Literature DB >> 22533640

Multidimensional epistasis and fitness landscapes in enzyme evolution.

Wei Zhang1, Daniel F A R Dourado, Pedro Alexandrino Fernandes, Maria João Ramos, Bengt Mannervik.   

Abstract

The conventional analysis of enzyme evolution is to regard one single salient feature as a measure of fitness, expressed in a milieu exposing the possible selective advantage at a given time and location. Given that a single protein may serve more than one function, fitness should be assessed in several dimensions. In the present study we have explored individual mutational steps leading to a triple-point-mutated human GST (glutathione transferase) A2-2 displaying enhanced activity with azathioprine. A total of eight alternative substrates were used to monitor the diverse evolutionary trajectories. The epistatic effects of the mutations on catalytic activity were variable in sign and magnitude and depended on the substrate used, showing that epistasis is a multidimensional quality. Evidently, the multidimensional fitness landscape can lead to alternative trajectories resulting in enzymes optimized for features other than the selectable markers relevant at the origin of the evolutionary process. In this manner the evolutionary response is robust and can adapt to changing environmental conditions.

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Year:  2012        PMID: 22533640     DOI: 10.1042/BJ20120136

Source DB:  PubMed          Journal:  Biochem J        ISSN: 0264-6021            Impact factor:   3.857


  10 in total

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3.  Evolution of broad spectrum β-lactam resistance in an engineered metallo-β-lactamase.

Authors:  Song Sun; Wei Zhang; Bengt Mannervik; Dan I Andersson
Journal:  J Biol Chem       Date:  2012-12-03       Impact factor: 5.157

4.  Deep mutational scanning: a new style of protein science.

Authors:  Douglas M Fowler; Stanley Fields
Journal:  Nat Methods       Date:  2014-08       Impact factor: 28.547

5.  A model of substitution trajectories in sequence space and long-term protein evolution.

Authors:  Dinara R Usmanova; Luca Ferretti; Inna S Povolotskaya; Peter K Vlasov; Fyodor A Kondrashov
Journal:  Mol Biol Evol       Date:  2014-11-17       Impact factor: 16.240

6.  Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome.

Authors:  Lianet Noda-García; Ana L Juárez-Vázquez; María C Ávila-Arcos; Ernesto A Verduzco-Castro; Gabriela Montero-Morán; Paul Gaytán; Mauricio Carrillo-Tripp; Francisco Barona-Gómez
Journal:  BMC Evol Biol       Date:  2015-06-10       Impact factor: 3.260

7.  Reducing the standard deviation in multiple-assay experiments where the variation matters but the absolute value does not.

Authors:  Pablo Echenique-Robba; María Alejandra Nelo-Bazán; José A Carrodeguas
Journal:  PLoS One       Date:  2013-10-30       Impact factor: 3.240

8.  Specificity Effects of Amino Acid Substitutions in Promiscuous Hydrolases: Context-Dependence of Catalytic Residue Contributions to Local Fitness Landscapes in Nearby Sequence Space.

Authors:  Christopher D Bayer; Bert van Loo; Florian Hollfelder
Journal:  Chembiochem       Date:  2017-05-02       Impact factor: 3.164

9.  Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity.

Authors:  Tushar Modi; Valeria A Risso; Sergio Martinez-Rodriguez; Jose A Gavira; Mubark D Mebrat; Wade D Van Horn; Jose M Sanchez-Ruiz; S Banu Ozkan
Journal:  Nat Commun       Date:  2021-03-25       Impact factor: 14.919

10.  TMEM106B is a genetic modifier of frontotemporal lobar degeneration with C9orf72 hexanucleotide repeat expansions.

Authors:  Michael D Gallagher; Eunran Suh; Murray Grossman; Lauren Elman; Leo McCluskey; John C Van Swieten; Safa Al-Sarraj; Manuela Neumann; Ellen Gelpi; Bernardino Ghetti; Jonathan D Rohrer; Glenda Halliday; Christine Van Broeckhoven; Danielle Seilhean; Pamela J Shaw; Matthew P Frosch; Irina Alafuzoff; Anna Antonell; Nenad Bogdanovic; William Brooks; Nigel J Cairns; Johnathan Cooper-Knock; Carl Cotman; Patrick Cras; Marc Cruts; Peter P De Deyn; Charles DeCarli; Carol Dobson-Stone; Sebastiaan Engelborghs; Nick Fox; Douglas Galasko; Marla Gearing; Ilse Gijselinck; Jordan Grafman; Päivi Hartikainen; Kimmo J Hatanpaa; J Robin Highley; John Hodges; Christine Hulette; Paul G Ince; Lee-Way Jin; Janine Kirby; Julia Kofler; Jillian Kril; John B J Kwok; Allan Levey; Andrew Lieberman; Albert Llado; Jean-Jacques Martin; Eliezer Masliah; Christopher J McDermott; Ann McKee; Catriona McLean; Simon Mead; Carol A Miller; Josh Miller; David G Munoz; Jill Murrell; Henry Paulson; Olivier Piguet; Martin Rossor; Raquel Sanchez-Valle; Mary Sano; Julie Schneider; Lisa C Silbert; Salvatore Spina; Julie van der Zee; Tim Van Langenhove; Jason Warren; Stephen B Wharton; Charles L White; Randall L Woltjer; John Q Trojanowski; Virginia M Y Lee; Vivianna Van Deerlin; Alice S Chen-Plotkin
Journal:  Acta Neuropathol       Date:  2014-01-19       Impact factor: 17.088

  10 in total

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