1
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Kang H, Park D, Kim J. Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs. Nucleic Acids Res 2024; 52:8595-8608. [PMID: 38943344 DOI: 10.1093/nar/gkae549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
The CRISPR-Cas system provides a versatile RNA-guided approach for a broad range of applications. Thanks to advances in RNA synthetic biology, the engineering of guide RNAs (gRNAs) has enabled the conditional control of the CRISPR-Cas system. However, achieving precise regulation of the CRISPR-Cas system for efficient modulation of internal metabolic processes remains challenging. In this work, we developed a robust dCas9 regulator with engineered conditional gRNAs to enable tight control of endogenous genes. Our conditional gRNAs in Escherichia coli can control gene expression upon specific interaction with trigger RNAs with a dynamic range as high as 130-fold, evaluating up to a three-input logic A OR (B AND C). The conditional gRNA-mediated targeting of endogenous metabolic genes, lacZ, malT and poxB, caused differential regulation of growth in Escherichia coli via metabolic flux control. Further, conditional gRNAs could regulate essential cytoskeleton genes, ftsZ and mreB, to control cell filamentation and division. Finally, three types of two-input logic gates could be applied for the conditional control of ftsZ regulation, resulting in morphological changes. The successful operation and application of conditional gRNAs based on programmable RNA interactions suggests that our system could be compatible with other Cas-effectors and implemented in other host organisms.
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Affiliation(s)
- Hansol Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Dongwon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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2
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Ranzani AT, Buchholz K, Blackholm M, Kopkin H, Möglich A. Induction of bacterial expression at the mRNA level by light. Nucleic Acids Res 2024:gkae678. [PMID: 39126322 DOI: 10.1093/nar/gkae678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/17/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Vital organismal processes, including development, differentiation and adaptation, involve altered gene expression. Although expression is frequently controlled at the transcriptional stage, various regulation mechanisms operate at downstream levels. Here, we leverage the photoreceptor NmPAL to optogenetically induce RNA refolding and the translation of bacterial mRNAs. Blue-light-triggered NmPAL binding disrupts a cis-repressed mRNA state, thereby relieves obstruction of translation initiation, and upregulates gene expression. Iterative probing and optimization of the circuit, dubbed riboptoregulator, enhanced induction to 30-fold. Given action at the mRNA level, the riboptoregulator can differentially regulate individual structural genes within polycistronic operons. Moreover, it is orthogonal to and can be wed with other gene-regulatory circuits for nuanced and more stringent gene-expression control. We thus advance the pAurora2 circuit that combines transcriptional and translational mechanisms to optogenetically increase bacterial gene expression by >1000-fold. The riboptoregulator strategy stands to upgrade numerous regulatory circuits and widely applies to expression control in microbial biotechnology, synthetic biology and materials science.
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Affiliation(s)
- Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Konrad Buchholz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Marius Blackholm
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Hayat Kopkin
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447 Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, 95447 Bayreuth, Germany
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3
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Liu M, Li Z, Huang J, Yan J, Zhao G, Zhang Y. OptoLacI: optogenetically engineered lactose operon repressor LacI responsive to light instead of IPTG. Nucleic Acids Res 2024; 52:8003-8016. [PMID: 38860425 PMCID: PMC11260447 DOI: 10.1093/nar/gkae479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Optogenetics' advancement has made light induction attractive for controlling biological processes due to its advantages of fine-tunability, reversibility, and low toxicity. The lactose operon induction system, commonly used in Escherichia coli, relies on the binding of lactose or isopropyl β-d-1-thiogalactopyranoside (IPTG) to the lactose repressor protein LacI, playing a pivotal role in controlling the lactose operon. Here, we harnessed the light-responsive light-oxygen-voltage 2 (LOV2) domain from Avena sativa phototropin 1 as a tool for light control and engineered LacI into two light-responsive variants, OptoLacIL and OptoLacID. These variants exhibit direct responsiveness to light and darkness, respectively, eliminating the need for IPTG. Building upon OptoLacI, we constructed two light-controlled E. coli gene expression systems, OptoE.coliLight system and OptoE.coliDark system. These systems enable bifunctional gene expression regulation in E. coli through light manipulation and show superior controllability compared to IPTG-induced systems. We applied the OptoE.coliDark system to protein production and metabolic flux control. Protein production levels are comparable to those induced by IPTG. Notably, the titers of dark-induced production of 1,3-propanediol (1,3-PDO) and ergothioneine exceeded 110% and 60% of those induced by IPTG, respectively. The development of OptoLacI will contribute to the advancement of the field of optogenetic protein engineering, holding substantial potential applications across various fields.
