The 'evolvability' of promiscuous protein functions

Nature Genetics

Volumn 37, Issue 1, 2005, Pages 73-76

  Aharoni, Amir ^a   Gaidukov, Leonid ^a   Khersonsky, Olga ^a   Gould, Stephen McQ ^a   Roodveldt, Cintia ^a   Tawfik, Dan S ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ENZYME SUBSTRATE; EVOLUTION; GENE DUPLICATION; GENE FUNCTION; GENE MUTATION; GENETIC VARIABILITY; MORPHOLOGICAL TRAIT; NONHUMAN; PLASTICITY; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FUNCTION; SURVIVAL;

ARYLDIALKYLPHOSPHATASE; BACTERIA; CARBONIC ANHYDRASE II; EVOLUTION, MOLECULAR; HUMANS; PHOSPHORIC TRIESTER HYDROLASES; POLYMERASE CHAIN REACTION; PROTEIN STRUCTURE, TERTIARY; VARIATION (GENETICS);

EID: 11244281311     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1482     Document Type: Article

References (30)

1. Jensen, R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409-425 (1976).
2. Copley, S.D. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. 7, 265-272 (2003).
3. James, L.C. & Tawfik, D.S. Conformational diversity and protein evolution - a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28, 361-368 (2003).
4. Arnold, F.H., Wintrode, P.L., Miyazaki, K. & Gershenson, A. How enzymes adapt: lessons from directed evolution. Trends Biochem. Sci. 26, 100-106 (2001).
5. Krebs, J.F., Ippolito, J.A., Christianson, D.W. & Fierke, C.A. Structural and functional importance of a conserved hydrogen bond network in human carbonic anhydrase II. J. Biol. Chem. 268, 27458-27466 (1993).
6. Raushel, F.M. & Holden, H.M. Phosphotriesterase: an enzyme in search of its natural substrate. Adv. Enzymol. Relat. Areas Mol. Biol. 74, 51-93 (2000).
7. Draganov, D.I. & La Du, B.N. Pharmacogenetics of paraoxonases: a brief review. Naunyn Schmiedebergs Arch. Pharmacol. 369, 78-88 (2004).
8. Stemmer, W.P.C. DNA Shuffling by Random Fragmentation and Reassembly - in-Vitro Recombination for Molecular Evolution. Proc. Natl. Acad. Sci. USA 91, 10747-10751 (1994).
9. Aharoni, A. et al. Directed evolution of mammalian paraoxonases PON1 and PON3 for bacterial expression and catalytic specialization. Proc. Natl. Acad. Sci. USA 101, 482-487 (2004).
10. Bone, R., Silen, J.L. & Agard, D.A. Structural plasticity broadens the specificity of an engineered protease. Nature 339, 191-195 (1989).
11. Perona, J.J. & Craik, C.S. Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold. J. Biol. Chem. 272, 29987-29990 (1997).
12. James, L.C. & Tawfik, D.S. The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness. Protein Sci. 12, 2183-2193 (2003).
13. Bornscheuer, U.T. & Kaziauskas, R.J. Catalytic plasticity in biocatalysis: using old enzymes to form new bonds and follow new pathways. Angew. Chem. Int. Ed. Engl. 43, 2-10 (2004).
14. O'Brien, P.J. & Herschlag, D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6, R91-R105 (1999).
15. Yang, K. & Metcalf, W.W. A new activity for an old enzyme: Escherichia coli bacterial alkaline phosphatase is a phosphite-dependent hydrogenase. Proc. Natl. Acad. Sci. USA 101, 7919-7924 (2004).
16. James, L., Roversi, P. & Tawfik, D. Antibody multi-specificity mediated by conformational diversity. Science 299, 1362-1367 (2003)
17. James, L.C. & Tawfik, D.S. Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution. Protein Sci. 10, 2600-2607 (2001).
18. Miller, B.G. & Raines, R.T. Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases. Biochemistry 43, 6387-6392 (2004).
19. Taverna, D.M. & Goldstein, R.A. Why are proteins so robust to site mutations? J. Mol. Biol. 315, 479-484 (2002).
20. Pata, J.D., Stirtan, W.G., Goldstein, S.W. & Steitz, T.A. Structure of HIV-1 reverse transcriptase bound to an inhibitor active against mutant reverse transcriptases resistant to other nonnucleoside inhibitors. Proc. Natl. Acad. Sci. USA 101, 10548-10553 (2004).
21. Chong, Y.H. & Chu, C.K. Understanding the molecular mechanism of drug resistance of anti-HIV nucleosides by molecular modeling. Front. Biosci. 9, 164-186 (2004).
22. Wouters, M.A., Liu, K., Riek, P. & Husain, A. A despecialization step underlying evolution of a family of serine proteases. Mol. Cell. 12, 343-354 (2003).
23. Matsumura, I. & Ellington, A.D. In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 305, 331-339 (2001).
24. Lynch, M. & Katju, V. The altered evolutionary trajectories of gene duplicates. Trends Genet. 20, 544-549 (2004).
25. Kirschner, M. & Gerhart, J. Evolvability. Proc. Natl. Acad. Sci. USA 95, 8420-8427 (1998).
26. Earl, D.J. & Deem, M.W. Evolvability is a selectable trait. Proc. Natl. Acad. Sci. USA 101, 11531-11536 (2004).
27. Radman, M., Matic, I. & Taddei, F. Evolution of evolvability. Ann. NY Acad. Sci. 870, 146-155 (1999).
28. Giraud, A. et al. Costs and benefits of high mutation rates: Adaptive evolution of bacteria in the mouse gut. Science 291, 2606-2608 (2001).
29. True, H.L. & Lindquist, S.L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477-483 (2000).
30. Harel, M. et al. Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes. Nat. Struct. Mol. Biol. 11, 412-419 (2004).