Literature DB >> 32444838

The developing toolkit of continuous directed evolution.

Mary S Morrison1,2,3,4, Christopher J Podracky1,2,4, David R Liu5,6,7.   

Abstract

Continuous directed evolution methods allow the key steps of evolution-gene diversification, selection, and replication-to proceed in the laboratory with minimal researcher intervention. As a result, continuous evolution can find solutions much more quickly than traditional discrete evolution methods. Continuous evolution also enables the exploration of longer and more numerous evolutionary trajectories, increasing the likelihood of accessing solutions that require many steps through sequence space and greatly facilitating the iterative refinement of selection conditions and targeted mutagenesis strategies. Here we review the historical advances that have expanded continuous evolution from its earliest days as an experimental curiosity to its present state as a powerful and surprisingly general strategy for generating tailor-made biomolecules, and discuss more recent improvements with an eye to the future.

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Year:  2020        PMID: 32444838     DOI: 10.1038/s41589-020-0532-y

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


  62 in total

1.  Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions.

Authors:  Kathleen E McGinness; Martin C Wright; Gerald F Joyce
Journal:  Chem Biol       Date:  2002-05

2.  Continuous in vitro evolution of ribozymes that operate under conditions of extreme pH.

Authors:  Henriette Kühne; Gerald F Joyce
Journal:  J Mol Evol       Date:  2003-09       Impact factor: 2.395

Review 3.  In vitro evolution of proteins.

Authors:  Tomoaki Matsuura; Tetsuya Yomo
Journal:  J Biosci Bioeng       Date:  2006-06       Impact factor: 2.894

4.  Emergence of a fast-reacting ribozyme that is capable of undergoing continuous evolution.

Authors:  Sarah B Voytek; Gerald F Joyce
Journal:  Proc Natl Acad Sci U S A       Date:  2007-09-18       Impact factor: 11.205

5.  Microbial Selection.

Authors:  V Bryson; W Szybalski
Journal:  Science       Date:  1952-07-18       Impact factor: 47.728

6.  Experiments with the Chemostat on spontaneous mutations of bacteria.

Authors:  A NOVICK; L SZILARD
Journal:  Proc Natl Acad Sci U S A       Date:  1950-12       Impact factor: 11.205

7.  The pH-auxostat as a tool for studying microbial dynamics in continuous fermentation.

Authors:  G Larsson; S O Enfors; H Pham
Journal:  Biotechnol Bioeng       Date:  1990-07       Impact factor: 4.530

8.  Continuous in vitro evolution of catalytic function.

Authors:  M C Wright; G F Joyce
Journal:  Science       Date:  1997-04-25       Impact factor: 47.728

9.  An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule.

Authors:  D R Mills; R L Peterson; S Spiegelman
Journal:  Proc Natl Acad Sci U S A       Date:  1967-07       Impact factor: 11.205

10.  Continuous in vitro evolution of bacteriophage RNA polymerase promoters.

Authors:  R R Breaker; A Banerji; G F Joyce
Journal:  Biochemistry       Date:  1994-10-04       Impact factor: 3.162

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  16 in total

Review 1.  Learning Strategies in Protein Directed Evolution.

Authors:  Xavier F Cadet; Jean Christophe Gelly; Aster van Noord; Frédéric Cadet; Carlos G Acevedo-Rocha
Journal:  Methods Mol Biol       Date:  2022

2.  Suicide prevention for enzymes using continuous directed evolution.

Authors:  Mehran Dastmalchi
Journal:  Plant Physiol       Date:  2022-02-04       Impact factor: 8.340

Review 3.  L-valine production in Corynebacterium glutamicum based on systematic metabolic engineering: progress and prospects.

Authors:  Jie Liu; Jian-Zhong Xu; Bingbing Wang; Zhi-Ming Rao; Wei-Guo Zhang
Journal:  Amino Acids       Date:  2021-08-16       Impact factor: 3.520

Review 4.  Methods for the directed evolution of biomolecular interactions.

Authors:  Victoria Cochran Xie; Matthew J Styles; Bryan C Dickinson
Journal:  Trends Biochem Sci       Date:  2022-05       Impact factor: 14.264

5.  An in vivo selection system with tightly regulated gene expression enables directed evolution of highly efficient enzymes.

Authors:  Parinthon Nearmnala; Manutsawee Thanaburakorn; Watanalai Panbangred; Pimchai Chaiyen; Narupat Hongdilokkul
Journal:  Sci Rep       Date:  2021-06-03       Impact factor: 4.379

Review 6.  Systems for in vivo hypermutation: a quest for scale and depth in directed evolution.

Authors:  Gordon Rix; Chang C Liu
Journal:  Curr Opin Chem Biol       Date:  2021-03-27       Impact factor: 8.972

Review 7.  Proteome expansion in the Potyviridae evolutionary radiation.

Authors:  Fabio Pasin; José-Antonio Daròs; Ioannis E Tzanetakis
Journal:  FEMS Microbiol Rev       Date:  2022-07-01       Impact factor: 15.177

Review 8.  Molecular Evolution of Transition Metal Bioavailability at the Host-Pathogen Interface.

Authors:  Giuliano T Antelo; Alejandro J Vila; David P Giedroc; Daiana A Capdevila
Journal:  Trends Microbiol       Date:  2020-09-18       Impact factor: 17.079

9.  A Framework for Implementing Metaheuristic Algorithms Using Intercellular Communication.

Authors:  Yerko Ortiz; Javier Carrión; Rafael Lahoz-Beltrá; Martín Gutiérrez
Journal:  Front Bioeng Biotechnol       Date:  2021-05-10

10.  Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis.

Authors:  Krysten A Jones; Harrison M Snodgrass; Ketaki Belsare; Bryan C Dickinson; Jared C Lewis
Journal:  ACS Cent Sci       Date:  2021-09-13       Impact factor: 14.553

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