Composability of regulatory sequences controlling transcription and translation in Escherichia coli
The inability to predict heterologous gene expression levels precisely hinders our ability to engineer biological systems. Using well-characterized regulatory elements offers a potential solution only if such elements behave predictably when combined. We synthesized 12,563 combinations of common pro...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences (U.S.)
2014
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| Online Access: | http://hdl.handle.net/1721.1/89095 https://orcid.org/0000-0003-3759-6883 |
| _version_ | 1826209685596798976 |
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| author | Kosuri, Sriram Goodman, Daniel Bryan Cambray, Guillaume Mutalik, Vivek K. Gao, Yuan Arkin, Adam P. Endy, Drew Church, George M. |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology Kosuri, Sriram Goodman, Daniel Bryan Cambray, Guillaume Mutalik, Vivek K. Gao, Yuan Arkin, Adam P. Endy, Drew Church, George M. |
| author_sort | Kosuri, Sriram |
| collection | MIT |
| description | The inability to predict heterologous gene expression levels precisely hinders our ability to engineer biological systems. Using well-characterized regulatory elements offers a potential solution only if such elements behave predictably when combined. We synthesized 12,563 combinations of common promoters and ribosome binding sites and simultaneously measured DNA, RNA, and protein levels from the entire library. Using a simple model, we found that RNA and protein expression were within twofold of expected levels 80% and 64% of the time, respectively. The large dataset allowed quantitation of global effects, such as translation rate on mRNA stability and mRNA secondary structure on translation rate. However, the worst 5% of constructs deviated from prediction by 13-fold on average, which could hinder large-scale genetic engineering projects. The ease and scale this of approach indicates that rather than relying on prediction or standardization, we can screen synthetic libraries for desired behavior. |
| first_indexed | 2024-09-23T14:27:11Z |
| format | Article |
| id | mit-1721.1/89095 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:27:11Z |
| publishDate | 2014 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/890952022-10-01T21:21:16Z Composability of regulatory sequences controlling transcription and translation in Escherichia coli Kosuri, Sriram Goodman, Daniel Bryan Cambray, Guillaume Mutalik, Vivek K. Gao, Yuan Arkin, Adam P. Endy, Drew Church, George M. Harvard University--MIT Division of Health Sciences and Technology Goodman, Daniel Bryan The inability to predict heterologous gene expression levels precisely hinders our ability to engineer biological systems. Using well-characterized regulatory elements offers a potential solution only if such elements behave predictably when combined. We synthesized 12,563 combinations of common promoters and ribosome binding sites and simultaneously measured DNA, RNA, and protein levels from the entire library. Using a simple model, we found that RNA and protein expression were within twofold of expected levels 80% and 64% of the time, respectively. The large dataset allowed quantitation of global effects, such as translation rate on mRNA stability and mRNA secondary structure on translation rate. However, the worst 5% of constructs deviated from prediction by 13-fold on average, which could hinder large-scale genetic engineering projects. The ease and scale this of approach indicates that rather than relying on prediction or standardization, we can screen synthetic libraries for desired behavior. Agilent Technologies Wyss Institute for Biologically Inspired Engineering National Science Foundation (U.S.). Graduate Research Fellowship 2014-08-28T17:31:22Z 2014-08-28T17:31:22Z 2013-08 2013-02 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/89095 Kosuri, S., D. B. Goodman, G. Cambray, V. K. Mutalik, Y. Gao, A. P. Arkin, D. Endy, and G. M. Church. “Composability of Regulatory Sequences Controlling Transcription and Translation in Escherichia Coli.” Proceedings of the National Academy of Sciences 110, no. 34 (August 7, 2013): 14024–14029. https://orcid.org/0000-0003-3759-6883 en_US http://dx.doi.org/10.1073/pnas.1301301110 Proceedings of the National Academy of Sciences 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 National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Kosuri, Sriram Goodman, Daniel Bryan Cambray, Guillaume Mutalik, Vivek K. Gao, Yuan Arkin, Adam P. Endy, Drew Church, George M. Composability of regulatory sequences controlling transcription and translation in Escherichia coli |
| title | Composability of regulatory sequences controlling transcription and translation in Escherichia coli |
| title_full | Composability of regulatory sequences controlling transcription and translation in Escherichia coli |
| title_fullStr | Composability of regulatory sequences controlling transcription and translation in Escherichia coli |
| title_full_unstemmed | Composability of regulatory sequences controlling transcription and translation in Escherichia coli |
| title_short | Composability of regulatory sequences controlling transcription and translation in Escherichia coli |
| title_sort | composability of regulatory sequences controlling transcription and translation in escherichia coli |
| url | http://hdl.handle.net/1721.1/89095 https://orcid.org/0000-0003-3759-6883 |
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