Literature DB >> 33441561

Contextual dependencies expand the re-usability of genetic inverters.

Huseyin Tas1, Lewis Grozinger2, Ruud Stoof2, Victor de Lorenzo3, Ángel Goñi-Moreno4,5.   

Abstract

The implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, the context in which the circuit performs is crucial for its outcome. We characterise 20 genetic NOT logic gates in up to 7 bacterial-based contexts each, to generate 135 different functions. The contexts we focus on are combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each gate shows seven different dynamic behaviours, depending on the context. That is, gates can be fine-tuned by changing only contextual parameters, thus improving the compatibility between gates. Finally, we analyse portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expands functionality, and advocate for considering context as a fundamental design parameter.

Entities:  

Year:  2021        PMID: 33441561     DOI: 10.1038/s41467-020-20656-5

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  32 in total

Review 1.  Synthetic biology devices for in vitro and in vivo diagnostics.

Authors:  Shimyn Slomovic; Keith Pardee; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-24       Impact factor: 11.205

Review 2.  Stochasticity in gene expression: from theories to phenotypes.

Authors:  Mads Kaern; Timothy C Elston; William J Blake; James J Collins
Journal:  Nat Rev Genet       Date:  2005-06       Impact factor: 53.242

Review 3.  Boolean network models of cellular regulation: prospects and limitations.

Authors:  Stefan Bornholdt
Journal:  J R Soc Interface       Date:  2008-08-06       Impact factor: 4.118

4.  Quantifying cellular capacity identifies gene expression designs with reduced burden.

Authors:  Francesca Ceroni; Rhys Algar; Guy-Bart Stan; Tom Ellis
Journal:  Nat Methods       Date:  2015-04-06       Impact factor: 28.547

5.  Synthetic analog computation in living cells.

Authors:  Ramiz Daniel; Jacob R Rubens; Rahul Sarpeshkar; Timothy K Lu
Journal:  Nature       Date:  2013-05-15       Impact factor: 49.962

6.  Genetic circuit design automation.

Authors:  Alec A K Nielsen; Bryan S Der; Jonghyeon Shin; Prashant Vaidyanathan; Vanya Paralanov; Elizabeth A Strychalski; David Ross; Douglas Densmore; Christopher A Voigt
Journal:  Science       Date:  2016-04-01       Impact factor: 47.728

Review 7.  Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems.

Authors:  Stefano Cardinale; Adam Paul Arkin
Journal:  Biotechnol J       Date:  2012-05-31       Impact factor: 4.677

8.  Designing and engineering evolutionary robust genetic circuits.

Authors:  Sean C Sleight; Bryan A Bartley; Jane A Lieviant; Herbert M Sauro
Journal:  J Biol Eng       Date:  2010-11-01       Impact factor: 4.355

Review 9.  Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis.

Authors:  Juhyun Kim; Manuel Salvador; Elizabeth Saunders; Jaime González; Claudio Avignone-Rossa; Jose Ignacio Jiménez
Journal:  Essays Biochem       Date:  2016-11-30       Impact factor: 8.000

10.  Isocost Lines Describe the Cellular Economy of Genetic Circuits.

Authors:  Andras Gyorgy; José I Jiménez; John Yazbek; Hsin-Ho Huang; Hattie Chung; Ron Weiss; Domitilla Del Vecchio
Journal:  Biophys J       Date:  2015-08-04       Impact factor: 4.033

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  9 in total

1.  Genetic context effects can override canonical cis regulatory elements in Escherichia coli.

Authors:  Scott A Scholz; Chase D Lindeboom; Peter L Freddolino
Journal:  Nucleic Acids Res       Date:  2022-10-14       Impact factor: 19.160

2.  Accurate characterization of dynamic microbial gene expression and growth rate profiles.

Authors:  Gonzalo Vidal; Carlos Vidal-Céspedes; Macarena Muñoz Silva; Carlos Castillo-Passi; Guillermo Yáñez Feliú; Fernán Federici; Timothy J Rudge
Journal:  Synth Biol (Oxf)       Date:  2022-10-15

3.  Picking the right metaphors for addressing microbial systems: economic theory helps understanding biological complexity.

Authors:  Juhyun Kim; Rafael Silva-Rocha; Víctor de Lorenzo
Journal:  Int Microbiol       Date:  2021-07-16       Impact factor: 2.479

Review 4.  Strategies for Improving Small-Molecule Biosensors in Bacteria.

Authors:  Corwin A Miller; Joanne M L Ho; Matthew R Bennett
Journal:  Biosensors (Basel)       Date:  2022-01-25

5.  Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor.

Authors:  Nahikari López-López; David San León; Sonia de Castro; Roberto Díez-Martínez; Manuel Iglesias-Bexiga; María José Camarasa; Margarita Menéndez; Juan Nogales; Junkal Garmendia
Journal:  mSystems       Date:  2022-03-16       Impact factor: 7.324

6.  Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study.

Authors:  Pablo I Nikel; Ilaria Benedetti; Nicolas T Wirth; Víctor de Lorenzo; Belén Calles
Journal:  Microb Biotechnol       Date:  2022-04-27       Impact factor: 6.575

7.  A Network Approach to Genetic Circuit Designs.

Authors:  Matthew Crowther; Anil Wipat; Ángel Goñi-Moreno
Journal:  ACS Synth Biol       Date:  2022-08-31       Impact factor: 5.249

8.  Local genetic context shapes the function of a gene regulatory network.

Authors:  Anna Nagy-Staron; Kathrin Tomasek; Caroline Caruso Carter; Elisabeth Sonnleitner; Bor Kavčič; Tiago Paixão; Calin C Guet
Journal:  Elife       Date:  2021-03-08       Impact factor: 8.140

9.  Functional biology in its natural context: A search for emergent simplicity.

Authors:  Joy Bergelson; Martin Kreitman; Dmitri A Petrov; Alvaro Sanchez; Mikhail Tikhonov
Journal:  Elife       Date:  2021-06-07       Impact factor: 8.140

  9 in total

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