Literature DB >> 32374988

Automated Continuous Evolution of Proteins in Vivo.

Ziwei Zhong1, Brandon G Wong2,3, Arjun Ravikumar1,2,3, Garri A Arzumanyan1, Ahmad S Khalil2,3,4, Chang C Liu1,5,6.   

Abstract

We present automated continuous evolution (ACE), a platform for the hands-free directed evolution of biomolecules. ACE pairs OrthoRep, a genetic system for continuous targeted mutagenesis of user-selected genes in vivo, with eVOLVER, a scalable and automated continuous culture device for precise, multiparameter regulation of growth conditions. By implementing real-time feedback-controlled tuning of selection stringency with eVOLVER, genes of interest encoded on OrthoRep autonomously traversed multimutation adaptive pathways to reach desired functions, including drug resistance and improved enzyme activity. The durability, scalability, and speed of biomolecular evolution with ACE should be broadly applicable to protein engineering as well as prospective studies on how selection parameters and schedules shape adaptation.

Entities:  

Keywords:  OrthoRep; continuous culture; continuous evolution; eVOLVER; orthogonal replication

Mesh：

Substances：

Year:  2020        PMID： 32374988      PMCID： PMC7370864          DOI： 10.1021/acssynbio.0c00135

Source DB:  PubMed          Journal:  ACS Synth Biol        ISSN： 2161-5063            Impact factor:   5.110


  21 in total

1.  Evolutionary history of a specialized p450 propane monooxygenase.

Authors:  Rudi Fasan; Yergalem T Meharenna; Christopher D Snow; Thomas L Poulos; Frances H Arnold
Journal:  J Mol Biol       Date:  2008-06-28       Impact factor: 5.469

2.  Intense neutral drifts yield robust and evolvable consensus proteins.

Authors:  Shimon Bershtein; Korina Goldin; Dan S Tawfik
Journal:  J Mol Biol       Date:  2008-04-16       Impact factor: 5.469

Review 3.  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

4.  CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window.

Authors:  Shakked O Halperin; Connor J Tou; Eric B Wong; Cyrus Modavi; David V Schaffer; John E Dueber
Journal:  Nature       Date:  2018-08-01       Impact factor: 49.962

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.  An orthogonal DNA replication system in yeast.

Authors:  Arjun Ravikumar; Adrian Arrieta; Chang C Liu
Journal:  Nat Chem Biol       Date:  2014-02-02       Impact factor: 15.040

8.  Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition.

Authors:  Erdal Toprak; Adrian Veres; Sadik Yildiz; Juan M Pedraza; Remy Chait; Johan Paulsson; Roy Kishony
Journal:  Nat Protoc       Date:  2013-02-21       Impact factor: 13.491

9.  Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER.

Authors:  Brandon G Wong; Christopher P Mancuso; Szilvia Kiriakov; Caleb J Bashor; Ahmad S Khalil
Journal:  Nat Biotechnol       Date:  2018-06-11       Impact factor: 54.908

10.  Environmental changes bridge evolutionary valleys.

Authors:  Barrett Steinberg; Marc Ostermeier
Journal:  Sci Adv       Date:  2016-01-22       Impact factor: 14.136
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  13 in total

Review 1.  Synthetic Biological Circuits within an Orthogonal Central Dogma.

Authors:  Alan Costello; Ahmed H Badran
Journal:  Trends Biotechnol       Date:  2020-06-22       Impact factor: 19.536

2.  Systematic molecular evolution enables robust biomolecule discovery.

Authors:  Erika A DeBenedictis; Emma J Chory; Dana W Gretton; Brian Wang; Stefan Golas; Kevin M Esvelt
Journal:  Nat Methods       Date:  2021-12-30       Impact factor: 28.547

3.  High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs.

Authors:  Tony P Huang; Zachary J Heins; Shannon M Miller; Brandon G Wong; Pallavi A Balivada; Tina Wang; Ahmad S Khalil; David R Liu
Journal:  Nat Biotechnol       Date:  2022-09-08       Impact factor: 68.164

4.  Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight.

Authors:  François Bertaux; Sebastián Sosa-Carrillo; Viktoriia Gross; Achille Fraisse; Chetan Aditya; Mariela Furstenheim; Gregory Batt
Journal:  Nat Commun       Date:  2022-06-11       Impact factor: 17.694

Review 5.  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

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

7.  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 8.  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

9.  Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities.

Authors:  Gordon Rix; Ella J Watkins-Dulaney; Patrick J Almhjell; Christina E Boville; Frances H Arnold; Chang C Liu
Journal:  Nat Commun       Date:  2020-11-06       Impact factor: 14.919

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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