Literature DB >> 24556867

Engineering reduced evolutionary potential for synthetic biology.

Brian A Renda1, Michael J Hammerling, Jeffrey E Barrick.   

Abstract

The field of synthetic biology seeks to engineer reliable and predictable behaviors in organisms from collections of standardized genetic parts. However, unlike other types of machines, genetically encoded biological systems are prone to changes in their designed sequences due to mutations in their DNA sequences after these devices are constructed and deployed. Thus, biological engineering efforts can be confounded by undesired evolution that rapidly breaks the functions of parts and systems, particularly when they are costly to the host cell to maintain. Here, we explain the fundamental properties that determine the evolvability of biological systems. Then, we use this framework to review current efforts to engineer the DNA sequences that encode synthetic biology devices and the genomes of their microbial hosts to reduce their ability to evolve and therefore increase their genetic reliability so that they maintain their intended functions over longer timescales.

Entities:  

Mesh:

Year:  2014        PMID: 24556867      PMCID: PMC4043932          DOI: 10.1039/c3mb70606k

Source DB:  PubMed          Journal:  Mol Biosyst        ISSN: 1742-2051


  89 in total

Review 1.  Origins of spontaneous mutations: specificity and directionality of base-substitution, frameshift, and sequence-substitution mutageneses.

Authors:  Hisaji Maki
Journal:  Annu Rev Genet       Date:  2002-06-11       Impact factor: 16.830

2.  Building a Parallel Metabolism within the Cell.

Authors:  Aleksandra Filipovska; Oliver Rackham
Journal:  ACS Chem Biol       Date:  2008-01-04       Impact factor: 5.100

3.  Genome evolution and adaptation in a long-term experiment with Escherichia coli.

Authors:  Jeffrey E Barrick; Dong Su Yu; Sung Ho Yoon; Haeyoung Jeong; Tae Kwang Oh; Dominique Schneider; Richard E Lenski; Jihyun F Kim
Journal:  Nature       Date:  2009-10-18       Impact factor: 49.962

Review 4.  Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition.

Authors:  Ben Ryall; Gustavo Eydallin; Thomas Ferenci
Journal:  Microbiol Mol Biol Rev       Date:  2012-09       Impact factor: 11.056

5.  Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.

Authors:  Jessica S Dymond; Sarah M Richardson; Candice E Coombes; Timothy Babatz; Héloïse Muller; Narayana Annaluru; William J Blake; Joy W Schwerzmann; Junbiao Dai; Derek L Lindstrom; Annabel C Boeke; Daniel E Gottschling; Srinivasan Chandrasegaran; Joel S Bader; Jef D Boeke
Journal:  Nature       Date:  2011-09-14       Impact factor: 49.962

6.  Genome engineering reveals large dispensable regions in Bacillus subtilis.

Authors:  Helga Westers; Ronald Dorenbos; Jan Maarten van Dijl; Jorrit Kabel; Tony Flanagan; Kevin M Devine; Florence Jude; Simone J Seror; Aaron C Beekman; Elise Darmon; Caroline Eschevins; Anne de Jong; Sierd Bron; Oscar P Kuipers; Alessandra M Albertini; Haike Antelmann; Michael Hecker; Nicola Zamboni; Uwe Sauer; Claude Bruand; Dusko S Ehrlich; Juan C Alonso; Margarita Salas; Wim J Quax
Journal:  Mol Biol Evol       Date:  2003-08-29       Impact factor: 16.240

Review 7.  Genome dynamics during experimental evolution.

Authors:  Jeffrey E Barrick; Richard E Lenski
Journal:  Nat Rev Genet       Date:  2013-10-29       Impact factor: 53.242

Review 8.  Microbial laboratory evolution in the era of genome-scale science.

Authors:  Tom M Conrad; Nathan E Lewis; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2011-07-05       Impact factor: 11.429

9.  Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs.

Authors:  Bálint Csörgo; Tamás Fehér; Edit Tímár; Frederick R Blattner; György Pósfai
Journal:  Microb Cell Fact       Date:  2012-01-20       Impact factor: 5.328

10.  A synthetic Escherichia coli predator-prey ecosystem.

Authors:  Frederick K Balagaddé; Hao Song; Jun Ozaki; Cynthia H Collins; Matthew Barnet; Frances H Arnold; Stephen R Quake; Lingchong You
Journal:  Mol Syst Biol       Date:  2008-04-15       Impact factor: 11.429

View more
  32 in total

Review 1.  Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Authors:  Bryan A Bartley; Kyung Kim; J Kyle Medley; Herbert M Sauro
Journal:  Biophys J       Date:  2017-03-28       Impact factor: 4.033

Review 2.  The dawn of evolutionary genome engineering.

Authors:  Csaba Pál; Balázs Papp; György Pósfai
Journal:  Nat Rev Genet       Date:  2014-05-28       Impact factor: 53.242

Review 3.  A critical comparison of cellular and cell-free bioproduction systems.

Authors:  Nico J Claassens; Simon Burgener; Bastian Vögeli; Tobias J Erb; Arren Bar-Even
Journal:  Curr Opin Biotechnol       Date:  2019-06-14       Impact factor: 9.740

Review 4.  Rational engineering of synthetic microbial systems: from single cells to consortia.

Authors:  Philip Bittihn; M Omar Din; Lev S Tsimring; Jeff Hasty
Journal:  Curr Opin Microbiol       Date:  2018-03-22       Impact factor: 7.934

5.  Mapping Protein-Protein Interaction Interface Peptides with Jun-Fos Assisted Phage Display and Deep Sequencing.

Authors:  Wanzhi Huang; Victoria Soeung; David M Boragine; Timothy Palzkill
Journal:  ACS Synth Biol       Date:  2020-06-23       Impact factor: 5.110

6.  A Modelling Framework Linking Resource-Based Stochastic Translation to the Optimal Design of Synthetic Constructs.

Authors:  Peter Sarvari; Duncan Ingram; Guy-Bart Stan
Journal:  Biology (Basel)       Date:  2021-01-07

Review 7.  Principles for designing synthetic microbial communities.

Authors:  Nathan I Johns; Tomasz Blazejewski; Antonio Lc Gomes; Harris H Wang
Journal:  Curr Opin Microbiol       Date:  2016-04-13       Impact factor: 7.934

8.  Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1.

Authors:  Brian A Renda; Cindy Chan; Kristin N Parent; Jeffrey E Barrick
Journal:  J Bacteriol       Date:  2016-11-04       Impact factor: 3.490

9.  Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator.

Authors:  Benjamin R Jack; Sean P Leonard; Dennis M Mishler; Brian A Renda; Dacia Leon; Gabriel A Suárez; Jeffrey E Barrick
Journal:  ACS Synth Biol       Date:  2015-07-01       Impact factor: 5.110

Review 10.  Genomes by design.

Authors:  Adrian D Haimovich; Paul Muir; Farren J Isaacs
Journal:  Nat Rev Genet       Date:  2015-08-11       Impact factor: 53.242

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.