1
|
Zhang Q, Song L, Fu M, He J, Yang G, Jiang Z. Optogenetics in oral and craniofacial research. J Zhejiang Univ Sci B 2024; 25:656-671. [PMID: 39155779 PMCID: PMC11337086 DOI: 10.1631/jzus.b2300322] [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: 05/10/2023] [Accepted: 10/17/2023] [Indexed: 08/20/2024]
Abstract
Optogenetics combines optics and genetic engineering to control specific gene expression and biological functions and has the advantages of precise spatiotemporal control, noninvasiveness, and high efficiency. Genetically modified photosensory sensors are engineered into proteins to modulate conformational changes with light stimulation. Therefore, optogenetic techniques can provide new insights into oral biological processes at different levels, ranging from the subcellular and cellular levels to neural circuits and behavioral models. Here, we introduce the origins of optogenetics and highlight the recent progress of optogenetic approaches in oral and craniofacial research, focusing on the ability to apply optogenetics to the study of basic scientific neural mechanisms and to establish different oral behavioral test models in vivo (orofacial movement, licking, eating, and drinking), such as channelrhodopsin (ChR), archaerhodopsin (Arch), and halorhodopsin from Natronomonas pharaonis (NpHR). We also review the synergic and antagonistic effects of optogenetics in preclinical studies of trigeminal neuralgia and maxillofacial cellulitis. In addition, optogenetic tools have been used to control the neurogenic differentiation of dental pulp stem cells in translational studies. Although the scope of optogenetic tools is increasing, there are limited large animal experiments and clinical studies in dental research. Potential future directions include exploring therapeutic strategies for addressing loss of taste in patients with coronavirus disease 2019 (COVID-19), studying oral bacterial biofilms, enhancing craniomaxillofacial and periodontal tissue regeneration, and elucidating the possible pathogenesis of dry sockets, xerostomia, and burning mouth syndrome.
Collapse
Affiliation(s)
- Qinmeng Zhang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Luyao Song
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengdie Fu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jin He
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guoli Yang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China.
- Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Zhiwei Jiang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China. ,
- Zhejiang University School of Medicine, Hangzhou 310058, China. ,
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Le Bec M, Pouzet S, Cordier C, Barral S, Scolari V, Sorre B, Banderas A, Hersen P. Optogenetic spatial patterning of cooperation in yeast populations. Nat Commun 2024; 15:75. [PMID: 38168087 PMCID: PMC10761962 DOI: 10.1038/s41467-023-44379-5] [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: 05/17/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial communities are shaped by complex metabolic interactions such as cooperation and competition for resources. Methods to control such interactions could lead to major advances in our ability to better engineer microbial consortia for synthetic biology applications. Here, we use optogenetics to control SUC2 invertase production in yeast, thereby shaping spatial assortment of cooperator and cheater cells. Yeast cells behave as cooperators (i.e., transform sucrose into hexose, a public good) upon blue light illumination or cheaters (i.e., consume hexose produced by cooperators to grow) in the dark. We show that cooperators benefit best from the hexoses they produce when their domain size is constrained between two cut-off length-scales. From an engineering point of view, the system behaves as a bandpass filter. The lower limit is the trace of cheaters' competition for hexoses, while the upper limit is defined by cooperators' competition for sucrose. Cooperation mostly occurs at the frontiers with cheater cells, which not only compete for hexoses but also cooperate passively by letting sucrose reach cooperators. We anticipate that this optogenetic method could be applied to shape metabolic interactions in a variety of microbial ecosystems.
Collapse
Affiliation(s)
- Matthias Le Bec
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Sylvain Pouzet
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Céline Cordier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Simon Barral
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Vittore Scolari
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005, Paris, France
| | - Benoit Sorre
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Alvaro Banderas
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
| | - Pascal Hersen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
| |
Collapse
|
4
|
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
Collapse
|
5
|
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: 5] [Impact Index Per Article: 5.0] [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.
