Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters
Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promot...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2014
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| Online Access: | http://hdl.handle.net/1721.1/84999 https://orcid.org/0000-0001-5409-1831 https://orcid.org/0000-0003-0844-4776 https://orcid.org/0000-0001-9364-6537 |
| _version_ | 1826194313806086144 |
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| author | Rhodius, Virgil A. Sharon, Brian D. Orlova, Ekaterina Tabakh, Hannah Burkhardt, David H. Clancy, Kevin Peterson, Todd C. Gross, Carol A. Segall-Shapiro, Thomas H. Ghodasara, Amar Navin Voigt, Christopher A. |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Rhodius, Virgil A. Sharon, Brian D. Orlova, Ekaterina Tabakh, Hannah Burkhardt, David H. Clancy, Kevin Peterson, Todd C. Gross, Carol A. Segall-Shapiro, Thomas H. Ghodasara, Amar Navin Voigt, Christopher A. |
| author_sort | Rhodius, Virgil A. |
| collection | MIT |
| description | Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σs as well as the specificity of their interaction with anti‐σs. DNA synthesis was used to build 86 ECF σs (two from every subgroup), their promoters, and 62 anti‐σs identified from the genomes of diverse bacteria. A subset of 20 σs and promoters were found to be highly orthogonal to each other. This set can be increased by combining the −35 and −10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σs, anti‐σs, and promoters were used to build synthetic genetic switches in Escherichia coli. This represents a genome‐scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well‐characterized regulatory parts will enable the construction of sophisticated gene expression programs. |
| first_indexed | 2024-09-23T09:54:08Z |
| format | Article |
| id | mit-1721.1/84999 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T09:54:08Z |
| publishDate | 2014 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/849992022-09-26T14:25:22Z Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters Rhodius, Virgil A. Sharon, Brian D. Orlova, Ekaterina Tabakh, Hannah Burkhardt, David H. Clancy, Kevin Peterson, Todd C. Gross, Carol A. Segall-Shapiro, Thomas H. Ghodasara, Amar Navin Voigt, Christopher A. Massachusetts Institute of Technology. Department of Biological Engineering Segall-Shapiro, Thomas H. Ghodasara, Amar Navin Voigt, Christopher A. Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σs as well as the specificity of their interaction with anti‐σs. DNA synthesis was used to build 86 ECF σs (two from every subgroup), their promoters, and 62 anti‐σs identified from the genomes of diverse bacteria. A subset of 20 σs and promoters were found to be highly orthogonal to each other. This set can be increased by combining the −35 and −10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σs, anti‐σs, and promoters were used to build synthetic genetic switches in Escherichia coli. This represents a genome‐scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well‐characterized regulatory parts will enable the construction of sophisticated gene expression programs. Life Technologies, Inc. United States. Defense Advanced Research Projects Agency (Chronicle of Lineage Indicative of Origins N66001-12-C-4018) United States. Office of Naval Research (N00014-10-1-0245) National Institutes of Health (U.S.) (NIH AI067699) National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (SA5284-11210) American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship Hertz Foundation (Fellowship) 2014-02-19T15:06:29Z 2014-02-19T15:06:29Z 2013-10 2013-05 Article http://purl.org/eprint/type/JournalArticle 1744-4292 http://hdl.handle.net/1721.1/84999 Rhodius, Virgil A, Thomas H Segall-Shapiro, Brian D Sharon, Amar Ghodasara, Ekaterina Orlova, Hannah Tabakh, David H Burkhardt, et al. “Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters.” Molecular Systems Biology 9 (October 29, 2013). Copyright © 2013 EMBO and Macmillan Publishers Limited https://orcid.org/0000-0001-5409-1831 https://orcid.org/0000-0003-0844-4776 https://orcid.org/0000-0001-9364-6537 en_US http://dx.doi.org/10.1038/msb.2013.58 Molecular Systems Biology http://creativecommons.org/licenses/by/3.0/ application/pdf Nature Publishing Group Nature Publishing Group |
| spellingShingle | Rhodius, Virgil A. Sharon, Brian D. Orlova, Ekaterina Tabakh, Hannah Burkhardt, David H. Clancy, Kevin Peterson, Todd C. Gross, Carol A. Segall-Shapiro, Thomas H. Ghodasara, Amar Navin Voigt, Christopher A. Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters |
| title | Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters |
| title_full | Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters |
| title_fullStr | Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters |
| title_full_unstemmed | Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters |
| title_short | Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters |
| title_sort | design of orthogonal genetic switches based on a crosstalk map of σs anti σs and promoters |
| url | http://hdl.handle.net/1721.1/84999 https://orcid.org/0000-0001-5409-1831 https://orcid.org/0000-0003-0844-4776 https://orcid.org/0000-0001-9364-6537 |
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