Massive thermal acceleration of the emergence of primordial chemistry, the incidence of spontaneous mutation, and the evolution of enzymes

Journal of Biological Chemistry

Volumn 289, Issue 44, 2014, Pages 30198-30204

  Richard, Wolfenden ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

THERMAL ACCELERATIONS;

AMINO ACID SEQUENCE; BASE PAIRING; CATALYSIS; DNA REPAIR; ENTHALPY; ENZYME ANALYSIS; ENZYME KINETICS; HEAT SENSITIVITY; HUMAN; MOLECULAR EVOLUTION; NATURAL SELECTION; REVIEW; SPONTANEOUS MUTATION; TEMPERATURE SENSITIVITY; THERMODYNAMICS; BIOCATALYSIS; CHEMISTRY; ENZYME STABILITY; GENETICS; HALF LIFE TIME; KINETICS; MUTATION;

ENZYME;

BIOCATALYSIS; ENZYME STABILITY; ENZYMES; EVOLUTION, MOLECULAR; HALF-LIFE; HUMANS; KINETICS; MUTATION; THERMODYNAMICS;

EID: 84908638699     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.R114.567081     Document Type: Review

References (40)

1. Wolfenden, R. (1972) Analog approaches to the transition state in enzyme reactions. Acc. Chem. Res. 5, 10-18
2. Wolfenden, R. (2003) Thermodynamic and extrathermodynamic requirements of enzyme catalysis. Biophys. Chem. 105, 559-572
3. Kahne, D., and Still, W. C. (1988) Hydrolysis of a peptide bond in neutral water. J. Am. Chem. Soc. 110, 7529-7534
4. Harcourt, A. V., and Esson, W. T. (1866) On the laws of connexion between the conditions of a chemical change and its amount. Phil. Trans. R. Soc. London 156, 193-221
5. Radzicka, A., and Wolfenden R., (1995) A proficient enzyme. Science 267, 90-93
6. Wolfenden, R. (2011) Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes. Anna. Rev. Biochem. 80, 645-667
7. Edwards, D. R., Lohman, D. C., and Wolfenden, R. (2012) Catalytic proficiency: the extreme case of S-O cleaving sulfatases. J. Am. Chem. Soc. 134, 525-531
8. Darwin, C. (1871) Letter to J. D. Hooker, February 1, 1871
9. Thomsen, W. (Lord Kelvin) (1871) On the origin of life. Presidential Address to the British Association for the Advancement of Science, Edinburgh, August 1871; reprinted in Kelvin's Popular Lectures and Addresses (2010), pp. 132-205, Nabu Press, Charleston, SC
10. Ball, P. (2011) Some like it hot. Nature 10.1038/news.2010.590
11. Wolfenden, R., Snider, M., Ridgway, C., and Miller, B. (1999) The temperature dependence of enzyme rate enhancements. J. Am. Chem. Soc. 121, 7419-7420
12. Woese, C. (1987) Bacterial evolution. Microbiol. Rev. 51, 221-271
13. Di Giulio, M. (2003) The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence. J. Theor. Biol. 221, 425-436
14. Huber, C., Kraus, F., Hanzlik, M., Eisenreich, W., and Wächtershäuser, G. (2012) Elements of metabolic evolution. Chemistry 18, 2063-2080
15. Risso, V. A., Gavira, J. A., Mejia-Carmona, D. F., Gaucher, E. A., and Sanchez-Ruiz J. M. (2013) Hyperstability and substrate promiscuity in laboratory resurrections of precambrian ß-lactamases. J. Am. Chem. Soc. 135, 2899-2902
16. Akanuma, S., Nakajima, Y., Yokobori, S., Kimura, M., Nemoto, N., Mase, T., Miyazono, K., Tanokura, M., and Yamagishi, A. (2013) Experimental evidence for the thermophilicity of ancestral life. Proc. Natl. Acad. Sci. U.S.A. 110, 11067-11072
17. Lad, C., Williams, N. H., and Wolfenden, R. (2003) The rate of hydrolysis of phosphomonoester dianions and the exceptional catalytic proficiencies of protein and inositol phosphatases. Proc. Natl. Acad. Sci. U.S.A. 100, 5607-5610
18. Snider M. G., Temple B. S., and Wolfenden, R. (2004) The path to the transition state in enzyme reactions: a survey of catalytic efficiencies. J. Phys. Org. Chem. 17, 586-591
