Ribozyme-based insulator parts buffer synthetic circuits from genetic context
Synthetic genetic programs are built from circuits that integrate sensors and implement temporal control of gene expression. Transcriptional circuits are layered by using promoters to carry the signal between circuits. In other words, the output promoter of one circuit serves as the input promoter t...
| Main Authors: | , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2014
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| Online Access: | http://hdl.handle.net/1721.1/89067 https://orcid.org/0000-0003-0844-4776 |
| _version_ | 1826189005955268608 |
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| author | Lou, Chunbo Stanton, Brynne Chen, Ying-Ja Munsky, Brian Voigt, Christopher A. |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Lou, Chunbo Stanton, Brynne Chen, Ying-Ja Munsky, Brian Voigt, Christopher A. |
| author_sort | Lou, Chunbo |
| collection | MIT |
| description | Synthetic genetic programs are built from circuits that integrate sensors and implement temporal control of gene expression. Transcriptional circuits are layered by using promoters to carry the signal between circuits. In other words, the output promoter of one circuit serves as the input promoter to the next. Thus, connecting circuits requires physically connecting a promoter to the next circuit. We show that the sequence at the junction between the input promoter and circuit can affect the input-output response (transfer function) of the circuit. A library of putative sequences that might reduce (or buffer) such context effects, which we refer to as 'insulator parts', is screened in Escherichia coli. We find that ribozymes that cleave the 5′ untranslated region (5′-UTR) of the mRNA are effective insulators. They generate quantitatively identical transfer functions, irrespective of the identity of the input promoter. When these insulators are used to join synthetic gene circuits, the behavior of layered circuits can be predicted using a mathematical model. The inclusion of insulators will be critical in reliably permuting circuits to build different programs. |
| first_indexed | 2024-09-23T08:08:22Z |
| format | Article |
| id | mit-1721.1/89067 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:08:22Z |
| publishDate | 2014 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/890672022-09-30T07:47:08Z Ribozyme-based insulator parts buffer synthetic circuits from genetic context Lou, Chunbo Stanton, Brynne Chen, Ying-Ja Munsky, Brian Voigt, Christopher A. Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Synthetic Biology Center Lou, Chunbo Stanton, Brynne Chen, Ying-Ja Voigt, Christopher A. Synthetic genetic programs are built from circuits that integrate sensors and implement temporal control of gene expression. Transcriptional circuits are layered by using promoters to carry the signal between circuits. In other words, the output promoter of one circuit serves as the input promoter to the next. Thus, connecting circuits requires physically connecting a promoter to the next circuit. We show that the sequence at the junction between the input promoter and circuit can affect the input-output response (transfer function) of the circuit. A library of putative sequences that might reduce (or buffer) such context effects, which we refer to as 'insulator parts', is screened in Escherichia coli. We find that ribozymes that cleave the 5′ untranslated region (5′-UTR) of the mRNA are effective insulators. They generate quantitatively identical transfer functions, irrespective of the identity of the input promoter. When these insulators are used to join synthetic gene circuits, the behavior of layered circuits can be predicted using a mathematical model. The inclusion of insulators will be critical in reliably permuting circuits to build different programs. Life Technologies, Inc. United States. Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4018) United States. Office of Naval Research (N00014-10-1-0245) National Science Foundation (U.S.) (CCF-0943385) National Institutes of Health (U.S.) (AI067699) National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (SynBERC, SA5284-11210) 2014-08-26T16:37:55Z 2014-08-26T16:37:55Z 2012-10 2012-05 Article http://purl.org/eprint/type/JournalArticle 1087-0156 1546-1696 http://hdl.handle.net/1721.1/89067 Lou, Chunbo, Brynne Stanton, Ying-Ja Chen, Brian Munsky, and Christopher A Voigt. “Ribozyme-Based Insulator Parts Buffer Synthetic Circuits from Genetic Context.” Nature Biotechnology 30, no. 11 (October 3, 2012): 1137–1142. https://orcid.org/0000-0003-0844-4776 en_US http://dx.doi.org/10.1038/nbt.2401 Nature Biotechnology Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Nature Publishing Group PMC |
| spellingShingle | Lou, Chunbo Stanton, Brynne Chen, Ying-Ja Munsky, Brian Voigt, Christopher A. Ribozyme-based insulator parts buffer synthetic circuits from genetic context |
| title | Ribozyme-based insulator parts buffer synthetic circuits from genetic context |
| title_full | Ribozyme-based insulator parts buffer synthetic circuits from genetic context |
| title_fullStr | Ribozyme-based insulator parts buffer synthetic circuits from genetic context |
| title_full_unstemmed | Ribozyme-based insulator parts buffer synthetic circuits from genetic context |
| title_short | Ribozyme-based insulator parts buffer synthetic circuits from genetic context |
| title_sort | ribozyme based insulator parts buffer synthetic circuits from genetic context |
| url | http://hdl.handle.net/1721.1/89067 https://orcid.org/0000-0003-0844-4776 |
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