A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits
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 av...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Springer Nature
2024
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| _version_ | 1797113144357683200 |
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| author | Sechkar, K Steel, H Perrino, G Stan, G-B |
| author_facet | Sechkar, K Steel, H Perrino, G Stan, G-B |
| author_sort | Sechkar, K |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-04-09T03:59:01Z |
| format | Journal article |
| id | oxford-uuid:7a19b29a-ade2-4cbb-aa4d-b8daafea4121 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-04-09T03:59:01Z |
| publishDate | 2024 |
| publisher | Springer Nature |
| record_format | dspace |
| spelling | oxford-uuid:7a19b29a-ade2-4cbb-aa4d-b8daafea41212024-04-05T16:04:19ZA coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuitsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:7a19b29a-ade2-4cbb-aa4d-b8daafea4121EnglishSymplectic ElementsSpringer Nature2024Sechkar, KSteel, HPerrino, GStan, G-BWithin 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. |
| spellingShingle | Sechkar, K Steel, H Perrino, G Stan, G-B A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits |
| title | A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits |
| title_full | A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits |
| title_fullStr | A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits |
| title_full_unstemmed | A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits |
| title_short | A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits |
| title_sort | coarse grained bacterial cell model for resource aware analysis and design of synthetic gene circuits |
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