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Affiliation(s)
- Meizi Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Zuhui Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- School of Biological Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jianfeng Huang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Junjun Yan
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yanfei Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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4
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Zhang H, Xiong X, Guo K, Zheng M, Cao T, Yang Y, Song J, Cen J, Zhang J, Jiang Y, Feng S, Tian L, Li X. A rapid aureochrome opto-switch enables diatom acclimation to dynamic light. Nat Commun 2024; 15:5578. [PMID: 38956103 PMCID: PMC11219949 DOI: 10.1038/s41467-024-49991-7] [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: 08/28/2023] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Diatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The identities and operational mechanisms of regulatory factors governing diatom acclimation to high light stress remain largely elusive. Here, we identified the AUREO1c protein from the coastal diatom Phaeodactylum tricornutum as a crucial regulator of non-photochemical quenching (NPQ), a photoprotective mechanism that dissipates excess energy as heat. AUREO1c detects light stress using a light-oxygen-voltage (LOV) domain and directly activates the expression of target genes, including LI818 genes that encode NPQ effector proteins, via its bZIP DNA-binding domain. In comparison to a kinase-mediated pathway reported in the freshwater green alga Chlamydomonas reinhardtii, the AUREO1c pathway exhibits a faster response and enables accumulation of LI818 transcript and protein levels to comparable degrees between continuous high-light and fluctuating-light treatments. We propose that the AUREO1c-LI818 pathway contributes to the resilience of diatoms under dynamic light conditions.
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Affiliation(s)
- Huan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaofeng Xiong
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Kangning Guo
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Mengyuan Zheng
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Tianjun Cao
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuqing Yang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jiaojiao Song
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jie Cen
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jiahuan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yanyou Jiang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shan Feng
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Lijin Tian
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Xiaobo Li
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
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5
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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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6
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Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
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Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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7
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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8
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Blanch-Asensio M, Tadimarri VS, Wilk A, Sankaran S. Discovery of a high-performance phage-derived promoter/repressor system for probiotic lactobacillus engineering. Microb Cell Fact 2024; 23:42. [PMID: 38326819 PMCID: PMC10848424 DOI: 10.1186/s12934-024-02302-7] [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: 12/05/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND The Lactobacillaceae family comprises many species of great importance for the food and healthcare industries, with numerous strains identified as beneficial for humans and used as probiotics. Hence, there is a growing interest in engineering these probiotic bacteria as live biotherapeutics for animals and humans. However, the genetic parts needed to regulate gene expression in these bacteria remain limited compared to model bacteria like E. coli or B. subtilis. To address this deficit, in this study, we selected and tested several bacteriophage-derived genetic parts with the potential to regulate transcription in lactobacilli. RESULTS We screened genetic parts from 6 different lactobacilli-infecting phages and identified one promoter/repressor system with unprecedented functionality in Lactiplantibacillus plantarum WCFS1. The phage-derived promoter was found to achieve expression levels nearly 9-fold higher than the previously reported strongest promoter in this strain and the repressor was able to almost completely repress this expression by reducing it nearly 500-fold. CONCLUSIONS The new parts and insights gained from their engineering will enhance the genetic programmability of lactobacilli for healthcare and industrial applications.
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Affiliation(s)
- Marc Blanch-Asensio
- Bioprogrammable Materials, INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Saarland University, 66123, Saarbrücken, Germany
| | - Varun Sai Tadimarri
- Bioprogrammable Materials, INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Saarland University, 66123, Saarbrücken, Germany
| | - Alina Wilk
- Bioprogrammable Materials, INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Saarland University, 66123, Saarbrücken, Germany
| | - Shrikrishnan Sankaran
- Bioprogrammable Materials, INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany.
