosphorus adsorption onto iron oxides. Nature 417: 159-162.
12. Black, S. (2000). A Theory of the Origin of Life Plus a Brief History of Biochemistry. Vantage Press, New York.
13. Brack, A. (Ed.) (1998). The Molecular Origins of Life. Cambridge University Press, Cambridge.
14. Brasier M. D., and J.F. Lindsay (1998). A billion years of environmental stability and the emergence of eukaryotes: New data from northern Australia. Geology 26: 555-559.
15. Brewin, N. (1972). Catalytic role for RNA in DNA replication. Nature 236: 101.
16. Briant, C. (Ed.) (1991). Metazoan Life without Oxygen. Chapman and Hall, London.
17. Brocks, J.J., G.A. Logan, R. Buick and R.E. Summons (1999). Archean molecular fossils and the early rise of eukaryotes. Science 285: 1033-1036.
18. Broda, E. (1975). The Evolution of Bioenergetic processes. Pergamon Press, Oxford.
19. Buss, L.W. (1987). The evolution of individuality. Princeton University Press, Princeton.
20. Cairns-Smith, A.G. (1982). Genetic Takeover and the Mineral Origins of Life. Cambridge University Press, Cambridge.
21. Cammack, R. (1983). Evolution and diversity in the iron-sulphur proteins. Chemica Scripta 21: 87-95.
22. Canfield, D.E. (1998). A new model for Proterozoic ocean chemistry. Nature 396: 450-453.
23. Canfield, D.E. and A. Teske (1996). Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies. Nature 382: 127-132.
24. Carroll, S.B., J.K. Grenier and S.D. Weatherbee (2001). From DNA to diversity. Molecular genetics and the evolution of animal design. Cambridge University Press, Cambridge.
25. Cavalier-Smith, T. (1987). The simultaneous symbiotic origin of mitochondria, chloroplasts, and microbodies. Annals of the New York Academy of Science 503: 55-71.
26. Cavalier-Smith, T. (2002). The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7-76.
27. Cech, T.R. (2000). The ribosome is a ribozyme. Science 289: 878-879.
28. Clothia, C. (1992). One thousand families for the molecular biologist. Nature 357: 543-544.
29. Daniel, R.M. and M.J Danson (1995). Did primitive microorganisms use nonhem iron proteins in place of NAD/P? Journal of Molecular Evolution 40: 559-563.
30. De Duve, C. (1984). A Guided Tour through the Living Cell. Freeman, New York.
31. De Duve, C. (2002). Life Evolving. Molecules, and Mind, and Meaning. Oxford University Press, Oxford.
32. Delwiche, C.F. and J.D. Palmer (1997). The origin of plastids and their spread via secondary symbiosis. Plant Systematics and Evolution (Supplement) 11: 53-86.
33. Dismukes, G.C., V.V. Klimov, S.V. Baranov, Yu. N. Kjslov, J. DasGupta and A. Tyryshkin (2001). The origin of atmospheric oxygen on Earth: the innovation of oxygenic photosynthesis. Proceedings of the National Academy of Sciences USA 98: 2170-2175.
34. Dorit, R.L., L. Schoenbach and W. Gilbert (1990). How big is the universe of exons? Science 250: 1377-1382.
35. Dyer, B.D. and R.A. Obar (1994). Tracing the History of Eukaryotic Cells. Columbia University Press, New York.
36. Eck, R. and M.O. Dayhoff (1966). Evolution of the structure of ferredoxin based on living relics of primitive amino acid sequences. Science 152: 363-366.
37. Elsasser, W.M. (1987). Reflections on a theory of organisms. Holism in biology. Johns Hopkins University Press, Baltimore.
38. Embley, T.M., D.A. Horner and R.P. Hirt (1997). Anaerobic eukaryote evolution: hydrogenosomes as biochemically modified mitochondria? Trends in Ecology and Evolution 12: 437-441.
39. Farquhar, J., H. Bas and M. Thiemens (2000). Atmospheric influence of Earth's earliest sulphur cycle. Science 289: 756-758.
40. Fedonkin, M.A. (1996). The oldest fossil animals in ecological perspective. In: Ghiselin, M.T. and G. Pinna (Eds). New Perspectives on the History of Life. Memoirs of the California Academy of Sciences 20: 31-45.
41. Fenchel, T. (2002). Origin and Early Evolution of Life. Oxford University Press, Oxford.
42. Ferris, J.P. (2002). From building blocks to the polymers of life. In: Schopf, J.W. (Ed.). Life's Origin. p. 113-139. University of California Press, Berkeley.
