Energy, genes and evolution: Introduction to an evolutionary synthesis

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 368, Issue 1622, 2013, Pages

  Lane, Nick ^a   Martin, William F ^b   Raven, John A ^c   Allen, John F ^a,d  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b HEINRICH HEINE UNIVERSITY   (Germany)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

^d QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Energy flow; Genomes; Mitochondria; Origin of life

Indexed keywords

ENERGY RESOURCE; ENVIRONMENTAL CHANGE; EUKARYOTE; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; GENOMICS; NICHE;

EUKARYOTA; PROKARYOTA;

ANIMAL; ENERGY METABOLISM; EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; GENOME; PHYSIOLOGY;

ANIMALS; BIOLOGICAL EVOLUTION; ENERGY METABOLISM; GENE EXPRESSION REGULATION; GENOME;

EID: 84892769922     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2012.0253     Document Type: Article

References (51)

1. Mitchell P. 1961 Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191, 144-148. (doi:10. 1038/191144a0)
2. Boyer PD, Chance B, Ernster L, Mitchell P, Racker E, Slater EC. 1977 Oxidative phosphorylation and photophosphorylation. Annu. Rev. Biochem. 46, 955-1026. (doi:10.1146/annurev.bi.46.070177. 004515)
3. Baradaran R, Berrisford JM, Minhas GS, Sazanov LA. 2013 Crystal structure of the entire respiratory complex. Nature 494, 443-448. (doi:10.1038/ nature11871)
4. Pesole G, Allen JF, Lane N, Martin W, Rand DM, Schatz G, Saccone C. 2012 The neglected genome. EMBO Rep. 13, 473-474. (doi:10.1038/embor. 2012.57)
5. Raven JA, Smith FA. 1976 Evolution of chemiosmotic energy coupling. J. Theoret. Biol. 57, 301-312. (doi:10.1016/0022-5193(76)90003-5)
6. Raven JA, Smith FA. 1982 Solute transport at the plasmalemma and the early evolution of cells. Biosystems 15, 13-26. (doi:10.1016/0303-2647(82) 90013-2)
7. Koch AL, Schmidt TM. 1991 The first cellular bioenergetic process: primitive generation of a proton-motive force. J. Mol. Evol. 33, 297-304. (doi:10.1007/BF02102860)
8. Mitchell P. 1957 The origin of life and the formation and organising functions of natural membranes. In Proceedings of the First International Symposium on the Origin of Life on the Earth (eds AI Oparin, AG Pasynski, AE Braunstein, TE Pavlovskaya), pp. 229-234. Moscow, Russia: USSR Academy of Sciences.
9. Zamzami N, Susin SA, Marchetti P, Hirsch T, Gomez-Monterrey I, Castedo M, Kroemer G. 1996 Mitochondrial control of nuclear apoptosis. J. Exp. Med. 183, 1533-1544. (doi:10.1084/jem. 183.4.1533)
10. Green DR, Galluzzi L, Kroemer G. 2011 Mitochondria and the autophagy-inflammation-cell death axis in organismal aging. Science 333, 1109-1112. (doi:10.1126/science.1201940)
11. Wallace DC. 2005 A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu. Rev. Genet. 39, 359-407. (doi:10.1146/annurev. genet.39.110304.095751)
12. Margulis L. 2004 Serial endosymbiosis theory (SET) and composite individuality. Microbiol. Today 31, 172-175.
13. Archibald JM. 2011 Origin of eukaryotic cells: 40 years on. Symbiosis 54, 69-86. (doi:10.1007/ s13199-011-0129-z)
14. Cavalier-Smith T. 2002 The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. System. Evol. Microbiol. 52, 297-354.
15. Martin W, Müller M. 1998 The hydrogen hypothesis for the first eukaryote. Nature 392, 37-41. (doi:10. 1038/32096)
16. Hjort K, Goldberg AV, Tsaousis AD, Hirst RP, Embley TM. 2010 Diversity and reductive evolution of mitochondria among microbial eukaryotes. Phil. Trans. R. Soc. B. 365, 713-727. (doi:10.1098/rstb. 2009.0224)
17. Lane N. 2011 Energetics and genetics across the prokaryote-eukaryote divide. Biol. Direct 6, 35. (doi:10.1186/1745-6150-6-35)
18. Hurst LD, Hamilton WD. 1992 Cytoplasmic fusion and the nature of sexes. Proc. R. Soc. Lond. B 247, 189-194. (doi:10.1098/rspb.1992.0027)
19. Allen JF. 1996 Separate sexes and the mitochondrial theory of ageing. J. Theoret. Biol. 180, 135-140. (doi:10.1006/jtbi.1996.0089)
20. Hadjivasiliou Z, Pomiankowski A, Seymour R, Lane N. 2012 Selection for mitonuclear coadaptation could favour the evolution of two sexes. Proc. R. Soc. B 279, 1865-1872. (doi:10.1098/rspb.2011.1871)
21. Martin W, Koonin EV. 2006 Introns and the origin of nucleus-cytosol compartmentalization. Nature 440, 41-45. (doi:10.1038/nature04531)
22. Blackstone NW, Green DR. 1999 The evolution of a mechanism of cell suicide. Bioessays 21, 84-88. (doi:10.1002/(SICI)1521-1878(199901)21:1,84:: AID-BIES11.3.0.CO;2-0)
23. Madigan MT, Martinko JM, Stahl DA, Clark DP. 2011 Brock biology of microorganisms. San Francisco, CA: Pearson Education.