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9
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Niu L, Yu L, Jin C, Jin K, Liu Z, Zhu T, Zhu X, Zhang Y, Wu Y. Living Materials Based Dynamic Information Encryption via Light-Inducible Bacterial Biosynthesis of Quantum Dots. Angew Chem Int Ed Engl 2024; 63:e202315251. [PMID: 38085166 DOI: 10.1002/anie.202315251] [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: 10/10/2023] [Indexed: 01/10/2024]
Abstract
Microbial biosynthesis, as an alternative method for producing quantum dots (QDs), has gained attention because it can be conducted under mild and environmentally friendly conditions, distinguishing it from conventional chemical and physical synthesis approaches. However, there is currently no method to selectively control this biosynthesis process in a subset of microbes within a population using external stimuli. In this study, we have attained precise and selective control over the microbial biosynthesis of QDs through the utilization of an optogenetically engineered Escherichia coli (E. coli). The recombinant E. coli is designed to express smCSE enzyme, under the regulation of eLightOn system, which can be activated by blue light. The smCSE enzymes use L-cysteine and Cd2+ as substrates to form CdS QDs. This system enables light-inducible bacterial biosynthesis of QDs in precise patterns within a hydrogel for information encryption. As the biosynthesis progresses, the optical characteristics of the QDs change, allowing living materials containing the recombinant E. coli to display time-dependent patterns that self-destruct after reading. Compared to static encryption using fluorescent QD inks, dynamic information encryption based on living materials offers enhanced security.
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Affiliation(s)
- Luqi Niu
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
| | - Lin Yu
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
- School of Medicine, Shanghai University, Nanchen Rd. 333, Shanghai, China
| | - Chenyang Jin
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
| | - Kai Jin
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
| | - Zhen Liu
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
| | - Tao Zhu
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
| | - Xiaohui Zhu
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
| | - Yong Zhang
- Department of Biomedical Engineering, The City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Yihan Wu
- Department of Environmental and Chemical Engineering, Shanghai University, Nanchen Rd. 333, Shanghai, China
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10
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Mathony J, Aschenbrenner S, Becker P, Niopek D. Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303496. [PMID: 37562980 PMCID: PMC10558690 DOI: 10.1002/advs.202303496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Domain insertion engineering is a promising approach to recombine the functions of evolutionarily unrelated proteins. Insertion of light-switchable receptor domains into a selected effector protein, for instance, can yield allosteric effectors with light-dependent activity. However, the parameters that determine domain insertion tolerance and allostery are poorly understood. Here, an unbiased screen is used to systematically assess the domain insertion permissibility of several evolutionary unrelated proteins. Training machine learning models on the resulting data allow to dissect features informative for domain insertion tolerance and revealed sequence conservation statistics as the strongest indicators of suitable insertion sites. Finally, extending the experimental pipeline toward the identification of switchable hybrids results in opto-chemogenetic derivatives of the transcription factor AraC that function as single-protein Boolean logic gates. The study reveals determinants of domain insertion tolerance and yielded multimodally switchable proteins with unique functional properties.
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Affiliation(s)
- Jan Mathony
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Sabine Aschenbrenner
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Philipp Becker
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Dominik Niopek
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
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11
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Nagasawa Y, Ueda HH, Kawabata H, Murakoshi H. LOV2-based photoactivatable CaMKII and its application to single synapses: Local Optogenetics. Biophys Physicobiol 2023; 20:e200027. [PMID: 38496236 PMCID: PMC10941968 DOI: 10.2142/biophysico.bppb-v20.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/02/2023] [Indexed: 03/19/2024] Open
Abstract
Optogenetic techniques offer a high spatiotemporal resolution to manipulate cellular activity. For instance, Channelrhodopsin-2 with global light illumination is the most widely used to control neuronal activity at the cellular level. However, the cellular scale is much larger than the diffraction limit of light (<1 μm) and does not fully exploit the features of the "high spatial resolution" of optogenetics. For instance, until recently, there were no optogenetic methods to induce synaptic plasticity at the level of single synapses. To address this, we developed an optogenetic tool named photoactivatable CaMKII (paCaMKII) by fusing a light-sensitive domain (LOV2) to CaMKIIα, which is a protein abundantly expressed in neurons of the cerebrum and hippocampus and essential for synaptic plasticity. Combining photoactivatable CaMKII with two-photon excitation, we successfully activated it in single spines, inducing synaptic plasticity (long-term potentiation) in hippocampal neurons. We refer to this method as "Local Optogenetics", which involves the local activation of molecules and measurement of cellular responses. In this review, we will discuss the characteristics of LOV2, the recent development of its derivatives, and the development and application of paCaMKII.