43. Fothergill-Gilmore, L.A. (1986). The evolution of the glycolytic pathway. Trends in Biochemical Sciences 11: 47-51.
44. Frausto da Silva, J.J.R. and R.J.P. Williams (1991). The Biological Chemistry of the Elements. The Inorganic Chemistry of Life. Clarendon Press, Oxford.
45. Gray, M.W. (1998). Rickettsia, typhus and the mitochondrial connection. Nature 396: 109-110.
46. Gray, M.W. (2000). Mitochondrial genes on the move. Nature 408: 302-305.
47. Guerrero, R. (1991). Predation as a prerequisite to organelle evolution: Daptobacter as example. In: Margulis, L. (Ed.). Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. pp. 106-117. MIT Press, Cambridge, Massachusetts.
48. Guerrero, R., C. Pedros-Alio, I. Esteve, J. Mas, D. Chase and L. Margulis (1986). Predatory prokaryotes and primary consumption evolved in bacteria. Proceedings of the National Academy of Sciences USA 83: 2138-2142.
49. Gupta, R.S. (1998). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbial and Molecular Biology Reviews 62: 1435-1491.
50. Gupta, R.S. and G.B. Golding (1996). The origin of the eukaryotic cell. Trends in Biochemical Science 21: 166-171.
51. Holland, H.D. (1994). Early Proterozoic atmospheric change. In: Bengtson, S. (Ed.) Early Life on Earth, p. 237-244. Nobel Symposium, 84. Columbia University Press, New York
52. Hopkin, S.P. (1989). Ecophysiology of metals in terrestrial invertebrates. Elsevier, London.
53. Howell, S.T., 1998. Molecular genetics of plant development. Cambridge University Press, Cambridge.
54. Joyce, G.F. (2002). The antiquity of RNA-based evolution. Nature 418: 214-221.
55. Kahne, D. and W.S. Still (1988). Hydrolysis of a peptide bond in neutral water. Journal of the American Chemical Society 110: 7529-7533.
56. Kashefi, K. and D.R. Lovley (2003). Extending the upper temperature limit of life. Science 301: 934.
57. Kauffman, S.A. (1993). The Origins of Order. Self-organization and Selection in Evolution. Oxford University Press, New York.
58. Kauffman, S.A. (2000). Investigations. Oxford University Press, New York.
59. Knoll, A.H. (1992). The early evolution of eukaryotes: a geological prospective. Science 256: 622-627.
60. Knoll, A.H. (1996). Breathing room for early animals. Nature 382: 111-112.
61. Koch, A.L. (1985). Primeval cells: possible energy-generating and cell-division mechanisms. Journal of Molecular Evolution 21: 270-277.
62. Kooijman, S.A.L.M. (2000). Dynamic energy and mass budgets in biological systems. Cambridge University Press, Cambridge.
63. Kooijman, S.A.L.M. and R. Hengeveld (in press). The symbiotic nature of metabolic evolution. In: Reydon, T.A.C. and L. Hemerik (Eds). Current Themes in Theoretical Biology: A Dutch Perspective. Kluwer Academic Publishers, Dordrecht.
64. Kooijman, S.A.L.M., P. Auger, J.C. Poggiale and B.W. Kooij (2003). Quantitative steps in symbiogenesis and the evolution of homeostasis. Biological Reviews 78: 435-463.
65. Lahav, N. (1999). Biogenesis. Theories of Life's Origin. Oxford University Press, Oxford.
66. Lambert, I.A., N.J. Beukes, C. Klein and J. Veizer (1992). Proterozoic mineral deposits through time. In: Schopf, J.W. and C. Klein (Eds). The Proterozoic Biosphere. A Multidisciplinary Study. Cambridge University Press, Cambridge.
67. Lang, B.F., M.W. Gray and G. Burger (1999). Mitochondrial genome evolution and the origin of the eukaryotic cell. Annual Review of Genetics 33: 351-397.
68. Lehninger, A.L. (1975). Biochemistry. 2nd Edition. Worth, New York.
69. Lowe, D.R. (1994). Early environments: constraints and opportunities for early evolution. In: Bengtson, S. (Ed.). Early Life on Earth. p. 25-35. Nobel Symposium, 84. Columbia University Press, New York.
70. Magnum C. (1991). Precambrian oxygen levels, the sulfide biosystem, and the origin of the Metazoa. Journal of Experimental Zoology 260: 33-42.
