Literature DB >> 24522979

Dynamics and constraints of enzyme evolution.

Miriam Kaltenbach1, Nobuhiko Tokuriki.   

Abstract

The wealth of distinct enzymatic functions found in nature is impressive and the on-going evolutionary divergence of enzymatic functions continues to generate new and efficient catalysts, which can be seen through the recent emergence of enzymes able to degrade xenobiotics. However, recreating such processes in the laboratory has been met with only moderate success. What are the factors that lead to suboptimal research outputs? In this review, we discuss constraints on enzyme evolution, which can restrict evolutionary trajectories and lead to evolutionary dead-ends. We highlight recent studies that have used experimental evolution to mimic different aspects of enzymatic adaptation under simple, controlled settings to shed light on evolutionary dynamics and constraints. A better understanding of these constraints will lead to the development of more efficient strategies for directed evolution and enzyme engineering.
© 2014 Wiley Periodicals, Inc.

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Year:  2014        PMID: 24522979     DOI: 10.1002/jez.b.22562

Source DB:  PubMed          Journal:  J Exp Zool B Mol Dev Evol        ISSN: 1552-5007            Impact factor:   2.656


  24 in total

1.  How mutational epistasis impairs predictability in protein evolution and design.

Authors:  Charlotte M Miton; Nobuhiko Tokuriki
Journal:  Protein Sci       Date:  2016-01-22       Impact factor: 6.725

2.  Reverse evolution leads to genotypic incompatibility despite functional and active site convergence.

Authors:  Miriam Kaltenbach; Colin J Jackson; Eleanor C Campbell; Florian Hollfelder; Nobuhiko Tokuriki
Journal:  Elife       Date:  2015-08-14       Impact factor: 8.140

3.  Pervasive Pairwise Intragenic Epistasis among Sequential Mutations in TEM-1 β-Lactamase.

Authors:  Courtney E Gonzalez; Marc Ostermeier
Journal:  J Mol Biol       Date:  2019-03-25       Impact factor: 5.469

4.  Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory.

Authors:  Mariano M González; Luciano A Abriata; Pablo E Tomatis; Alejandro J Vila
Journal:  Mol Biol Evol       Date:  2016-03-15       Impact factor: 16.240

5.  Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme.

Authors:  Merijn L M Salverda; Jeroen Koomen; Bertha Koopmanschap; Mark P Zwart; J Arjan G M de Visser
Journal:  Proc Natl Acad Sci U S A       Date:  2017-11-13       Impact factor: 11.205

6.  Protein Evolution is Potentially Governed by Protein Stability: Directed Evolution of an Esterase from the Hyperthermophilic Archaeon Sulfolobus tokodaii.

Authors:  Ryo Kurahashi; Satoshi Sano; Kazufumi Takano
Journal:  J Mol Evol       Date:  2018-04-20       Impact factor: 2.395

7.  Escherichia coli D-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway.

Authors:  Anastassia A Vorobieva; Mohammad Shahneawz Khan; Patrice Soumillion
Journal:  J Biol Chem       Date:  2014-08-26       Impact factor: 5.157

8.  Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.

Authors:  Gloria Yang; Dave W Anderson; Florian Baier; Elias Dohmen; Nansook Hong; Paul D Carr; Shina Caroline Lynn Kamerlin; Colin J Jackson; Erich Bornberg-Bauer; Nobuhiko Tokuriki
Journal:  Nat Chem Biol       Date:  2019-10-21       Impact factor: 15.040

9.  Automated Design of Efficient and Functionally Diverse Enzyme Repertoires.

Authors:  Olga Khersonsky; Rosalie Lipsh; Ziv Avizemer; Yacov Ashani; Moshe Goldsmith; Haim Leader; Orly Dym; Shelly Rogotner; Devin L Trudeau; Jaime Prilusky; Pep Amengual-Rigo; Victor Guallar; Dan S Tawfik; Sarel J Fleishman
Journal:  Mol Cell       Date:  2018-09-27       Impact factor: 17.970

Review 10.  The Classification and Evolution of Enzyme Function.

Authors:  Sergio Martínez Cuesta; Syed Asad Rahman; Nicholas Furnham; Janet M Thornton
Journal:  Biophys J       Date:  2015-05-15       Impact factor: 4.033

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