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Affiliation(s)
- Yutaro Nagasawa
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hiromi H Ueda
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Haruka Kawabata
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hideji Murakoshi
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
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12
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Arancibia D, Pol I, Vargas-Fernández M, Zárate RV, Signorelli JR, Zamorano P. OPTO-BLUE: An Integrated Bidirectional Optogenetic Lentiviral Platform for Controlled Light-Induced Gene Expression. Int J Mol Sci 2023; 24:ijms24119537. [PMID: 37298488 DOI: 10.3390/ijms24119537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Regulated systems for transgene expression are useful tools in basic research and a promising platform in biomedicine due to their regulated transgene expression by an inducer. The emergence of optogenetics expression systems enabled the construction of light-switchable systems, enhancing the spatial and temporal resolution of a transgene. The LightOn system is an optogenetic tool that regulates the expression of a gene of interest using blue light as an inducer. This system is based on a photosensitive protein (GAVPO), which dimerizes and binds to the UASG sequence in response to blue light, triggering the expression of a downstream transgene. Previously, we adapted the LightOn system to a dual lentiviral vector system for neurons. Here, we continue the optimization and assemble all components of the LightOn system into a single lentiviral plasmid, the OPTO-BLUE system. For functional validation, we used enhanced green fluorescent protein (EGFP) as an expression reporter (OPTO-BLUE-EGFP) and evaluated the efficiency of EGFP expression by transfection and transduction in HEK293-T cells exposed to continuous blue-light illumination. Altogether, these results prove that the optimized OPTO-BLUE system allows the light-controlled expression of a reporter protein according to a specific time and light intensity. Likewise, this system should provide an important molecular tool to modulate gene expression of any protein by blue light.
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Affiliation(s)
- Duxan Arancibia
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Iracy Pol
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Martín Vargas-Fernández
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Rafaella V Zárate
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
- Instituto Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Janetti R Signorelli
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Pedro Zamorano
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
- Instituto Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile
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13
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Mao M, Qian Y, Zhang W, Zhou S, Wang Z, Chen X, Yang Y. Controlling protein stability with SULI, a highly sensitive tag for stabilization upon light induction. Nat Commun 2023; 14:2172. [PMID: 37061509 PMCID: PMC10105765 DOI: 10.1038/s41467-023-37830-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Optogenetics tools for precise temporal and spatial control of protein abundance are valuable in studying diverse complex biological processes. In the present study, we engineer a monomeric tag of stabilization upon light induction (SULI) for yeast and zebrafish based on a single light-oxygen-voltage domain from Neurospora crassa. Proteins of interest fused with SULI are stable upon light illumination but are readily degraded after transfer to dark conditions. SULI shows a high dynamic range and a high tolerance to fusion at different positions of the target protein. Further studies reveal that SULI-mediated degradation occurs through a lysine ubiquitination-independent proteasome pathway. We demonstrate the usefulness of SULI in controlling the cell cycle in yeast and regulating protein stability in zebrafish, respectively. Overall, our data indicate that SULI is a simple and robust tool to quantitatively and spatiotemporally modulate protein levels for biotechnological or biomedical applications.
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Affiliation(s)
- Miaowei Mao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yajie Qian
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Wenyao Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Siyu Zhou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Zefeng Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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14
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Qian Y, Li T, Zhou S, Chen X, Yang Y. A Single-Component Optogenetic Gal4-UAS System Allows Stringent Control of Gene Expression in Zebrafish and Drosophila. ACS Synth Biol 2023; 12:664-671. [PMID: 36891673 PMCID: PMC10029753 DOI: 10.1021/acssynbio.2c00410] [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: 07/30/2022] [Indexed: 03/10/2023]
Abstract
The light-regulated Gal4-UAS system has offered new ways to control cellular activities with precise spatial and temporal resolution in zebrafish and Drosophila. However, the existing optogenetic Gal4-UAS systems suffer from having multiple protein components and a dependence on extraneous light-sensitive cofactors, which increase the technical complexity and limit the portability of these systems. To overcome these limitations, we herein describe the development of a novel optogenetic Gal4-UAS system (ltLightOn) for both zebrafish and Drosophila based on a single light-switchable transactivator, termed GAVPOLT, which dimerizes and binds to gene promoters to activate transgene expression upon blue light illumination. The ltLightOn system is independent of exogenous cofactors and exhibits a more than 2400-fold ON/OFF gene expression ratio, allowing quantitative, spatial, and temporal control of gene expression. We further demonstrate the usefulness of the ltLightOn system in regulating zebrafish embryonic development by controlling the expression of lefty1 by light. We believe that this single-component optogenetic system will be immensely useful in understanding the gene function and behavioral circuits in zebrafish and Drosophila.
