Energy flows, metabolism and translation

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 366, Issue 1580, 2011, Pages 2949-2958

  Pascal, Robert ^a   Boiteau, Laurent ^a  

^a UNIVERSITÉ DE MONTPELLIER   (France)

Author keywords

Aminoacyl adenylates; Aminoacylation; Carbon metabolism; Chemiosmosis; Heterotrophic hypothesis; Methanogenesis

Indexed keywords

BIOCHEMISTRY; CHEMICAL BONDING; ENERGY FLOW; METABOLISM; METHANOGENESIS; SELF ORGANIZATION; THERMODYNAMICS;

EID: 80052932273     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2011.0135     Document Type: Review

References (63)

1. Pross, A. 2004 Causation and the origin of life. Metabolism or replication first? Orig. Life Evol. Biosph. 34, 307-321. (doi:10.1023/B:ORIG.0000016446.51012.bc)
2. Orgel, L. E. 2008 The implausibility of metabolic cycles on the prebiotic earth. PLoS Biol. 6, 5-13. (doi:10.1371/ journal.pbio.0060018)
3. Shapiro, R. 2006 Small molecule interactions were central to the origin of life. Q. Rev. Biol. 81, 106-125.
4. Fry, I. 2011 The role of natural selection in the origin of life. Orig. Life Evol. Biosph. 41, 3-16. (doi:10.1007/ s11084-010-9214-1)
5. T. 2003 The principles of life. Oxford, UK: Oxford University Press.
6. G. 1988 Before enzymes and templates: theory of surface metabolism. Microbiol. Rev. 52, 452-484.
7. Martin, W. & Russell, M. J. 2003 On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Phil. Trans. R. Soc. Lond. B 358, 59-85. (doi:10.1098/rstb.2002.1183)
8. Oparin, A. I. 1924 The origin of life. Proiskhodenie Zhini, pp. 199-234. [English transl.: Bernal, J. D. 1967 The origin of life. The Weidenfeld and Nicolson Natural History (ed. R. Carrington). London, UK: Readers Union].
9. Haldane, J. B. S. 1929 The origin of life. The rationalist annual, pp. 242-249. [Reprinted in: Bernal, J. D. 1967 The origin of life. The Weidenfeld and Nicolson Natural History (ed. R. Carrington). London, UK: Readers Union.].
10. Eschenmoser, A. 2007 Question 1: commentary referring to the statement 'The Origin of Life can be Traced Back to the Origin of Kinetic Control'. Orig. Life Evol. Biosph. 37, 309-314. (doi:10.1007/s11084-007-9102-5)
11. Boiteau, L. & Pascal, R. 2011 Energy sources, selforganization, and the origin of life. Orig. Life Evol. Biosph. 40, 23-33. (doi:10.1007/s11084-010-9209-y)
12. Pross, A. 2009 Seeking the chemical roots of Darwinism: bridging between chemistry and biology. Chem. Eur. J. 15, 8374-8381. (doi:10.1002/chem.200900805)
13. E. 1946 What's life. New York, NY: McMillan.
14. Lotka, A. J. 1922 Contribution to the energetics of evolution. Proc. Natl Acad. Sci. USA 8, 147-151. (doi:10.1073/pnas.8.6.147)
15. Lotka, A. J. 1922 Natural selection as a physical principle. Proc. Natl Acad. Sci. USA 8, 151-154. (doi:10.1073/pnas.8.6.151)
16. Nicolis, G. & Prigogine, I. 1977 Self-organization in nonequilibrium systems. New York, NY: Wiley.
17. Morowitz, H. & Smith, E. 2007 Energy flow and the organization of life. Complexity 13, 51-59. (doi:10.1002/cplx.20191)
18. Chyba, C. & Sagan, C. 1992 Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: an inventory for the origins of life. Nature 355, 125-132. (doi:10.1038/355125a0)
19. Tian, F., Toon, O. B., Pavlov, A. A. & De Sterck, H.2005 A hydrogen-rich early earth atmosphere. Science 308, 1014-1017. (doi:10.1126/science.1106983)
20. H.J.,Chalmers, J. H., Lazcano, A., Miller, S. L. & Bada, J. L. 2008 A reassessment of prebiotic organic synthesis in neutral planetary atmospheres. Orig. Life Evol. Biosph. 38, 105-115. (doi:10.1007/s11084-007-9120-3)
