Literature DB >> 33784581

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

Gordon Rix1, Chang C Liu2.   

Abstract

Traditional approaches to the directed evolution of genes of interest (GOIs) place constraints on the scale of experimentation and depth of evolutionary search reasonably achieved. Engineered genetic systems that dramatically elevate the mutation of target GOIs in vivo relieve these constraints by enabling continuous evolution, affording new strategies in the exploration of sequence space and fitness landscapes for GOIs. We describe various in vivo hypermutation systems for continuous evolution, discuss how different architectures for in vivo hypermutation facilitate evolutionary search scale and depth in their application to problems in protein evolution and engineering, and outline future opportunities for the field.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Continuous evolution; Directed evolution; Hypermutation; Protein evolution

Mesh:

Substances:

Year:  2021        PMID: 33784581      PMCID: PMC8464631          DOI: 10.1016/j.cbpa.2021.02.008

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.972


  39 in total

1.  The 'evolvability' of promiscuous protein functions.

Authors:  Amir Aharoni; Leonid Gaidukov; Olga Khersonsky; Stephen McQ Gould; Cintia Roodveldt; Dan S Tawfik
Journal:  Nat Genet       Date:  2004-11-28       Impact factor: 38.330

2.  A constant rate of spontaneous mutation in DNA-based microbes.

Authors:  J W Drake
Journal:  Proc Natl Acad Sci U S A       Date:  1991-08-15       Impact factor: 11.205

Review 3.  Machine-learning-guided directed evolution for protein engineering.

Authors:  Kevin K Yang; Zachary Wu; Frances H Arnold
Journal:  Nat Methods       Date:  2019-07-15       Impact factor: 28.547

4.  Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor.

Authors:  Haiqi Chen; Sophia Liu; Samuel Padula; Daniel Lesman; Kettner Griswold; Allen Lin; Tongtong Zhao; Jamie L Marshall; Fei Chen
Journal:  Nat Biotechnol       Date:  2019-12-16       Impact factor: 54.908

5.  Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds.

Authors:  Arjun Ravikumar; Garri A Arzumanyan; Muaeen K A Obadi; Alex A Javanpour; Chang C Liu
Journal:  Cell       Date:  2018-11-08       Impact factor: 41.582

6.  Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells.

Authors:  Gaelen T Hess; Laure Frésard; Kyuho Han; Cameron H Lee; Amy Li; Karlene A Cimprich; Stephen B Montgomery; Michael C Bassik
Journal:  Nat Methods       Date:  2016-10-31       Impact factor: 28.547

7.  Using phage-assisted continuous evolution (PACE) to evolve human PD1.

Authors:  Xiaoxiao Ye; Min Tu; Mingxin Piao; Liang Yang; Zeng Zhou; Zhaopeng Li; Meiyu Lin; Zhenming Yang; Zecheng Zuo
Journal:  Exp Cell Res       Date:  2020-08-27       Impact factor: 3.905

8.  Targeted Diversification in the S. cerevisiae Genome with CRISPR-Guided DNA Polymerase I.

Authors:  Connor J Tou; David V Schaffer; John E Dueber
Journal:  ACS Synth Biol       Date:  2020-06-16       Impact factor: 5.110

9.  Phage-assisted continuous and non-continuous evolution.

Authors:  Shannon M Miller; Tina Wang; David R Liu
Journal:  Nat Protoc       Date:  2020-11-16       Impact factor: 13.491

10.  In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9.

Authors:  Beatriz Álvarez; Mario Mencía; Víctor de Lorenzo; Luis Ángel Fernández
Journal:  Nat Commun       Date:  2020-12-22       Impact factor: 14.919

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  5 in total

1.  Rapid generation of potent antibodies by autonomous hypermutation in yeast.

Authors:  Alon Wellner; Conor McMahon; Morgan S A Gilman; Jonathan R Clements; Sarah Clark; Kianna M Nguyen; Ming H Ho; Vincent J Hu; Jung-Eun Shin; Jared Feldman; Blake M Hauser; Timothy M Caradonna; Laura M Wingler; Aaron G Schmidt; Debora S Marks; Jonathan Abraham; Andrew C Kruse; Chang C Liu
Journal:  Nat Chem Biol       Date:  2021-06-24       Impact factor: 16.174

2.  Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases.

Authors:  Jaya Joshi; Qiang Li; Jorge D García-García; Bryan J Leong; You Hu; Steven D Bruner; Andrew D Hanson
Journal:  Biochem J       Date:  2021-09-17       Impact factor: 3.857

3.  Using continuous directed evolution to improve enzymes for plant applications.

Authors:  Jorge D García-García; Kristen Van Gelder; Jaya Joshi; Ulschan Bathe; Bryan J Leong; Steven D Bruner; Chang C Liu; Andrew D Hanson
Journal:  Plant Physiol       Date:  2022-02-04       Impact factor: 8.340

Review 4.  Genome editor-directed in vivo library diversification.

Authors:  Cristina Cheng; Mi Zhou; Qiwen Su; Alexandra Steigmeyer; Jia Niu
Journal:  Cell Chem Biol       Date:  2021-06-08       Impact factor: 9.039

5.  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

  5 in total

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