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Affiliation(s)
- Yajie Qian
- Optogenetics
& Synthetic Biology Interdisciplinary Research Center, State Key
Laboratory of Bioreactor Engineering, East
China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
- Shanghai
Frontiers Science Center of Optogenetic Techniques for Cell Metabolism,
School of Pharmacy, East China University
of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Ting Li
- Optogenetics
& Synthetic Biology Interdisciplinary Research Center, State Key
Laboratory of Bioreactor Engineering, East
China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
- Shanghai
Frontiers Science Center of Optogenetic Techniques for Cell Metabolism,
School of Pharmacy, East China University
of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Siyu Zhou
- Optogenetics
& Synthetic Biology Interdisciplinary Research Center, State Key
Laboratory of Bioreactor Engineering, East
China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
- Shanghai
Frontiers Science Center of Optogenetic Techniques for Cell Metabolism,
School of Pharmacy, East China University
of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Xianjun Chen
- Optogenetics
& Synthetic Biology Interdisciplinary Research Center, State Key
Laboratory of Bioreactor Engineering, East
China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
- Shanghai
Frontiers Science Center of Optogenetic Techniques for Cell Metabolism,
School of Pharmacy, East China University
of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
| | - Yi Yang
- Optogenetics
& Synthetic Biology Interdisciplinary Research Center, State Key
Laboratory of Bioreactor Engineering, East
China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
- Shanghai
Frontiers Science Center of Optogenetic Techniques for Cell Metabolism,
School of Pharmacy, East China University
of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
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15
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Multamäki E, García de Fuentes A, Sieryi O, Bykov A, Gerken U, Ranzani A, Köhler J, Meglinski I, Möglich A, Takala H. Optogenetic Control of Bacterial Expression by Red Light. ACS Synth Biol 2022; 11:3354-3367. [PMID: 35998606 PMCID: PMC9594775 DOI: 10.1021/acssynbio.2c00259] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In optogenetics, as in nature, sensory photoreceptors serve to control cellular processes by light. Bacteriophytochrome (BphP) photoreceptors sense red and far-red light via a biliverdin chromophore and, in response, cycle between the spectroscopically, structurally, and functionally distinct Pr and Pfr states. BphPs commonly belong to two-component systems that control the phosphorylation of cognate response regulators and downstream gene expression through histidine kinase modules. We recently demonstrated that the paradigm BphP from Deinococcus radiodurans exclusively acts as a phosphatase but that its photosensory module can control the histidine kinase activity of homologous receptors. Here, we apply this insight to reprogram two widely used setups for bacterial gene expression from blue-light to red-light control. The resultant pREDusk and pREDawn systems allow gene expression to be regulated down and up, respectively, uniformly under red light by 100-fold or more. Both setups are realized as portable, single plasmids that encode all necessary components including the biliverdin-producing machinery. The triggering by red light affords high spatial resolution down to the single-cell level. As pREDusk and pREDawn respond sensitively to red light, they support multiplexing with optogenetic systems sensitive to other light colors. Owing to the superior tissue penetration of red light, the pREDawn system can be triggered at therapeutically safe light intensities through material layers, replicating the optical properties of the skin and skull. Given these advantages, pREDusk and pREDawn enable red-light-regulated expression for diverse use cases in bacteria.
