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Lookup NU author(s): Dr Lewis Grozinger, Ruud Stoof, Dr Angel Goni-Moreno
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2021, The Author(s).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.
Author(s): Tas H, Grozinger L, Stoof R, de Lorenzo V, Goni-Moreno A
Publication type: Article
Publication status: Published
Journal: Nature Communications
Year: 2021
Volume: 12
Issue: 1
Online publication date: 13/01/2021
Acceptance date: 02/12/2020
Date deposited: 25/08/2023
ISSN (electronic): 2041-1723
Publisher: Nature Research
URL: https://doi.org/10.1038/s41467-020-20656-5
DOI: 10.1038/s41467-020-20656-5
Data Access Statement: Availability of data, genetic material and supporting software. The flow cytometry data used for analysis in this study is available as a figshare repository at https://data.ncl.ac.uk/ndownloader/articles/12073479/versions/1. This SBOL files for the genetic constructs used in the study are available at https://github.com/lgrozinger/pyolin/tree/master/results/sbol. The constructs themselves are retained at SEVA bank (http://seva-plasmids.com) at CNB-CSIC, Madrid, Spain and ready for distribution for research purposes. Code availability The Python package used to perform all the analysis presented, the preprocessing of the raw cytometry data, and to generate the figures shown here, is made available at https://github.com/lgrozinger/pyolin.
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