Experimental evolution of proteins and molecular networks.
Evolution provides the theoretical framework by which we can understand biology. Understanding evolutionary processes is also crucial for engineering new proteins, metabolic pathways and organisms. My group uses ‘experimental evolution’ to reconstruct evolutionary trajectories of biological molecules in the laboratory, and to perform deep characterization of evolutionary trajectories and intermediates to examine various aspect of evolutionary dynamics. In experimental evolution, all parameters such as mutation rate and type, selection pressure and the environment are tunable, thus we can controllably test various aspects of molecular evolution. The evolutionary intermediates obtained in the experiments represent a molecular “fossil record”, and enable us to explore step-by-step evolution of molecular function. Moreover, functional and structural characterization of the intermediates significantly contributes to the long-standing question in protein science of “how function and structure are related”.
The research process specifically involves i) recreating evolutionary processes to acquire a new protein function or a new and protein network in the laboratory using synthetic biology and experimental evolution. This typically involves iterative cycles of gene diversification and gene library screening/selection. ii) Characterizing the effects of mutations obtained in evolution to identify how epistasis (interaction between mutations) restricts evolutionary trajectories, and reveal mechanisms underlying the epistasis. In particular, how and why the order of mutations accumulated in the evolution is crucial to accomplish functional and structural transition. iii) Characterizing intermediates in the evolution with various biochemical and biophysical techniques to investigate the relationship between sequence, function and structure, and in particular the interplay between multiple functionality and conformational diversity. iv) Applying our knowledge of molecular evolution to create de novo proteins and metabolic pathways for industrial and medical uses.
- Baier F, Copp JN, Tokuriki N* "Evolution of enzyme superfamilies: comprehensive exploration of sequence-function relationships" in revision
- Kaltenbach M, Emond S, Hollfelder F and Tokuriki N* “Functional trade-offs in promiscuous enzymes cannot be explained by intrinsic mutational robustness of the native activity” PLos Gen in press
- Yang G, Hong N, Baier F, Jackson CJ*, Tokuriki N* “Conformational tinkering through indirect effects of mutations drives evolution of a promiscuous activity” Biochemistry in press
- Campbell E, Kaltenbach M, Carr P, Livingstone E, Jurnou L, Weik M, Tokuriki N*, Jackson CJ*, “The role of protein dynamics in the evolution of new enzyme function” Nat Chem Biol in press
- Miton CM and Tokuriki N* " How mutational epistasis impairs predictability in protein evolution and design” Protein Sci 2016 Jan 12.
- Kaltenbach M, Jackson CJ, Campbell EC, Hollfelder F, Tokuriki N*"Reverse evolution leads to genotypic incompatibility despite functional and active-site convergence."Elife, 2015 Aug 14.
- Baier F, Chen J, Solomonson M, Strynadka NC, Tokuriki N*"Distinct Metal Isoforms Underlie Promiscuous Activity Profiles of Metalloenzymes."ACS Chem Biol, 2015 Apr 16.
- Baier F, Tokuriki N*"Connectivity between catalytic landscapes of the metallo-β-lactamase superfamily." J Mol Biol, 426, 2442-56, 2014
- Kaltenbach M, Tokuriki N*"Dynamics and constraints of enzyme evolution."J Exp Zool B Mol Dev Evol, 322(7), 468-87, 2014
- Wyganowski KT, Kaltenbach M, Tokuriki N*"GroEL/ES buffering and compensatory mutations promote protein evolution by stabilizing folding intermediates" J Mol Biol, 425, 3403-14, 2013
- Tokuriki N*, Jackson CJ, Afriat-Jurnou L, Wygnowski KT, Tang, R., Tawfik DS*, “Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme” Nature Communications, 3:1257, 2012
- Tokuriki N & Tawfik DS “Chaperonin overexpression promote genetic variation and enzyme evolution” Nature, 459, 668-673, 2009.
- Tokuriki N & Tawfik DS “Protein dynamism and evolvability” Science, 324, 203-207, 2009
- Bershtein S, Segal M, Bekerman R, Tokuriki N, & Tawfik DS “Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein” Nature, 444 (7121) 929-932, 2006
For a complete publication list, please see Tokurikilab website.