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Affiliation(s)
- Elina Multamäki
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland
| | | | - Oleksii Sieryi
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Alexander Bykov
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Uwe Gerken
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | | | - Jürgen Köhler
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | - Igor Meglinski
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland,College
of Engineering and Physical Sciences, Aston
University, Birmingham B4 7ET, U.K.
| | - Andreas Möglich
- Lehrstuhl
für Biochemie, Photobiochemie, Universität
Bayreuth, Bayreuth 95447, Germany,. Phone: +49 921 55
7835
| | - Heikki Takala
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland,Department
of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla 40014, Finland,. Phone: +358 46 923 6211
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16
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Ranzani AT, Wehrmann M, Kaiser J, Juraschitz M, Weber AM, Pietruschka G, Gerken U, Mayer G, Möglich A. Light-Dependent Control of Bacterial Expression at the mRNA Level. ACS Synth Biol 2022; 11:3482-3492. [PMID: 36129831 DOI: 10.1021/acssynbio.2c00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sensory photoreceptors mediate numerous light-dependent adaptations across organisms. In optogenetics, photoreceptors achieve the reversible, non-invasive, and spatiotemporally precise control by light of gene expression and other cellular processes. The light-oxygen-voltage receptor PAL binds to small RNA aptamers with sequence specificity upon blue-light illumination. By embedding the responsive aptamer in the ribosome-binding sequence of genes of interest, their expression can be downregulated by light. We developed the pCrepusculo and pAurora optogenetic systems that are based on PAL and allow to down- and upregulate, respectively, bacterial gene expression using blue light. Both systems are realized as compact, single plasmids that exhibit stringent blue-light responses with low basal activity and up to several 10-fold dynamic range. As PAL exerts light-dependent control at the RNA level, it can be combined with other optogenetic circuits that control transcription initiation. By integrating regulatory mechanisms operating at the DNA and mRNA levels, optogenetic circuits with emergent properties can thus be devised. As a case in point, the pEnumbra setup permits to upregulate gene expression under moderate blue light whereas strong blue light shuts off expression again. Beyond providing novel signal-responsive expression systems for diverse applications in biotechnology and synthetic biology, our work also illustrates how the light-dependent PAL-aptamer interaction can be harnessed for the control and interrogation of RNA-based processes.
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Affiliation(s)
- Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Markus Wehrmann
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Jennifer Kaiser
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Marc Juraschitz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Anna M Weber
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany
| | - Georg Pietruschka
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany
| | - Uwe Gerken
- Lehrstuhl für Spektroskopie weicher Materie, University of Bayreuth, 95447 Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany.,Center of Aptamer Research & Development, University of Bonn, 53121 Bonn, Germany
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.,Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447 Bayreuth, Germany.,North-Bavarian NMR Center, Universität Bayreuth, 95447 Bayreuth, Germany
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17
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
- *Correspondence: Andreas Möglich,
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18
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Lee TA, Steel H. Cybergenetic control of microbial community composition. Front Bioeng Biotechnol 2022; 10:957140. [PMID: 36277404 PMCID: PMC9582452 DOI: 10.3389/fbioe.2022.957140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The use of bacterial communities in bioproduction instead of monocultures has potential advantages including increased productivity through division of labour, ability to utilise cheaper substrates, and robustness against perturbations. A key challenge in the application of engineered bacterial communities is the ability to reliably control the composition of the community in terms of its constituent species. This is crucial to prevent faster growing species from outcompeting others with a lower relative fitness, and to ensure that all species are present at an optimal ratio during different steps in a biotechnological process. In contrast to purely biological approaches such as synthetic quorum sensing circuits or paired auxotrophies, cybergenetic control techniques - those in which computers interface with living cells-are emerging as an alternative approach with many advantages. The community composition is measured through methods such as fluorescence intensity or flow cytometry, with measured data fed real-time into a computer. A control action is computed using a variety of possible control algorithms and then applied to the system, with actuation taking the form of chemical (e.g., inducers, nutrients) or physical (e.g., optogenetic, mechanical) inputs. Subsequent changes in composition are then measured and the cycle repeated, maintaining or driving the system to a desired state. This review discusses recent and future developments in methods for implementing cybergenetic control systems, contrasts their capabilities with those of traditional biological methods of population control, and discusses future directions and outstanding challenges for the field.
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19
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McCue AC, Kuhlman B. Design and engineering of light-sensitive protein switches. Curr Opin Struct Biol 2022; 74:102377. [PMID: 35461160 PMCID: PMC9968517 DOI: 10.1016/j.sbi.2022.102377] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 11/03/2022]
Abstract
Engineered, light-sensitive protein switches are used to interrogate a broad variety of biological processes. These switches are typically constructed by genetically fusing naturally occurring light-responsive protein domains with functional domains from other proteins. Protein activity can be controlled using a variety of mechanisms including light-induced colocalization, caging, and allosteric regulation. Protein design efforts have focused on reducing background signaling, maximizing the change in activity upon light stimulation, and perturbing the kinetics of switching. It is common to combine structure-based modeling with experimental screening to identify ideal fusion points between domains and discover point mutations that optimize switching. Here, we introduce commonly used light-sensitive domains and summarize recent progress in using them to regulate protein activity.