71. Maniatis, T. and R. Reed (1987). The role of small nuclear ribonucleoprotein particles in pre-mRNA splicing. Nature 325: 673-678.
72. Margulis, L. (1970). Origin of Eukaryotic Cells. Yale University Press, New Haven.
73. Margulis, L. (1981). Symbiosis in Cell Evolution. Freeman, New York.
74. Martin, W. (2002). A powerhouse divided. Science 287: 1219-1221.
75. Martin, W. and R.G. Herrmann (1998). Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiology 118: 9-17.
76. Martin, W. and M. Müller (1998). The hydrogen hypothesis for the first eukaryotes. Nature 392: 37-48.
77. Martin, W. and M.J. Russell (2003). On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemiautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions of the Royal Society of London B 358: 59-85.
78. McMenamin, M.A.S. and D.L.S. McMenamin (1990). The Emergence of Animals. The Cambrian Breakthrough. Columbia University Press, New York.
79. Meyer, A. (2003). Duplication, duplication. Nature 421: 31-32.
80. Miller, S.L. (1953). The production of amino acids under possible primitive earth conditions. Science 117: 528-529.
81. Mitchell, P. (1961). Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism. Nature 191: 144-148.
82. Mitchell, P. (1979). Keilin's respiratory chain concept and its chemiosmotic consequences. Science 206: 1148-1159.
83. Morowitz, H.J. (1978). Proton semiconductors and energy transduction in biological systems. American Journal of Physiology 235: R99-R114.
84. Morowitz, H.J. (1981). Phase separation, charge separation and biogenesis. BioSystems 14: 41-47.
85. Morowitz, H.J. (1992). Beginnings of Cellular Life. Metabolism recapitulates biogenesis. Yale University Press, New Haven.
86. Müller, M. and W. Martin (1999). The genome of Rickettsia prowazekii and some thoughts on the origin of mitochondria and hydrogenosomes. BioEssays 27: 377-381.
87. Navarro-Gonzalez, R., C.P. McKay and D.N. Mvondo (2001). A possible nitrogen crisis for Archaean life due to reduced nitrogen fixation by lightning. Nature 412: 61-64.
88. Ogata, H., S. Audic, P. Renesto-Audiffren, P.-E. Fournier, V. Barbe, D. Samson, V. Roux, P. Cossart, J. Weissenbach, J.-M. Claverie and D. Raoult (2001). Mechanisms of evolution in Rickettsia coroni and R. prowazekii. Science 293: 2093-2098.
89. Overmann, J. and K. Schubert (2002). Phototrophic consortia: model systems for symbiontic interrelations between prokaryotes. Archives of Microbiology 177: 201-208.
90. Paterson, H.E.H. (1985). The recognition concept of species. In: Vrba, E. (Ed.). Species and speciation. p. 21-29. Transvaal Museum, Pretoria.
91. Piaget, J. (1968). Le Structuralisme. Presses Universitaires de France, Paris.
92. Ponnamperuma, C. (1972). The Origins of Life. Thames and Hudson, London.
93. Prigogine, I. and I. Stengers (1984). Order out of Chaos. Man's New Dialogue with Nature. Heinemann, London.
94. Pullman, B. (1972). Electronic factors in biochemical evolution. In: Ponnamperuma, C. (Ed.). Exobiology. p. 136-169. North Holland Publishing Company, Amsterdam.
95. Pullman, B. and A. Pullman (1961). Submolecular structure of the nucleic acids. Nature 189: 725-727.
96. Pullman, B. and A. Pullman (1962). Electronic delocalisation and biochemical evolution. Nature 196: 1137-1142.
97. Pullman, B., P. Claverie and J. Caillet (1966). On the exclusivity of hydrogen-bonded pairing between Watson-Crick complementary bases. Journal of Molecular Biology 22: 373-375.
98. Reanney, D. (1979). RNA splicing and polynucleotide evolution. Nature 277: 598-600.
99. Rizzotti, M. (1996). Defining Life: the Central Problem in Theoretical Biology. University of Padua, Padua.
100. Rizzotti, M. (2000). Early Evolution. From the Appearance of the First Cell to the First Modern Organisms. Birkhauser, Basel.
101. Ronneberg, T.A, L. F. Landweber and S.J. Freeland (2000). Testing a biosynthetic theory on the genetic code: fact or artifact? Proceedings of the National Academy of Sciences USA 97: 13690-13695.
102. Russell, M.J. and A.J. Hall (1997). The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. Journal of the Geological Society of London 154: 377-402.
