Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
Abstract 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 t...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2013-10-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2013.58 |
| _version_ | 1826990418577850368 |
|---|---|
| author | Virgil A Rhodius Thomas H Segall‐Shapiro Brian D Sharon Amar Ghodasara Ekaterina Orlova Hannah Tabakh David H Burkhardt Kevin Clancy Todd C Peterson Carol A Gross Christopher A Voigt |
| author_facet | Virgil A Rhodius Thomas H Segall‐Shapiro Brian D Sharon Amar Ghodasara Ekaterina Orlova Hannah Tabakh David H Burkhardt Kevin Clancy Todd C Peterson Carol A Gross Christopher A Voigt |
| author_sort | Virgil A Rhodius |
| collection | DOAJ |
| description | Abstract 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 | 2024-03-11T21:49:07Z |
| format | Article |
| id | doaj.art-008a5930ca7040cdb7fd5b0a748f5ffe |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2025-02-18T08:20:11Z |
| publishDate | 2013-10-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-008a5930ca7040cdb7fd5b0a748f5ffe2024-11-03T12:56:20ZengSpringer NatureMolecular Systems Biology1744-42922013-10-019111310.1038/msb.2013.58Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promotersVirgil A Rhodius0Thomas H Segall‐Shapiro1Brian D Sharon2Amar Ghodasara3Ekaterina Orlova4Hannah Tabakh5David H Burkhardt6Kevin Clancy7Todd C Peterson8Carol A Gross9Christopher A Voigt10Department of Microbiology and Immunology, University of California San FranciscoDepartment of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of TechnologyGraduate Group in Biophysics, University of California San FranciscoDepartment of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of TechnologyDepartment of Microbiology and Immunology, University of California San FranciscoDepartment of Microbiology and Immunology, University of California San FranciscoGraduate Group in Biophysics, University of California San FranciscoSynthetic Biology Research and Development, Life TechnologiesSynthetic Biology Research and Development, Life TechnologiesDepartment of Microbiology and Immunology, University of California San FranciscoDepartment of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of TechnologyAbstract 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.https://doi.org/10.1038/msb.2013.58compilergenetic circuitpart miningsynthetic biologysystems biology |
| spellingShingle | Virgil A Rhodius Thomas H Segall‐Shapiro Brian D Sharon Amar Ghodasara Ekaterina Orlova Hannah Tabakh David H Burkhardt Kevin Clancy Todd C Peterson Carol A Gross Christopher A Voigt Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters Molecular Systems Biology compiler genetic circuit part mining synthetic biology systems biology |
| 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 |
| topic | compiler genetic circuit part mining synthetic biology systems biology |
| url | https://doi.org/10.1038/msb.2013.58 |
| work_keys_str_mv | AT virgilarhodius designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT thomashsegallshapiro designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT briandsharon designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT amarghodasara designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT ekaterinaorlova designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT hannahtabakh designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT davidhburkhardt designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT kevinclancy designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT toddcpeterson designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT carolagross designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters AT christopheravoigt designoforthogonalgeneticswitchesbasedonacrosstalkmapofssantissandpromoters |