Dynamic control of endogenous metabolism with combinatorial logic circuits
Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of s...
| Main Authors: | , , , , , |
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| Format: | Article |
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Nature Publishing Group
2019
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| Online Access: | http://hdl.handle.net/1721.1/121120 https://orcid.org/0000-0002-7762-3084 https://orcid.org/0000-0002-3036-7183 https://orcid.org/0000-0001-5409-1831 https://orcid.org/0000-0002-6788-2429 https://orcid.org/0000-0003-0844-4776 |
| _version_ | 1826212632686755840 |
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| author | Moser, Felix Espah Borujeni, Amin Ghodasara, Amar Navin Cameron, Douglas Park, YongJin Voigt, Christopher A. |
| author2 | Massachusetts Institute of Technology. Institute for Medical Engineering & Science |
| author_facet | Massachusetts Institute of Technology. Institute for Medical Engineering & Science Moser, Felix Espah Borujeni, Amin Ghodasara, Amar Navin Cameron, Douglas Park, YongJin Voigt, Christopher A. |
| author_sort | Moser, Felix |
| collection | MIT |
| description | Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post-translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed (pta or poxB) and respond by turning off the corresponding gene. This work demonstrates how simple circuits can be implemented to enable customizable dynamic gene regulation. |
| first_indexed | 2024-09-23T15:31:09Z |
| format | Article |
| id | mit-1721.1/121120 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T15:31:09Z |
| publishDate | 2019 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/1211202022-09-29T14:51:03Z Dynamic control of endogenous metabolism with combinatorial logic circuits Moser, Felix Espah Borujeni, Amin Ghodasara, Amar Navin Cameron, Douglas Park, YongJin Voigt, Christopher A. Massachusetts Institute of Technology. Institute for Medical Engineering & Science Massachusetts Institute of Technology. Department of Biological Engineering Moser, Felix Espah Borujeni, Amin Ghodasara, Amar Navin Cameron, Douglas Park, YongJin Voigt, Christopher A. Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post-translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed (pta or poxB) and respond by turning off the corresponding gene. This work demonstrates how simple circuits can be implemented to enable customizable dynamic gene regulation. Synthetic Biology Engineering Research Center (SynBERC EEC0540879) United States. Office of Naval Research. Multidisciplinary University Research Initiative (N00014‐13‐1‐0074) United States. Department of Energy (DE‐SC0018368) 2019-03-29T19:41:50Z 2019-03-29T19:41:50Z 2018-11 2019-02-28T14:26:11Z Article http://purl.org/eprint/type/JournalArticle 1744-4292 http://hdl.handle.net/1721.1/121120 Moser, Felix, Amin Espah Borujeni, Amar N. Ghodasara, Ewen Cameron, Yongjin Park, and Christopher A. Voigt. “Dynamic Control of Endogenous Metabolism with Combinatorial Logic Circuits.” Molecular Systems Biology 14, no. 11 (November 2018): e8605. © 2018 The Authors https://orcid.org/0000-0002-7762-3084 https://orcid.org/0000-0002-3036-7183 https://orcid.org/0000-0001-5409-1831 https://orcid.org/0000-0002-6788-2429 https://orcid.org/0000-0003-0844-4776 http://dx.doi.org/10.15252/msb.20188605 Molecular Systems Biology Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Nature Publishing Group Molecular Systems Biology |
| spellingShingle | Moser, Felix Espah Borujeni, Amin Ghodasara, Amar Navin Cameron, Douglas Park, YongJin Voigt, Christopher A. Dynamic control of endogenous metabolism with combinatorial logic circuits |
| title | Dynamic control of endogenous metabolism with combinatorial logic circuits |
| title_full | Dynamic control of endogenous metabolism with combinatorial logic circuits |
| title_fullStr | Dynamic control of endogenous metabolism with combinatorial logic circuits |
| title_full_unstemmed | Dynamic control of endogenous metabolism with combinatorial logic circuits |
| title_short | Dynamic control of endogenous metabolism with combinatorial logic circuits |
| title_sort | dynamic control of endogenous metabolism with combinatorial logic circuits |
| url | http://hdl.handle.net/1721.1/121120 https://orcid.org/0000-0002-7762-3084 https://orcid.org/0000-0002-3036-7183 https://orcid.org/0000-0001-5409-1831 https://orcid.org/0000-0002-6788-2429 https://orcid.org/0000-0003-0844-4776 |
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