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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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Harmer Z, Thompson JC, Cole DL, Venturelli OS, Zavala VM, McClean MN. Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro. ACS Synth Biol 2024; 13:1424-1433. [PMID: 38684225 PMCID: PMC11106771 DOI: 10.1021/acssynbio.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/31/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation, we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive split transcription factors in the budding yeast, Saccharomyces cerevisiae. We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering.
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Affiliation(s)
- Zachary
P. Harmer
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Jaron C. Thompson
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - David L. Cole
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ophelia S. Venturelli
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Bacteriology, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Victor M. Zavala
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Mathematics
and Computer Science Division, Argonne National
Laboratory, Lemont, Illinois 60439. United States
| | - Megan N. McClean
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
- University
of Wisconsin Carbone Cancer Center, University
of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, United States
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Harmer ZP, Thompson JC, Cole DL, Zavala VM, McClean MN. Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572411. [PMID: 38187522 PMCID: PMC10769237 DOI: 10.1101/2023.12.19.572411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive spit transcription factors in the budding yeast, Saccharomyces cerevisiae . We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering. Graphical abstract
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Harmer Z, McClean MN. Lustro: High-Throughput Optogenetic Experiments Enabled by Automation and a Yeast Optogenetic Toolkit. ACS Synth Biol 2023; 12:1943-1951. [PMID: 37434272 PMCID: PMC10368012 DOI: 10.1021/acssynbio.3c00215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Indexed: 07/13/2023]
Abstract
Optogenetic systems use genetically encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light; however, these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae. We expand the yeast optogenetic toolkit to include variants of the cryptochromes and enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to the high-throughput characterization of optogenetic systems across a range of biological systems and applications.
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Affiliation(s)
- Zachary
P. Harmer
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Megan N. McClean
- Department
of Biomedical Engineering, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
- University
of Wisconsin Carbone Cancer Center, University
of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, United States
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Harmer ZP, McClean MN. Lustro: High-throughput optogenetic experiments enabled by automation and a yeast optogenetic toolkit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536078. [PMID: 37066312 PMCID: PMC10104134 DOI: 10.1101/2023.04.07.536078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Optogenetic systems use genetically-encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light, however these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae . We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to high-throughput characterization of optogenetic systems across a range of biological systems and applications.
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