Abstract
How proteins with new functions (e.g., drug or antibiotic resistance or degradation of man-made chemicals) evolve in a matter of months or years is still unclear. This ability is dependent on the induction of new phenotypic traits by a small number of mutations (plasticity). But mutations often have deleterious effects on functions that are essential for survival. How are these seemingly conflicting demands met at the single-protein level? Results from directed laboratory evolution experiments indicate that the evolution of a new function is driven by mutations that have little effect on the native function but large effects on the promiscuous functions that serve as starting point. Thus, an evolving protein can initially acquire increased fitness for a new function without losing its original function. Gene duplication and the divergence of a completely new protein may then follow.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Accession codes
References
Jensen, R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409–425 (1976).
Copley, S.D. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. 7, 265–272 (2003).
James, L.C. & Tawfik, D.S. Conformational diversity and protein evolution - a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28, 361–368 (2003).
Arnold, F.H., Wintrode, P.L., Miyazaki, K. & Gershenson, A. How enzymes adapt: lessons from directed evolution. Trends Biochem. Sci. 26, 100–106 (2001).
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).
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).
Draganov, D.I. & La Du, B.N. Pharmacogenetics of paraoxonases: a brief review. Naunyn Schmiedebergs Arch. Pharmacol. 369, 78–88 (2004).
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).
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).
Bone, R., Silen, J.L. & Agard, D.A. Structural plasticity broadens the specificity of an engineered protease. Nature 339, 191–195 (1989).
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).
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).
Bornscheuer, U.T. & Kazlauskas, 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).
O'Brien, P.J. & Herschlag, D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6, R91–R105 (1999).
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).
James, L., Roversi, P. & Tawfik, D. Antibody multi-specificity mediated by conformational diversity. Science 299, 1362–1367 (2003).
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).
Miller, B.G. & Raines, R.T. Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases. Biochemistry 43, 6387–6392 (2004).
Taverna, D.M. & Goldstein, R.A. Why are proteins so robust to site mutations? J. Mol. Biol. 315, 479–484 (2002).
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).
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).
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).
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).
Lynch, M. & Katju, V. The altered evolutionary trajectories of gene duplicates. Trends Genet. 20, 544–549 (2004).
Kirschner, M. & Gerhart, J. Evolvability. Proc. Natl. Acad. Sci. USA 95, 8420–8427 (1998).
Earl, D.J. & Deem, M.W. Evolvability is a selectable trait. Proc. Natl. Acad. Sci. USA 101, 11531–11536 (2004).
Radman, M., Matic, I. & Taddei, F. Evolution of evolvability. Ann. NY Acad. Sci. 870, 146–155 (1999).
Giraud, A. et al. Costs and benefits of high mutation rates: Adaptive evolution of bacteria in the mouse gut. Science 291, 2606–2608 (2001).
True, H.L. & Lindquist, S.L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477–483 (2000).
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).
Acknowledgements
We thank F. Kondrashov for his constructive and insightful criticism. We acknowledge financial support from the Benoziyo Institute of Molecular Medicine, the Minerva foundation and the Israel Science Foundation. S.G. is funded by the EU's ENDIRPRO program. D.S.T. is the incumbent of the Elaine Blond Career Development Chair.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Fig. 1
PON1, PTE and CAII substrates used in the different directed evolution experiments. (PDF 43 kb)
Supplementary Table 1
PON1 variants with improved γ-butyrolactonase activity. (PDF 35 kb)
Supplementary Table 2
PON1 variants with improved long-chain acyl esterase activity. (PDF 17 kb)
Supplementary Table 3
PON1 variants with improved acetoxy coumarin esterase activity. (PDF 67 kb)
Supplementary Table 4
PON1 variants evolved for an OP substrate. (PDF 103 kb)
Supplementary Table 5
PON1 variants analyzed for phenyl acetate, paraoxon, dihydrocoumain, δ-valerolactone and γ-heptaolid. (PDF 32 kb)
Supplementary Table 6
Analysis of the bacterial PTE variants evolved for 2-Naphtyl acetate hydrolysis. (PDF 58 kb)
Supplementary Table 7
Analysis of the newly evolved Carbonic anhydrase II (CAII) variants. (PDF 107 kb)
Supplementary Table 8
Examples for variants exhibiting large improvements in promiscuous activities and small changes in native activity. (PDF 90 kb)
Rights and permissions
About this article
Cite this article
Aharoni, A., Gaidukov, L., Khersonsky, O. et al. The 'evolvability' of promiscuous protein functions. Nat Genet 37, 73–76 (2005). https://doi.org/10.1038/ng1482
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng1482
This article is cited by
-
Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation
Journal of Molecular Evolution (2024)
-
Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes
Nature Communications (2022)
-
Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability
Nature Ecology & Evolution (2022)
-
Bypassing evolutionary dead ends and switching the rate-limiting step of a human immunotherapeutic enzyme
Nature Catalysis (2022)
-
Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities
Nature Communications (2020)