Collapse
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
| |
Collapse
|
6
|
Portius M, Danneberg C, Pompe T. Biomaterial approaches for engineering and analyzing structure and metabolic states of microbial consortia within biofilms. Curr Opin Biotechnol 2023; 81:102916. [PMID: 36870250 DOI: 10.1016/j.copbio.2023.102916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/25/2023] [Accepted: 02/03/2023] [Indexed: 03/06/2023]
Abstract
Microbial consortia within biofilms are frequently found in structured organization in nature and are thought to bear great potential for productive biotechnological applications, such as the degradation of complex substrates, biosensing, or the production of chemical compounds. However, in-depth understanding of their organizational principles, as well as comprehensive design criteria of structured microbial consortia for industrial applications are still limited. It is hypothesized that biomaterial engineering of such consortia within scaffolds can advance the field by providing defined in vitro mimics of naturally occurring and industrially applicable biofilms. Such systems will allow for adjustment of important microenvironmental parameters and in-depth analysis with high temporal and spatial resolution. In this review, we provide the background of biomaterial engineering of structured biofilm consortia, show approaches for their design, and demonstrate tools to analyze their metabolic state.
Collapse
Affiliation(s)
- Matthias Portius
- Institute of Biochemistry, Leipzig University, Germany; Research and Transfer Center for Bioactive Matter, bioACTmatter, Leipzig University, Germany
| | | | - Tilo Pompe
- Institute of Biochemistry, Leipzig University, Germany; Research and Transfer Center for Bioactive Matter, bioACTmatter, Leipzig University, Germany.
| |
Collapse
|
7
|
Sheets MB, Tague N, Dunlop MJ. An optogenetic toolkit for light-inducible antibiotic resistance. Nat Commun 2023; 14:1034. [PMID: 36823420 PMCID: PMC9950086 DOI: 10.1038/s41467-023-36670-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Antibiotics are a key control mechanism for synthetic biology and microbiology. Resistance genes are used to select desired cells and regulate bacterial populations, however their use to-date has been largely static. Precise spatiotemporal control of antibiotic resistance could enable a wide variety of applications that require dynamic control of susceptibility and survival. Here, we use light-inducible Cre recombinase to activate expression of drug resistance genes in Escherichia coli. We demonstrate light-activated resistance to four antibiotics: carbenicillin, kanamycin, chloramphenicol, and tetracycline. Cells exposed to blue light survive in the presence of lethal antibiotic concentrations, while those kept in the dark do not. To optimize resistance induction, we vary promoter, ribosome binding site, and enzyme variant strength using chromosome and plasmid-based constructs. We then link inducible resistance to expression of a heterologous fatty acid enzyme to increase production of octanoic acid. These optogenetic resistance tools pave the way for spatiotemporal control of cell survival.
Collapse
Affiliation(s)
- Michael B Sheets
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Nathan Tague
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Biological Design Center, Boston University, Boston, MA, 02215, USA.
| |
Collapse
|
8
|
Rojas V, Larrondo LF. Coupling Cell Communication and Optogenetics: Implementation of a Light-Inducible Intercellular System in Yeast. ACS Synth Biol 2023; 12:71-82. [PMID: 36534043 PMCID: PMC9872819 DOI: 10.1021/acssynbio.2c00338] [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: 06/28/2022] [Indexed: 12/23/2022]
Abstract
Cell communication is a widespread mechanism in biology, allowing the transmission of information about environmental conditions. In order to understand how cell communication modulates relevant biological processes such as survival, division, differentiation, and apoptosis, different synthetic systems based on chemical induction have been successfully developed. In this work, we coupled cell communication and optogenetics in the budding yeast Saccharomyces cerevisiae. Our approach is based on two strains connected by the light-dependent production of α-factor pheromone in one cell type, which induces gene expression in the other type. After the individual characterization of the different variants of both strains, the optogenetic intercellular system was evaluated by combining the cells under contrasting illumination conditions. Using luciferase as a reporter gene, specific co-cultures at a 1:1 ratio displayed activation of the response upon constant blue light, which was not observed for the same cell mixtures grown in darkness. Then, the system was assessed at several dark/blue-light transitions, where the response level varies depending on the moment in which illumination was delivered. Furthermore, we observed that the amplitude of response can be tuned by modifying the initial ratio between both strains. Finally, the two-population system showed higher fold inductions in comparison with autonomous strains. Altogether, these results demonstrated that external light information is propagated through a diffusible signaling molecule to modulate gene expression in a synthetic system involving microbial cells, which will pave the road for studies allowing optogenetic control of population-level dynamics.