21. Deamer, D. & Weber, A. L. 2010 Bioenergetics and life's origins. Cold Spring Harb. Perspect. Biol. 2, a00492. (doi:10.1101/cshperspect.a004929)
22. Wolfenden, R. 2006 Degrees of difficulty of waterconsuming reactions in the absence of enzymes. Chem. Rev. 106, 3379-3396. (doi:10.1021/cr050311y)
23. Hoehler, T. M. 2007 An energy balance concept for habitability. Astrobiology 7, 824-838. (doi:10.1089/ast.2006.0095)
24. McCollom, T. M. & Amend, J. P. 2005 A thermodynamic assessment of energy requirements for biomass synthesis by chemolithoautotrophic micro-organisms in oxic and anoxic environments. Geobiology 3, 135-144. (doi:10.1111/j.1472-4669.2005.00045.x)
25. Butlerov, A. M. 1861 Formation synthe ́tique d'une substance sucre ́e. Comptes Rendus Acad. Sci. 53, 145-147.
26. Miller, S. L. 1953 A production of amino acids under possible primitive earth conditions. Science 117, 528-529. (doi:10.1126/science.117.3046.528)
27. Weber, A. L. 2000 Sugars as the optimal biosynthetic carbon substrate of aqueous life throughout the universe. Orig. Life Evol. Biosph. 30, 33-43. (doi:10.1023/ A:1006627406047)
28. Weber, A. L. 2002 Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions. Orig. Life Evol. Biosph. 32, 333-357. (doi:10.1023/A:1020588925703)
29. Urey, H. C. 1952 On the early chemical history of the earth and the origin of life. Proc. Natl Acad. Sci. USA 38, 351-363. (doi:10.1073/pnas.38.4.351)
30. Deamer, D. W. 1997 The first living systems: a bioenergetic perspective. Microbiol. Mol. Biol. Rev. 61, 239-261.
31. Hanczyc, M. M. & Szostak, J. W. 2004 Replicating vesicles as models of primitive cell growth and division. Curr. Opin. Chem. Biol. 8, 660-664. (doi:10.1016/j. cbpa.2004.10.002)
32. Benner, S. A., Kim, H.-J., Kim, M.-J. & Ricardo, A. 2010 Planetary organic chemistry and the origins of biomolecules. Cold Spring Harb. Perspect. Biol. 2, a003467. (doi:10.1101/cshperspect.a003467)
33. Cleaves, H. J. 2008 The prebiotic geochemistry of formaldehyde. Precamb. Res. 164, 111-118. (doi:10.1016/ j.precamres.2008.04.002)
34. Jencks, W. P. 1969 Catalysis in chemistry and enzymology. New York, NY: McGraw-Hill.
35. Thaddeus, P. 2006 The prebiotic molecules observed in the interstellar gas. Phil. Trans. R. Soc. B 361, 1681-1687. (doi:10.1098/rstb.2006.1897)
36. Miller, S. L. & Parris, M. 1964 Synthesis of pyrophosphate under primitive Earth conditions. Nature 204, 1248-1250. (doi:10.1038/2041248a0)
37. Orgel, L. E. & Lohrmann, R. 1974 Prebiotic chemistry and nucleic acid replication. Acc. Chem. Res. 7, 368-377. (doi:10.1021/ar50083a002)
38. Powner, M. W., Gerland, B. & Sutherland, J. D. 2009 Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239-242. (doi:10.1038/nature08013)
39. Miller, S. L. 1998 The endogenous synthesis of organic compounds. In The molecular origins of life. Assembling pieces of the puzzle (ed. A. Brack), pp. 59-85. Cambridge, UK: Cambridge University Press.
40. Kasting, J. F. & Brown, L. L. 1998 The early atmosphere as a source of biogenic compounds. In The molecular origins of life. Assembling pieces of the puzzle (ed. A. Brack), pp. 35-56. Cambridge, UK: Cambridge University Press.
41. Russell, M. J., Hall, A. J. & Martin, W. 2010 Serpentinization as a source of energy at the origin of life. Geobiology 8, 355-371. (doi:10.1111/j.1472-4669.2010.00249.x)
42. Lane, N., Allen, J. F. & Martin, W. 2010 How did LUCA make a living? Chemiosmosis in the origin of life. BioEssays 32, 271-280. (doi:10.1002/bies.200900131)
43. 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)
44. Madigan, M. T., Martinko, J. M. & Parker, J. 2003 Brock biology of microorganisms. Upper Saddle River, NJ: Prentice Hall.