103. Russell, M.J. and A.J. Hall (2003). From geochemistry to biochemistry. Chemiosmotic coupling and transition element clusters in the onset of life and photosynthesis. Geochemical News 153: 6-12.
104. Russell, M.J., A.J. Hall, and A.R. Mellersh (2003). On the dissipation of thermal and chemical energies on the early Earth: the onset of hydrothermal convection, chemiosmosis, genetically regulated metabolism and oxygenic photosynthesis. In: Ikan, R. (Ed.) Natural and Laboratory-Simulated Thermal Geochemical Processes. p.325-388. Kluwer, Dordrecht.
105. Schopf, J.W. and C. Klein (1992). The Proterozoic Biosphere. A Multidisciplinary Study. Cambridge University Press, Cambridge.
106. Schrödinger, E. (1944). What is Life? The Physical Aspect of the Living Cell. Cambridge University Press, Cambridge.
107. Shapiro, R. (1986). Origins. A Skeptic's Guide to the Creation of Life on Earth. Heinemann, New York.
108. Shapiro, R. (1988). Prebiotic ribose syntheses: a critical analysis. Origins of Life and Evolution of the Biosphere 18: 71-85.
109. Shapiro, R. (1995). The prebiotic role of adenine: a critical analysis. Origins of Life and Evolution of the Biosphere 25: 83-98.
110. Tielens, A.G.M., C. Rotte, J.J. van Helmond and W. Martin (2002). Mitochondria as we don't know them. Trends in Biochemical Sciences 27: 564-572.
111. Trifonov, E.N. (2000). Leap into life's beginnings. Tracking the chronology of amino acids. Science Spectra 20: 62-71.
112. Trifonov, E.N. and T. Bettecken (1997). Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene 205: 1-6.
113. Van den Ent F., L.A. Amos and J. Lowe (2001). Prokaryotic origin of the actin cytoskeleton. Nature 413: 39-44.
114. Van der Giezen, M., D.J. Slotboom, D.S. Horner, P.J. Dyal, M. Harding, G.P. Xue, T.M. Embley and E.R.S. Kunji (2002). Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin of both organelles. EMBO Journal 21: 572-579.
115. Van Dover, C.L. (2000). The Ecology of Deep-Sea Hydrothermal Vents. Princeton University Press, Princeton.
116. Van Holde, K.E. (1980). The origin of life: a thermodynamic critique. In: Halverson, H.O. and K.E. Van Holde (Eds). The Origins of Life and Evolution. p. 31-46. Liss, New York.
117. Vellai, T., K. Takacs and G. Vida (1998). A new aspect to the origin and evolution of eukaryotes. Journal of Molecular Evolution 46: 499-507.
118. Wächtershäuser, G. (1998a). Before enzymes and templates: theory of surface metabolism. Microbiological Reviews 52: 452-484.
119. Wächtershäuser, G. (1998b). Towards a reconstruction of ancestral genomes by gene cluster alignment. Systematic and Applied Microbiology 27: 473-477.
120. Wald, G. (1962). Life in the second and third periods; or why phosphorus and sulphur for high-energy bonds? In: Kasha, M. and B. Pullman (Eds). Horizons in Biochemistry. p. 127-142. Academic Press, New York.
121. Westheimer, F.H. (1987). Why nature choose phosphates. Science 235: 373-1178.
122. White, H.B. (1976). Coenzymes as fossils of an earlier metabolic phase. Journal of Molecular Evolution 7: 101-104.
123. White, H.B. (1982). Evolution of coenzymes and the origin of pyridine nucleotides. In: Everse, J., B. Anderson and K-S. You (Eds). The Pyridine Nucleotide Coenzymes. p. 2-17. Academic Press, New York.
124. Wilde, S.A., J.W. Valley, W.H. Peck and C.M. Graham (2001). Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago. Nature 409: 175-178.
125. Williams, R.J.P. (1981). Natural selection of chemical elements. Proceedings of the Royal Society of London B 213: 361-397.
126. Williams, R.J.P. and J.J.R. Frausto da Silva (1996). The Natural Selection of the Chemical Elements. The Environment and Life's Chemistry. Clarendon Press, Oxford.
127. Williams, R.J.P. and J.J.R. Frausto da Silva (1999). Bringing Chemistry to Life. From Matter to Man. Oxford University Press, Oxford.
128. Zubay, S. (2000). Origins of Life on the Earth and in the Cosmos. 2nd Edition. Academic Press, San Diego.