Collapse
Affiliation(s)
- Vicente Rojas
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Luis F. Larrondo
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| |
Collapse
|
9
|
Figueroa D, Baeza C, Ruiz D, Inzunza C, Romero A, Toro R, Salinas F. Expanding the molecular versatility of an optogenetic switch in yeast. Front Bioeng Biotechnol 2022; 10:1029217. [PMID: 36457859 PMCID: PMC9705753 DOI: 10.3389/fbioe.2022.1029217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, the FUN-LOV (FUNgal Light Oxygen and Voltage) optogenetic switch enables high levels of light-activated gene expression in a reversible and tunable fashion. The FUN-LOV components, under identical promoter and terminator sequences, are encoded in two different plasmids, which limits its future applications in wild and industrial yeast strains. In this work, we aim to expand the molecular versatility of the FUN-LOV switch to increase its biotechnological applications. Initially, we generated new variants of this system by replacing the promoter and terminator sequences and by cloning the system in a single plasmid (FUN-LOVSP). In a second step, we included the nourseothricin (Nat) or hygromycin (Hph) antibiotic resistances genes in the new FUN-LOVSP plasmid, generating two new variants (FUN-LOVSP-Nat and FUN-LOVSP-Hph), to allow selection after genome integration. Then, we compared the levels of light-activated expression for each FUN-LOV variants using the luciferase reporter gene in the BY4741 yeast strain. The results indicate that FUN-LOVSP-Nat and FUN-LOVSP-Hph, either episomally or genome integrated, reached higher levels of luciferase expression upon blue-light stimulation compared the original FUN-LOV system. Finally, we demonstrated the functionality of FUN-LOVSP-Hph in the 59A-EC1118 wine yeast strain, showing similar levels of reporter gene induction under blue-light respect to the laboratory strain, and with lower luciferase expression background in darkness condition. Altogether, the new FUN-LOV variants described here are functional in different yeast strains, expanding the biotechnological applications of this optogenetic tool.
Collapse
Affiliation(s)
- David Figueroa
- Laboratorio de Genómica Funcional, Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Camila Baeza
- Laboratorio de Genómica Funcional, Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Diego Ruiz
- Laboratorio de Genómica Funcional, Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Claudia Inzunza
- Laboratorio de Genómica Funcional, Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Andrés Romero
- Laboratorio de Genómica Funcional, Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Rodrigo Toro
- Laboratorio de Genómica Funcional, Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Francisco Salinas
- Laboratorio de Genómica Funcional, Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| |
Collapse
|
10
|
Kumar S, Khammash M. Platforms for Optogenetic Stimulation and Feedback Control. Front Bioeng Biotechnol 2022; 10:918917. [PMID: 35757811 PMCID: PMC9213687 DOI: 10.3389/fbioe.2022.918917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the potential of optogenetics in biology requires methodologies from different disciplines ranging from biology, to mechatronics engineering, to control engineering. Light stimulation of a synthetic optogenetic construct in a given biological species can only be achieved via a suitable light stimulation platform. Emerging optogenetic applications entail a consistent, reproducible, and regulated delivery of light adapted to the application requirement. In this review, we explore the evolution of light-induction hardware-software platforms from simple illumination set-ups to sophisticated microscopy, microtiter plate and bioreactor designs, and discuss their respective advantages and disadvantages. Here, we examine design approaches followed in performing optogenetic experiments spanning different cell types and culture volumes, with induction capabilities ranging from single cell stimulation to entire cell culture illumination. The development of automated measurement and stimulation schemes on these platforms has enabled researchers to implement various in silico feedback control strategies to achieve computer-controlled living systems—a theme we briefly discuss in the last part of this review.
Collapse
Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
| |
Collapse
|
11
|
Mazraeh D, Di Ventura B. Synthetic microbiology applications powered by light. Curr Opin Microbiol 2022; 68:102158. [PMID: 35660240 DOI: 10.1016/j.mib.2022.102158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
Synthetic biology is a field of research in which molecular parts (mostly nucleic acids and proteins) are de novo created or modified and then used either alone or in combination to achieve new functions that can help solve the problems of our modern society. In synthetic microbiology, microbes are employed rather than other organisms or cell-free systems. Optogenetics, a relatively recently established technology that relies on the use of genetically encoded photosensitive proteins to control biological processes with high spatiotemporal precision, offers the possibility to empower synthetic (micro)biology applications due to the many positive features that light has as an external trigger. In this review, we describe recent synthetic microbiology applications that made use of optogenetics after briefly introducing the molecular mechanism behind some of the most employed optogenetic tools. We highlight the power and versatility of this technique, which opens up new horizons for both research and industry.
Collapse
Affiliation(s)
- Daniel Mazraeh
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
| |
Collapse
|