Abstract
Neutral drift is a recently developed experimental technique used to identify superior starting points for protein engineering. Neutral drift explores accessible sequence space by repeated rounds of mutagenesis and selection to maintain wild-type function. Mutations that are largely neutral for the native function accumulate, and those that are highly detrimental are purged, yielding a library of high diversity and quality. This technique is useful in situations where laboratory evolution is at a dead end, i.e., when the enzyme activity intended for evolution proves recalcitrant to improvements or is too low to be detected.
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Hartl DL, Dykhuizen DE, Dean AM (1985) Limits of adaptation: the evolution of selective neutrality. Genetics 111(3):655–674
Huynen MA, Stadler PF, Fontana W (1996) Smoothness within ruggedness: the role of neutrality in adaptation. Proc Natl Acad Sci U S A 93(1):397–401
Dalby PA (2011) Strategy and success for the directed evolution of enzymes. Curr Opin Struct Biol 21(4):473–480
Goldsmith M, Tawfik DS (2012) Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 22(4):406–412
Amitai G, Gupta RD, Tawfik DS (2007) Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J 1(1):67–78
Bershtein S, Goldin K, Tawfik D (2008) Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol 379(5):1029–1044
Bershtein S, Tawfik DS (2008) Ohno’s model revisited: measuring the frequency of potentially adaptive mutations under various mutational drifts. Mol Biol Evol 25(11):2311–2318
Bloom JD et al (2007) Evolution favors protein mutational robustness in sufficiently large populations. BMC Biol 5:29
Bloom JD, Romero PA, Lu Z, Arnold FH (2007) Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct 2:17
Gupta RD, Tawfik DS (2008) Directed enzyme evolution via small and effective neutral drift libraries. Nat Methods 5(11):939–942
Tokuriki N, Tawfik DS (2009) Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 19(5):596–604
Tokuriki N et al (2012) Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat Commun 3:1257
Aharoni A, Amitai G, Bernath K, Magdassi S, Tawfik DS (2005) High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. Chem Biol 12(12):1281–1289
Goldsmith M, Kiss C, Bradbury AR, Tawfik DS (2007) Avoiding and controlling double transformation artifacts. Protein Eng Des Sel 20(7):315–318
Tokuriki N, Stricher F, Serrano L, Tawfik DS (2008) How protein stability and new functions trade off. PLoS Comput Biol 4(2):e1000002
Aharoni A et al (2005) The ‘evolvability’ of promiscuous protein functions. Nat Genet 37(1):73–76
Stemmer WP (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A 91(22):10747–10751
Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16(3):258–261
Tokuriki N, Tawfik DS (2009) Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature 459(7247):668–673
Acknowledgments
This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) and Canada Institutes of Health Research (CIHR). N.T. is a Michael Smith Foundation for Health Research Scholar.
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Kaltenbach, M., Tokuriki, N. (2014). Generation of Effective Libraries by Neutral Drift. In: Gillam, E., Copp, J., Ackerley, D. (eds) Directed Evolution Library Creation. Methods in Molecular Biology, vol 1179. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-1053-3_5
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DOI: https://doi.org/10.1007/978-1-4939-1053-3_5
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