19. Snider, M. J., Gaunitz, S., Ridgway, C., and Short, S. A., and Wolfenden, R. (2000) Temperature effects on the catalytic efficiency, rate enhancement and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor". Biochemistry 39, 9746-9753
20. Zabinski, R. F., and Toney, M. D. (2001) Metal ion inhibition of nonenzymatic pyridoxal catalyzed decarboxylation and transamination. J. Am. Chem. Soc. 123, 193-198
21. Bracken, K., Moss, R. A., and Ragunathan, K. G.(1997) Remarkably rapid cleavage of a model phosphodiester by complexed ceric ions in aqueous micellar solutions. J Am. Chem. Soc. 119, 9323-9324
22. Maldonado, A. L., and Yatsimirsky A. K. (2005) Kinetics of phosphodiester cleavage by differently generated cerium (IV) oxo species in neutral solution. Org. Biomol. Chem. 3, 2859-2867
23. Stockbridge, R. B., Lewis, C. A., Jr., Yuan, Y., and Wolfenden, R. (2010) Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes. Proc. Natl. Acad. Sci. U.S.A. 107, 22102-22105
24. Pedersen, K. J. (1934) The velocity of bromination of acetoacetic ethyl ester. II. The general basic catalysis. J. Phys. Chem. 38, 601-621
25. Jencks, W. P., and Gilchrist, M. (1966) General base catalysis of the aminolysis of phenyl acetate. J. Am. Chem. Soc. 88, 104-108
26. Stockbridge, R. B., and Wolfenden, R. (2009) The intrinsic reactivity of ATP and the catalytic proficiencies of kinases acting on glucose, N-acetylgalactosamine, and homoserine: a thermodynamic analysis. J. Biol. Chem. 284, 22747-22757
27. Bruice, T. C., and Schmir, G. L. (1957) Imidazole catalysis. I. The catalysis of the hydrolysis of phenyl acetates by imidazole. J. Am. Chem. Soc. 79, 1663-1667
28. Stockbridge, R. B., and Wolfenden, R. (2010) The hydrolysis of phosphate diesters in cyclohexane and acetone. Chem. Comm. 46, 4306-4308
29. Hilvert, D., Carpenter, S. H., Nared, K. D., and Auditor, M-T. M. (1988) Catalysis of concerted reactions by antibodies: the Claisen rearrangement. Proc. Natl. Acad. Sci. U.S.A. 85, 4953-4955
30. Lewis, C., Krämer, T., Robinson, S., and Hilvert, D. (1991) Medium effects in antibody-catalyzed reactions. Science 253, 1019-1022
31. Xu, J., Deng, Q., Chen, J., Houk, K. N., Bartek, J., Hilvert, D., and Wilson, I. A. (1999) Evolution of shape complementarity and catalytic efficiency from a primordial antibody template. Science 286, 2345-2348
32. Sievers, A., Beringer, M., Rodnina, M. V., and Wolfenden, R. (2004) The ribosome as an entropy trap. Proc. Natl. Acad. Sci. U.S.A. 101, 7897-7901
33. Schroeder, G. K., and Wolfenden, R. (2007) The rate enhancement produced by the ribosome: an improved model. Biochemistry 46, 4037-4044
34. Wolfenden, R., and Kati, W. M. (1991) Testing the limits of protein-ligand binding discrimination with transition-state analogue inhibitors. Acc. Chem. Res. 23, 209-215
35. Kauzmann, W. A. (1959) Some factors involved in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1-63
36. Petersheim, M., and Turner, D. H. (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp and ACCGGUp. Biochemistry 22, 256-263
37. Frederico, L. A., Kunkel, T. A., and Shaw, B. R. (1990) A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry 29, 2532-2537
38. Frederico, L. A., Kunkel, T. A., Shaw, B.R. (1993) Cytosine deamination in mismatched base pairs. Biochemistry 32, 6523-6530
39. Drake, J. W., and Baltz, R. H. (1976) The biochemistry of mutagenesis. Anna. Rev. Biochem. 45, 11-37
40. Schroeder, G. K., and Wolfenden, R. (2007) Rates of spontaneous disintegration of DNA, and the rate enhancements produced by DNA glycosylases and deaminases. Biochemistry 46, 13638-13647