Literature DB >> 24781324

Principles of genetic circuit design.

Jennifer A N Brophy1, Christopher A Voigt1.   

Abstract

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.

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Year:  2014        PMID: 24781324      PMCID: PMC4230274          DOI: 10.1038/nmeth.2926

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  222 in total

1.  Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli.

Authors:  Tae Seok Moon; Elizabeth J Clarke; Eli S Groban; Alvin Tamsir; Ryan M Clark; Matthew Eames; Tanja Kortemme; Christopher A Voigt
Journal:  J Mol Biol       Date:  2010-12-23       Impact factor: 5.469

2.  Causes and effects of N-terminal codon bias in bacterial genes.

Authors:  Daniel B Goodman; George M Church; Sriram Kosuri
Journal:  Science       Date:  2013-09-26       Impact factor: 47.728

3.  j5 DNA assembly design automation software.

Authors:  Nathan J Hillson; Rafael D Rosengarten; Jay D Keasling
Journal:  ACS Synth Biol       Date:  2011-12-20       Impact factor: 5.110

4.  Translational control of IS10 transposition.

Authors:  R W Simons; N Kleckner
Journal:  Cell       Date:  1983-09       Impact factor: 41.582

5.  Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.

Authors:  Karsten Temme; Dehua Zhao; Christopher A Voigt
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-16       Impact factor: 11.205

6.  The integrase family of site-specific recombinases: regional similarities and global diversity.

Authors:  P Argos; A Landy; K Abremski; J B Egan; E Haggard-Ljungquist; R H Hoess; M L Kahn; B Kalionis; S V Narayana; L S Pierson
Journal:  EMBO J       Date:  1986-02       Impact factor: 11.598

7.  Design, construction and characterization of a set of insulated bacterial promoters.

Authors:  Joseph H Davis; Adam J Rubin; Robert T Sauer
Journal:  Nucleic Acids Res       Date:  2010-09-15       Impact factor: 16.971

8.  Engineering the Salmonella type III secretion system to export spider silk monomers.

Authors:  Daniel M Widmaier; Danielle Tullman-Ercek; Ethan A Mirsky; Rena Hill; Sridhar Govindarajan; Jeremy Minshull; Christopher A Voigt
Journal:  Mol Syst Biol       Date:  2009-09-15       Impact factor: 11.429

9.  Engineering synthetic TAL effectors with orthogonal target sites.

Authors:  Abhishek Garg; Jason J Lohmueller; Pamela A Silver; Thomas Z Armel
Journal:  Nucleic Acids Res       Date:  2012-05-11       Impact factor: 16.971

10.  Programming gene expression with combinatorial promoters.

Authors:  Robert Sidney Cox; Michael G Surette; Michael B Elowitz
Journal:  Mol Syst Biol       Date:  2007-11-13       Impact factor: 11.429

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  225 in total

Review 1.  Recent advances and opportunities in synthetic logic gates engineering in living cells.

Authors:  Vijai Singh
Journal:  Syst Synth Biol       Date:  2014-08-28

2.  Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites.

Authors:  Tiebin Wang; Nathan Tague; Stephen A Whelan; Mary J Dunlop
Journal:  Nucleic Acids Res       Date:  2021-01-25       Impact factor: 16.971

3.  Rethinking risk assessment for emerging technology first-in-human trials.

Authors:  Anna Genske; Sabrina Engel-Glatter
Journal:  Med Health Care Philos       Date:  2016-03

4.  Robust, tunable genetic memory from protein sequestration combined with positive feedback.

Authors:  Tatenda Shopera; William R Henson; Andrew Ng; Young Je Lee; Kenneth Ng; Tae Seok Moon
Journal:  Nucleic Acids Res       Date:  2015-09-17       Impact factor: 16.971

5.  Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications.

Authors:  Mitchell S Weisenberger; Tara L Deans
Journal:  J Ind Microbiol Biotechnol       Date:  2018-03-19       Impact factor: 3.346

Review 6.  Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics.

Authors:  Zachary Js Mays; Nikhil U Nair
Journal:  Curr Opin Biotechnol       Date:  2018-03-15       Impact factor: 9.740

7.  The paths of mortality: how understanding the biology of aging can help explain systems behavior of single cells.

Authors:  Matthew M Crane; Matt Kaeberlein
Journal:  Curr Opin Syst Biol       Date:  2017-12-06

Review 8.  Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities.

Authors:  Xinyun Cao; Joshua J Hamilton; Ophelia S Venturelli
Journal:  Biochemistry       Date:  2018-11-20       Impact factor: 3.162

9.  Synthetic metabolic computation in a bioluminescence-sensing system.

Authors:  Natalia Barger; Phyana Litovco; Ximing Li; Mouna Habib; Ramez Daniel
Journal:  Nucleic Acids Res       Date:  2019-11-04       Impact factor: 16.971

10.  Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design.

Authors:  Shuyi Zhang; Christopher A Voigt
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971

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