Design principles for engineering bacteria to maximise chemical production from batch cultures
Abstract Bacteria can be engineered to manufacture chemicals, but it is unclear how to optimally engineer a single cell to maximise production performance from batch cultures. Moreover, the performance of engineered production pathways is affected by competition for the host’s native resources. Here...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55347-y |
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| _version_ | 1841559262674812928 |
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| author | Ahmad A. Mannan Alexander P. S. Darlington Reiko J. Tanaka Declan G. Bates |
| author_facet | Ahmad A. Mannan Alexander P. S. Darlington Reiko J. Tanaka Declan G. Bates |
| author_sort | Ahmad A. Mannan |
| collection | DOAJ |
| description | Abstract Bacteria can be engineered to manufacture chemicals, but it is unclear how to optimally engineer a single cell to maximise production performance from batch cultures. Moreover, the performance of engineered production pathways is affected by competition for the host’s native resources. Here, using a ‘host-aware’ computational framework which captures competition for both metabolic and gene expression resources, we uncover design principles for engineering the expression of host and production enzymes at the cell level which maximise volumetric productivity and yield from batch cultures. However, this does not break the fundamental growth-synthesis trade-off which limits production performance. We show that engineering genetic circuits to switch cells to a high synthesis-low growth state after first growing to a large population can further improve performance. By analysing different circuit topologies, we show that highest performance is achieved by circuits that inhibit host metabolism to redirect it to product synthesis. Our results should facilitate construction of microbial cell factories with high and efficient production capabilities. |
| format | Article |
| id | doaj-art-0c96afb36f924bfeaf5c745281da4c22 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-0c96afb36f924bfeaf5c745281da4c222025-01-05T12:38:45ZengNature PortfolioNature Communications2041-17232025-01-0116111010.1038/s41467-024-55347-yDesign principles for engineering bacteria to maximise chemical production from batch culturesAhmad A. Mannan0Alexander P. S. Darlington1Reiko J. Tanaka2Declan G. Bates3Department of Bioengineering, Imperial College LondonWarwick Integrative Synthetic Biology Centre, School of Engineering, University of WarwickDepartment of Bioengineering, Imperial College LondonWarwick Integrative Synthetic Biology Centre, School of Engineering, University of WarwickAbstract Bacteria can be engineered to manufacture chemicals, but it is unclear how to optimally engineer a single cell to maximise production performance from batch cultures. Moreover, the performance of engineered production pathways is affected by competition for the host’s native resources. Here, using a ‘host-aware’ computational framework which captures competition for both metabolic and gene expression resources, we uncover design principles for engineering the expression of host and production enzymes at the cell level which maximise volumetric productivity and yield from batch cultures. However, this does not break the fundamental growth-synthesis trade-off which limits production performance. We show that engineering genetic circuits to switch cells to a high synthesis-low growth state after first growing to a large population can further improve performance. By analysing different circuit topologies, we show that highest performance is achieved by circuits that inhibit host metabolism to redirect it to product synthesis. Our results should facilitate construction of microbial cell factories with high and efficient production capabilities.https://doi.org/10.1038/s41467-024-55347-y |
| spellingShingle | Ahmad A. Mannan Alexander P. S. Darlington Reiko J. Tanaka Declan G. Bates Design principles for engineering bacteria to maximise chemical production from batch cultures Nature Communications |
| title | Design principles for engineering bacteria to maximise chemical production from batch cultures |
| title_full | Design principles for engineering bacteria to maximise chemical production from batch cultures |
| title_fullStr | Design principles for engineering bacteria to maximise chemical production from batch cultures |
| title_full_unstemmed | Design principles for engineering bacteria to maximise chemical production from batch cultures |
| title_short | Design principles for engineering bacteria to maximise chemical production from batch cultures |
| title_sort | design principles for engineering bacteria to maximise chemical production from batch cultures |
| url | https://doi.org/10.1038/s41467-024-55347-y |
| work_keys_str_mv | AT ahmadamannan designprinciplesforengineeringbacteriatomaximisechemicalproductionfrombatchcultures AT alexanderpsdarlington designprinciplesforengineeringbacteriatomaximisechemicalproductionfrombatchcultures AT reikojtanaka designprinciplesforengineeringbacteriatomaximisechemicalproductionfrombatchcultures AT declangbates designprinciplesforengineeringbacteriatomaximisechemicalproductionfrombatchcultures |