Letter | Published:

The 'evolvability' of promiscuous protein functions

Nature Genetics volume 37, pages 7376 (2005) | Download Citation

Subjects

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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Protein Data Bank

References

  1. 1.

    Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409–425 (1976).

  2. 2.

    Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. 7, 265–272 (2003).

  3. 3.

    & Conformational diversity and protein evolution - a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28, 361–368 (2003).

  4. 4.

    , , & How enzymes adapt: lessons from directed evolution. Trends Biochem. Sci. 26, 100–106 (2001).

  5. 5.

    , , & Structural and functional importance of a conserved hydrogen bond network in human carbonic anhydrase II. J. Biol. Chem. 268, 27458–27466 (1993).

  6. 6.

    & Phosphotriesterase: an enzyme in search of its natural substrate. Adv. Enzymol. Relat. Areas Mol. Biol. 74, 51–93 (2000).

  7. 7.

    & Pharmacogenetics of paraoxonases: a brief review. Naunyn Schmiedebergs Arch. Pharmacol. 369, 78–88 (2004).

  8. 8.

    DNA Shuffling by Random Fragmentation and Reassembly - in-Vitro Recombination for Molecular Evolution. Proc. Natl. Acad. Sci. USA 91, 10747–10751 (1994).

  9. 9.

    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. 10.

    , & Structural plasticity broadens the specificity of an engineered protease. Nature 339, 191–195 (1989).

  11. 11.

    & Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold. J. Biol. Chem. 272, 29987–29990 (1997).

  12. 12.

    & The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness. Protein Sci. 12, 2183–2193 (2003).

  13. 13.

    & 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. 14.

    & Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6, R91–R105 (1999).

  15. 15.

    & 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. 16.

    , & Antibody multi-specificity mediated by conformational diversity. Science 299, 1362–1367 (2003).

  17. 17.

    & 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. 18.

    & Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases. Biochemistry 43, 6387–6392 (2004).

  19. 19.

    & Why are proteins so robust to site mutations? J. Mol. Biol. 315, 479–484 (2002).

  20. 20.

    , , & 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. 21.

    & Understanding the molecular mechanism of drug resistance of anti-HIV nucleosides by molecular modeling. Front. Biosci. 9, 164–186 (2004).

  22. 22.

    , , & A despecialization step underlying evolution of a family of serine proteases. Mol. Cell. 12, 343–354 (2003).

  23. 23.

    & In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 305, 331–339 (2001).

  24. 24.

    & The altered evolutionary trajectories of gene duplicates. Trends Genet. 20, 544–549 (2004).

  25. 25.

    & Evolvability. Proc. Natl. Acad. Sci. USA 95, 8420–8427 (1998).

  26. 26.

    & Evolvability is a selectable trait. Proc. Natl. Acad. Sci. USA 101, 11531–11536 (2004).

  27. 27.

    , & Evolution of evolvability. Ann. NY Acad. Sci. 870, 146–155 (1999).

  28. 28.

    et al. Costs and benefits of high mutation rates: Adaptive evolution of bacteria in the mouse gut. Science 291, 2606–2608 (2001).

  29. 29.

    & A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477–483 (2000).

  30. 30.

    et al. Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes. Nat. Struct. Mol. Biol. 11, 412–419 (2004).

Download references

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

Author notes

    • Leonid Gaidukov
    • , Stephen McQ Gould
    •  & Cintia Roodveldt

    These authors contributed equally to this work.

Affiliations

  1. Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.

    • Amir Aharoni
    • , Leonid Gaidukov
    • , Olga Khersonsky
    • , Stephen McQ Gould
    • , Cintia Roodveldt
    •  & Dan S Tawfik

Authors

  1. Search for Amir Aharoni in:

  2. Search for Leonid Gaidukov in:

  3. Search for Olga Khersonsky in:

  4. Search for Stephen McQ Gould in:

  5. Search for Cintia Roodveldt in:

  6. Search for Dan S Tawfik in:

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dan S Tawfik.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    PON1, PTE and CAII substrates used in the different directed evolution experiments.

  2. 2.

    Supplementary Table 1

    PON1 variants with improved γ-butyrolactonase activity.

  3. 3.

    Supplementary Table 2

    PON1 variants with improved long-chain acyl esterase activity.

  4. 4.

    Supplementary Table 3

    PON1 variants with improved acetoxy coumarin esterase activity.

  5. 5.

    Supplementary Table 4

    PON1 variants evolved for an OP substrate.

  6. 6.

    Supplementary Table 5

    PON1 variants analyzed for phenyl acetate, paraoxon, dihydrocoumain, δ-valerolactone and γ-heptaolid.

  7. 7.

    Supplementary Table 6

    Analysis of the bacterial PTE variants evolved for 2-Naphtyl acetate hydrolysis.

  8. 8.

    Supplementary Table 7

    Analysis of the newly evolved Carbonic anhydrase II (CAII) variants.

  9. 9.

    Supplementary Table 8

    Examples for variants exhibiting large improvements in promiscuous activities and small changes in native activity.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ng1482

Further reading