A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits
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Author(s)
Sechkar, Kirill
Harrison, Steel
Perrino, Giansimone
Stan, Guy-Bart
Stan, Guy-Bart
Type
Journal Article
Abstract
Within a cell, synthetic and native genes compete for expression machinery, influencing cellular process dynamics through resource couplings. Models that simplify competitive resource binding kinetics can guide the design of strategies for countering these couplings. However, in bacteria resource availability and cell growth rate are interlinked, which complicates resource-aware biocircuit design. Capturing this interdependence requires coarse-grained bacterial cell models that balance accurate representation of metabolic regulation against simplicity and interpretability. We propose a coarse-grained E. coli cell model that combines the ease of simplified resource coupling analysis with appreciation of bacterial growth regulation mechanisms and the processes relevant for biocircuit design. Reliably capturing known growth phenomena, it provides a unifying explanation to disparate empirical relations between growth and synthetic gene expression. Considering a biomolecular controller that makes cell-wide ribosome availability robust to perturbations, we showcase our model’s usefulness in numerically prototyping biocircuits and deriving analytical relations for design guidance.
Date Issued
2024-03-04
Date Acceptance
2024-02-27
Citation
Nature Communications, 2024, 15
ISSN
2041-1723
Publisher
Springer Nature
Journal / Book Title
Nature Communications
Volume
15
Copyright Statement
© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Copyright URL
Identifier
https://www.nature.com/articles/s41467-024-46410-9
Publication Status
Published
Article Number
1981
Date Publish Online
2024-03-04