Distributed implementation of Boolean functions by transcriptional synthetic circuits
Copyright © 2020 American Chemical Society. Starting in the early 2000s, sophisticated technologies have been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in order t...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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American Chemical Society (ACS)
2021
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| Online Access: | https://hdl.handle.net/1721.1/133603 |
| _version_ | 1811086544631496704 |
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| author | Al-Radhawi, M Ali Tran, Anh Phong Ernst, Elizabeth A Chen, Tianchi Voigt, Christopher A Sontag, Eduardo D |
| author_facet | Al-Radhawi, M Ali Tran, Anh Phong Ernst, Elizabeth A Chen, Tianchi Voigt, Christopher A Sontag, Eduardo D |
| author_sort | Al-Radhawi, M Ali |
| collection | MIT |
| description | Copyright © 2020 American Chemical Society. Starting in the early 2000s, sophisticated technologies have been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in order to achieve greater computational power has been hampered by many constraints, including repressor toxicity and the lack of large sets of mutually orthogonal repressors. As a consequence, a typical circuit contains no more than roughly seven repressor-based gates per cell. A possible way around this scalability problem is to distribute the computation among multiple cell types, each of which implements a small subcircuit, which communicate among themselves using diffusible small molecules (DSMs). Examples of DSMs are those employed by quorum sensing systems in bacteria. This paper focuses on systematic ways to implement this distributed approach, in the context of the evaluation of arbitrary Boolean functions. The unique characteristics of genetic circuits and the properties of DSMs require the development of new Boolean synthesis methods, distinct from those classically used in electronic circuit design. In this work, we propose a fast algorithm to synthesize distributed realizations for any Boolean function, under constraints on the number of gates per cell and the number of orthogonal DSMs. The method is based on an exact synthesis algorithm to find the minimal circuit per cell, which in turn allows us to build an extensive database of Boolean functions up to a given number of inputs. For concreteness, we will specifically focus on circuits of up to 4 inputs, which might represent, for example, two chemical inducers and two light inputs at different frequencies. Our method shows that, with a constraint of no more than seven gates per cell, the use of a single DSM increases the total number of realizable circuits by at least 7.58-fold compared to centralized computation. Moreover, when allowing two DSM's, one can realize 99.995% of all possible 4-input Boolean functions, still with at most 7 gates per cell. The methodology introduced here can be readily adapted to complement recent genetic circuit design automation software. A toolbox that uses the proposed algorithm was created and made available at https://github.com/sontaglab/DBC/. |
| first_indexed | 2024-09-23T13:27:39Z |
| format | Article |
| id | mit-1721.1/133603 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T13:27:39Z |
| publishDate | 2021 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/1336032021-10-28T03:51:41Z Distributed implementation of Boolean functions by transcriptional synthetic circuits Al-Radhawi, M Ali Tran, Anh Phong Ernst, Elizabeth A Chen, Tianchi Voigt, Christopher A Sontag, Eduardo D Copyright © 2020 American Chemical Society. Starting in the early 2000s, sophisticated technologies have been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in order to achieve greater computational power has been hampered by many constraints, including repressor toxicity and the lack of large sets of mutually orthogonal repressors. As a consequence, a typical circuit contains no more than roughly seven repressor-based gates per cell. A possible way around this scalability problem is to distribute the computation among multiple cell types, each of which implements a small subcircuit, which communicate among themselves using diffusible small molecules (DSMs). Examples of DSMs are those employed by quorum sensing systems in bacteria. This paper focuses on systematic ways to implement this distributed approach, in the context of the evaluation of arbitrary Boolean functions. The unique characteristics of genetic circuits and the properties of DSMs require the development of new Boolean synthesis methods, distinct from those classically used in electronic circuit design. In this work, we propose a fast algorithm to synthesize distributed realizations for any Boolean function, under constraints on the number of gates per cell and the number of orthogonal DSMs. The method is based on an exact synthesis algorithm to find the minimal circuit per cell, which in turn allows us to build an extensive database of Boolean functions up to a given number of inputs. For concreteness, we will specifically focus on circuits of up to 4 inputs, which might represent, for example, two chemical inducers and two light inputs at different frequencies. Our method shows that, with a constraint of no more than seven gates per cell, the use of a single DSM increases the total number of realizable circuits by at least 7.58-fold compared to centralized computation. Moreover, when allowing two DSM's, one can realize 99.995% of all possible 4-input Boolean functions, still with at most 7 gates per cell. The methodology introduced here can be readily adapted to complement recent genetic circuit design automation software. A toolbox that uses the proposed algorithm was created and made available at https://github.com/sontaglab/DBC/. 2021-10-27T19:53:45Z 2021-10-27T19:53:45Z 2020 2021-09-10T16:46:56Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/133603 en 10.1021/ACSSYNBIO.0C00228 ACS Synthetic Biology Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf American Chemical Society (ACS) bioRxiv |
| spellingShingle | Al-Radhawi, M Ali Tran, Anh Phong Ernst, Elizabeth A Chen, Tianchi Voigt, Christopher A Sontag, Eduardo D Distributed implementation of Boolean functions by transcriptional synthetic circuits |
| title | Distributed implementation of Boolean functions by transcriptional synthetic circuits |
| title_full | Distributed implementation of Boolean functions by transcriptional synthetic circuits |
| title_fullStr | Distributed implementation of Boolean functions by transcriptional synthetic circuits |
| title_full_unstemmed | Distributed implementation of Boolean functions by transcriptional synthetic circuits |
| title_short | Distributed implementation of Boolean functions by transcriptional synthetic circuits |
| title_sort | distributed implementation of boolean functions by transcriptional synthetic circuits |
| url | https://hdl.handle.net/1721.1/133603 |
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