Genomic mining of prokaryotic repressors for orthogonal logic gates
Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply 'part mining' to build a library of 73 TetR...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Nature Publishing Group
2015
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| Online Access: | http://hdl.handle.net/1721.1/99526 https://orcid.org/0000-0003-0844-4776 https://orcid.org/0000-0003-2171-8460 |
| _version_ | 1826202944531333120 |
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| author | Tamsir, Alvin Clancy, Kevin Peterson, Todd Stanton, Brynne C. Nielsen, Alec Andrew Voigt, Christopher A. |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Tamsir, Alvin Clancy, Kevin Peterson, Todd Stanton, Brynne C. Nielsen, Alec Andrew Voigt, Christopher A. |
| author_sort | Tamsir, Alvin |
| collection | MIT |
| description | Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply 'part mining' to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method, and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and exhibit minimal interactions with other promoters. Each repressor-promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOT/NOR gates, there are >10[superscript 54] circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits. |
| first_indexed | 2024-09-23T12:28:12Z |
| format | Article |
| id | mit-1721.1/99526 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T12:28:12Z |
| publishDate | 2015 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/995262022-09-28T08:03:06Z Genomic mining of prokaryotic repressors for orthogonal logic gates Tamsir, Alvin Clancy, Kevin Peterson, Todd Stanton, Brynne C. Nielsen, Alec Andrew Voigt, Christopher A. Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Synthetic Biology Center Stanton, Brynne C. Nielsen, Alec Andrew Voigt, Christopher A. Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply 'part mining' to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method, and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and exhibit minimal interactions with other promoters. Each repressor-promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOT/NOR gates, there are >10[superscript 54] circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits. United States. Air Force Office of Scientific Research (Award FA9550-11-C-0028) American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship (32 CFR 168a) United States. Defense Advanced Research Projects Agency. Chronical of Lineage Indicative of Origins (N66001-12-C-4016) United States. Office of Naval Research (N00014-13-1-0074) National Institutes of Health (U.S.) (GM095765) National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (SA5284-11210) 2015-10-30T15:51:51Z 2015-10-30T15:51:51Z 2013-12 2013-08 Article http://purl.org/eprint/type/JournalArticle 1552-4450 1552-4469 http://hdl.handle.net/1721.1/99526 Stanton, Brynne C, Alec A K Nielsen, Alvin Tamsir, Kevin Clancy, Todd Peterson, and Christopher A Voigt. “Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates.” Nat Chem Biol 10, no. 2 (December 8, 2013): 99–105. https://orcid.org/0000-0003-0844-4776 https://orcid.org/0000-0003-2171-8460 en_US http://dx.doi.org/10.1038/nchembio.1411 Nature Chemical Biology Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Nature Publishing Group PMC |
| spellingShingle | Tamsir, Alvin Clancy, Kevin Peterson, Todd Stanton, Brynne C. Nielsen, Alec Andrew Voigt, Christopher A. Genomic mining of prokaryotic repressors for orthogonal logic gates |
| title | Genomic mining of prokaryotic repressors for orthogonal logic gates |
| title_full | Genomic mining of prokaryotic repressors for orthogonal logic gates |
| title_fullStr | Genomic mining of prokaryotic repressors for orthogonal logic gates |
| title_full_unstemmed | Genomic mining of prokaryotic repressors for orthogonal logic gates |
| title_short | Genomic mining of prokaryotic repressors for orthogonal logic gates |
| title_sort | genomic mining of prokaryotic repressors for orthogonal logic gates |
| url | http://hdl.handle.net/1721.1/99526 https://orcid.org/0000-0003-0844-4776 https://orcid.org/0000-0003-2171-8460 |
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