24. Baross JA, Hoffman SE. 1985 Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life. Origins Life Evol. Biosph. 15, 327-345. (doi:10.1007/BF01808177)
25. Kelley DS et al. 2001 An off-axis hydrothermal vent field near the Mid-Atlantic Ridge at 308N. Nature 412, 145-149. (doi:10.1038/35084000)
26. Russell MJ, Daniel RM, Hall A. 1993 On the emergence of life via catalytic iron-sulphide membranes. Terra Nova 5, 343-347. (doi:10.1111/j. 1365-3121.1993.tb00267.x)
27. Russell MJ, Hall AJ. 1997 The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. J. Geol. Soc. Lond. 154, 377-402. (doi:10.1144/gsjgs.154.3.0377)
28. Lane N, Allen JF, Martin W. 2010 How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays 32, 271-280. (doi:10.1002/bies. 200900131)
29. Lane N, Martin WF. 2012 The origin of membrane bioenergetics. Cell 151, 1406-1416. (doi:10.1016/j. cell.2012.11.050)
30. Russell MJ, Martin W. 2004 The rocky roots of the acetyl-CoA pathway. Trends Biochem. Sci. 29, 358-363. (doi:10.1016/j.tibs.2004.05.007)
31. Koonin EV, Martin W. 2005 On the origin of genomes and cells within inorganic compartments. Trends Genet. 21, 647-654. (doi:10.1016/j.tig.2005. 09.006)
32. Lane N, Martin W. 2010 The energetics of genome complexity. Nature 467, 929-934. (doi:10.1038/ nature09486)
33. Lane N. 2011 Mitonuclear match: optimizing fitness and fertility over generations drives aging within generations. BioEssays, 33, 860-869. (doi:10.1002/ bies.201100051)
34. Allen JF. 1993 Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J. Theoret. Biol. 165, 609-631. (doi:10.1006/jtbi.1993.1210)
35. Allen JF. 2003 The function of genomes in bioenergetic organelles. Phil. Trans. R. Soc. Lond. B 358, 19-37. (doi:10.1098/rstb.2002.1191)
36. Amend JP, LaRowe DE, McCollom TM, Shock EL. 2013 The energetics of organic synthesis inside and outside the cell. Phil. Trans. R. Soc. B 368, 20120255. (doi:10.1098/rstb.2012.0255)
37. Russell MJ, Nitschke W, Branscomb E. 2013 The inevitable journey to being. Phil. Trans. R. Soc. B 368, 20120254. (doi:10.1098/rstb.2012.0254)
38. Nitschke W, Russell MJ. 2013 Beating the acetylcoenzyme A-pathway to the origin of life. Phil. Trans. R. Soc. B 368, 20120258. (doi:10.1098/rstb. 2012.0258)
39. Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira IAC, Allen JF, Lane N, Martin WF. 2013 Early bioenergetic evolution. Phil. Trans. R. Soc. B 368, 20130088. (doi:10.1098/rstb.2013.0088)
40. Kim JD, Senn S, Harel A, Jelen BI, Falkowski PG. 2013 Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases. Phil. Trans. R. Soc. B 368, 20120257. (doi:10.1098/rstb.2013.0257)
41. Macalady JL, Hamilton TL, Grettenberger CL, Jones DS, Tsao LE, Burgos WD. 2013 Energy, ecology and the distribution of microbial life. Phil. Trans. R. Soc. B 368, 20120383. (doi:10.1098/rstb.2012.0383)
42. Yin L, Bauer CE. 2013 Controlling the delicate balance of tetrapyrrole biosynthesis. Phil. Trans. R. Soc. B 368, 20120262. (doi:10.1098/rstb. 2012.0262)
43. Decker K, Jungermann K, Thauer RK. 1970 Energy production in anaerobic microbes. Angew. Chem. Int. Ed. 9, 138-158. (doi:10.1002/anie.197001381)
44. Raven JA, Beardall J, Larkum AWD, Sánchez-Baracaldo P. 2013 Interactions of photosynthesis with genome size and function. Phil. Trans. R. Soc. B 368, 20120264. (doi:10.1098/rstb.2012.0264)
45. Müller M et al. 2012 Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev. 76, 444-95. (doi:10.1128/ MMBR.05024-11)
46. Blackstone NW. 2013 Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation. Phil. Trans. R. Soc. B 368, 20120266. (doi:10.1098/rstb.2012.0266)
47. Bernard DG, Netz DJA, Lagny TJ, Pierik AJ, Balk J. 2013 Requirements of the cytosolic iron-sulfur cluster assembly pathway in Arabidopsis. Phil Trans. R. Soc. B 368, 20120259. (doi:10.1098/rstb. 2012.0259)
48. Puthiyaveetil S, Ibrahim IM, Allen JF. 2013 Evolutionary rewiring: a modified prokaryotic gene-regulatory pathway in chloroplasts. Phil. Trans. R. Soc. B. 368, 20120260. (doi:10.1098/rstb. 2012.0260)
49. de Paula WBM, Lucas CH, Agip A-NA, Vizcay- Barrena G, Allen JF. 2013 Energy, ageing, fidelity and sex: oocyte mitochondrial DNA as a protected genetic template. Phil. Trans. R. Soc. B 368, 20120263. (doi:10.1098/rstb.2012.0263)
50. Wallace DC. 2013 Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases. Phil. Trans. R. Soc. B 368, 20120267. (doi:10.1098/rstb.2012.0267)
51. Fu Q et al. 2013 A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553-559. (doi:10.1016/j.cub.2013.02.044)