Literature DB >> 25461718

In vivo continuous directed evolution.

Ahmed H Badran1, David R Liu2.   

Abstract

The development and application of methods for the laboratory evolution of biomolecules has rapidly progressed over the last few decades. Advancements in continuous microbe culturing and selection design have facilitated the development of new technologies that enable the continuous directed evolution of proteins and nucleic acids. These technologies have the potential to support the extremely rapid evolution of biomolecules with tailor-made functional properties. Continuous evolution methods must support all of the key steps of laboratory evolution - translation of genes into gene products, selection or screening, replication of genes encoding the most fit gene products, and mutation of surviving genes - in a self-sustaining manner that requires little or no researcher intervention. Continuous laboratory evolution has been historically used to study problems including antibiotic resistance, organismal adaptation, phylogenetic reconstruction, and host-pathogen interactions, with more recent applications focusing on the rapid generation of proteins and nucleic acids with useful, tailor-made properties. The advent of increasingly general methods for continuous directed evolution should enable researchers to address increasingly complex questions and to access biomolecules with more novel or even unprecedented properties.
Copyright © 2014. Published by Elsevier Ltd.

Entities:  

Mesh:

Year:  2014        PMID: 25461718      PMCID: PMC4308500          DOI: 10.1016/j.cbpa.2014.09.040

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  44 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

Review 2.  Whole organism biocatalysis.

Authors:  Takeru Ishige; Kohsuke Honda; Sakayu Shimizu
Journal:  Curr Opin Chem Biol       Date:  2005-04       Impact factor: 8.822

Review 3.  The promise and peril of continuous in vitro evolution.

Authors:  Glenn C Johns; Gerald F Joyce
Journal:  J Mol Evol       Date:  2005-06-27       Impact factor: 2.395

4.  Experimental phylogenetics: generation of a known phylogeny.

Authors:  D M Hillis; J J Bull; M E White; M R Badgett; I J Molineux
Journal:  Science       Date:  1992-01-31       Impact factor: 47.728

5.  Continuous in vitro evolution of catalytic function.

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

Review 6.  Selection and evolution of bacteriophages in cellstat.

Authors:  Y Husimi
Journal:  Adv Biophys       Date:  1989

7.  A Heritable Recombination system for synthetic Darwinian evolution in yeast.

Authors:  Dante W Romanini; Pamela Peralta-Yahya; Vanessa Mondol; Virginia W Cornish
Journal:  ACS Synth Biol       Date:  2012-12-21       Impact factor: 5.110

Review 8.  Exploring protein fitness landscapes by directed evolution.

Authors:  Philip A Romero; Frances H Arnold
Journal:  Nat Rev Mol Cell Biol       Date:  2009-12       Impact factor: 94.444

9.  Genome replication engineering assisted continuous evolution (GREACE) to improve microbial tolerance for biofuels production.

Authors:  Guodong Luan; Zhen Cai; Yin Li; Yanhe Ma
Journal:  Biotechnol Biofuels       Date:  2013-09-27       Impact factor: 6.040

10.  A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations.

Authors:  Bryan C Dickinson; Michael S Packer; Ahmed H Badran; David R Liu
Journal:  Nat Commun       Date:  2014-10-30       Impact factor: 14.919

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  23 in total

Review 1.  Methods for the directed evolution of proteins.

Authors:  Michael S Packer; David R Liu
Journal:  Nat Rev Genet       Date:  2015-06-09       Impact factor: 53.242

2.  Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.

Authors:  Jacob B Bale; Rachel U Park; Yuxi Liu; Shane Gonen; Tamir Gonen; Duilio Cascio; Neil P King; Todd O Yeates; David Baker
Journal:  Protein Sci       Date:  2015-08-06       Impact factor: 6.725

3.  Tools and systems for evolutionary engineering of biomolecules and microorganisms.

Authors:  Sungho Jang; Minsun Kim; Jaeseong Hwang; Gyoo Yeol Jung
Journal:  J Ind Microbiol Biotechnol       Date:  2019-05-27       Impact factor: 3.346

Review 4.  A mechanistic view of enzyme evolution.

Authors:  Gloria Yang; Charlotte M Miton; Nobuhiko Tokuriki
Journal:  Protein Sci       Date:  2020-08       Impact factor: 6.725

5.  VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells.

Authors:  Justin G English; Reid H J Olsen; Katherine Lansu; Michael Patel; Karoline White; Adam S Cockrell; Darshan Singh; Ryan T Strachan; Daniel Wacker; Bryan L Roth
Journal:  Cell       Date:  2019-07-04       Impact factor: 41.582

6.  Probing pathways of adaptation with continuous evolution.

Authors:  Ziwei Zhong; Chang C Liu
Journal:  Curr Opin Syst Biol       Date:  2019-02-13

Review 7.  Modern methods for laboratory diversification of biomolecules.

Authors:  Sinisa Bratulic; Ahmed H Badran
Journal:  Curr Opin Chem Biol       Date:  2017-11-02       Impact factor: 8.822

8.  Switching promotor recognition of phage RNA polymerase in silico along lab-directed evolution path.

Authors:  Chao E; Liqiang Dai; Jin Yu
Journal:  Biophys J       Date:  2022-01-11       Impact factor: 4.033

9.  Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication.

Authors:  Andreas K Brödel; Alfonso Jaramillo; Mark Isalan
Journal:  Nat Protoc       Date:  2017-08-10       Impact factor: 13.491

Review 10.  Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics.

Authors:  Xiao Tan; Justin H Letendre; James J Collins; Wilson W Wong
Journal:  Cell       Date:  2021-02-10       Impact factor: 41.582

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