45. Voet, D., Voet, J. G. & Pratt, C. W. 2006 Fundamentals of biochemistry, 2nd edn. New York, NY: Wiley.
46. Mansy, S. S. 2010 Membrane transport in primitive cells. Cold Spring Harb. Perspect. Biol. 2, a002188. (doi:10.1101/cshperspect.a002188)
47. Chen, I. A. & Szostak, J. W. 2004 Membrane growth can generate a transmembrane pH gradient in fatty acid vesicles. Proc. Natl Acad. Sci. USA 101, 7965-7970. (doi:10.1073/pnas.0308045101)
48. Eigen, M. 1964 Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Angew. Chem. Int. Ed. Engl. 3, 1-19. (doi:10.1002/anie.196400011)
49. Reece, S. Y., Hodgkiss, J. M., Stubbe, J. & Nocera, D. G. 2006 Proton-coupled electron transfer: the mechanistic underpinning for radical transport and catalysis in biology. Phil. Trans. R. Soc. B 361, 1351-1364. (doi:10.1098/rstb.2006.1874)
50. Pascal, R., Boiteau, L. & Commeyras, A. 2005 From the prebiotic synthesis of a-amino acids towards a primitive translation apparatus for the synthesis of peptides. Top. Curr. Chem. 259, 69-122. (doi:10.1007/b136707)
51. Jencks, W. P. 1976 Free energies of hydrolysis and decarboxylation. In Handbook of biochemistry and molecular biology, vol. 1 (ed. G. D. Fasman), pp. 296-304. 3rd edn, Cleveland, OH: CRC Press.
52. Sievers, A., Beringer, M., Rodnina, M. V. & Wolfenden, R. 2004 The ribosome as an entropy trap. Proc. Natl Acad. Sci. USA 101, 7897-7901. (doi:10.1073/pnas.0402488101)
53. Pascal, R. et al. 2006 Prebiotic chemistry-biochemistry-emergence of life (4.4-2 Ga). Earth Moon Planets 98, 153-203. (doi:10.1007/s11038-006-9089-3)
54. Noller, H. F. 2004 The driving force for molecular evolution of translation. RNA 10, 1833-1837. (doi:10.1261/ rna.7142404)
55. Wells, T. N. C., Ho, C. K. & Fersht, A. R. 1986 Free energy of hydrolysis of tyrosyl adenylate and its binding to wild-type and engineered mutant tyrosyl-tRNA synthetases. Biochemistry 25, 6603-6608. (doi:10.1021/ bi00369a040)
56. Schimmel, P. & Henderson, B. 1994 Possible role of aminoacyl- RNA complexes in noncoded peptide synthesis and origin of coded synthesis. Proc. Natl Acad. Sci. USA 91, 11 283-11 286. (doi:10.1073/pnas.91.24.11283)
57. Pascal, R. & Boiteau, L. 2010 Energetic constraints on prebiotic pathways: application to the emergence of translation. In Origins and evolution of life: an astrobiological perspective (eds M. Gargaud, P. López-Garcìa & H. Martin), pp. 247-258. Cambridge, UK: Cambridge University Press.
58. Leman, L., Orgel, L. & Ghadiri, M. R. 2004 Carbonyl sulfide-mediated prebiotic formation of peptides. Science 306, 283-286. (doi:10.1126/science.1102722)
59. Danger, G., Boiteau, L., Cottet, H. & Pascal, R. 2006 The peptide formation mediated by cyanate revisited. N-carboxyanhydrides as accessible intermediates in the decomposition of N-carbamoylaminoacids. J. Am. Chem. Soc. 128, 7412-7413. (doi:10.1021/ja061339+)
60. Biron, J.-P., Parkes, A. L., Pascal, R. & Sutherland, J. D. 2005 Expeditious, potentially primordial, aminoacylation of nucleotides. Angew. Chem. Int. Ed. 44, 6731-6734. (doi:10.1002/anie.200501591)
61. Leman, L. J., Orgel, L. E. & Ghadiri, M. R. 2006 Amino acid dependent formation of phosphate anhydrides in water mediated by carbonyl sulfide. J. Am. Chem. Soc. 128, 20-21. (doi:10.1021/ja056036e)
62. Brack, A. 1987 Selective emergence and survival of early polypeptides in water. Origins Life 17, 367-379. (doi:10.1007/BF02386475)
63. Zahnle, K., Schaefer, L. & Fegley, B. 2010 Earth's earliest atmospheres. Cold Spring Harb. Perspect. Biol. 2, a004895. (doi:10.1101/cshperspect.a004895)