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Affiliation(s)
- Amelia C McCue
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27514, USA.
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20
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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.
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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.
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21
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Baumschlager A. Engineering Light-Control in Biology. Front Bioeng Biotechnol 2022; 10:901300. [PMID: 35573251 PMCID: PMC9096073 DOI: 10.3389/fbioe.2022.901300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Unraveling the transformative power of optogenetics in biology requires sophisticated engineering for the creation and optimization of light-regulatable proteins. In addition, diverse strategies have been used for the tuning of these light-sensitive regulators. This review highlights different protein engineering and synthetic biology approaches, which might aid in the development and optimization of novel optogenetic proteins (Opto-proteins). Focusing on non-neuronal optogenetics, chromophore availability, general strategies for creating light-controllable functions, modification of the photosensitive domains and their fusion to effector domains, as well as tuning concepts for Opto-proteins are discussed. Thus, this review shall not serve as an encyclopedic summary of light-sensitive regulators but aims at discussing important aspects for the engineering of light-controllable proteins through selected examples.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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22
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Liu R, Yang J, Yao J, Zhao Z, He W, Su N, Zhang Z, Zhang C, Zhang Z, Cai H, Zhu L, Zhao Y, Quan S, Chen X, Yang Y. Optogenetic control of RNA function and metabolism using engineered light-switchable RNA-binding proteins. Nat Biotechnol 2022; 40:779-786. [PMID: 34980910 DOI: 10.1038/s41587-021-01112-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins (RBPs) play an essential role in regulating the function of RNAs in a cellular context, but our ability to control RBP activity in time and space is limited. Here, we describe the engineering of LicV, a photoswitchable RBP that binds to a specific RNA sequence in response to blue light irradiation. When fused to various RNA effectors, LicV allows for optogenetic control of RNA localization, splicing, translation and stability in cell culture. Furthermore, LicV-assisted CRISPR-Cas systems allow for efficient and tunable photoswitchable regulation of transcription and genomic locus labeling. These data demonstrate that the photoswitchable RBP LicV can serve as a programmable scaffold for the spatiotemporal control of synthetic RNA effectors.
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Affiliation(s)
- Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhou Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wei He
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zeyi Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Chenxia Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haibo Cai
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Shu Quan
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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23
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Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
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24
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Komera I, Gao C, Guo L, Hu G, Chen X, Liu L. Bifunctional optogenetic switch for improving shikimic acid production in E. coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:13. [PMID: 35418155 PMCID: PMC8822657 DOI: 10.1186/s13068-022-02111-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND Biomass formation and product synthesis decoupling have been proven to be promising to increase the titer of desired value add products. Optogenetics provides a potential strategy to develop light-induced circuits that conditionally control metabolic flux redistribution for enhanced microbial production. However, the limited number of light-sensitive proteins available to date hinders the progress of light-controlled tools. RESULTS To address these issues, two optogenetic systems (TPRS and TPAS) were constructed by reprogramming the widely used repressor TetR and protease TEVp to expand the current optogenetic toolkit. By merging the two systems, a bifunctional optogenetic switch was constructed to enable orthogonally regulated gene transcription and protein accumulation. Application of this bifunctional switch to decouple biomass formation and shikimic acid biosynthesis allowed 35 g/L of shikimic acid production in a minimal medium from glucose, representing the highest titer reported to date by E. coli without the addition of any chemical inducers and expensive aromatic amino acids. This titer was further boosted to 76 g/L when using rich medium fermentation. CONCLUSION The cost effective and light-controlled switch reported here provides important insights into environmentally friendly tools for metabolic pathway regulation and should be applicable to the production of other value-add chemicals.
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Affiliation(s)
- Irene Komera
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
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25
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Wang S, Luo Y, Jiang W, Li X, Qi Q, Liang Q. Development of Optogenetic Dual-Switch System for Rewiring Metabolic Flux for Polyhydroxybutyrate Production. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030617. [PMID: 35163885 PMCID: PMC8838604 DOI: 10.3390/molecules27030617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 11/30/2022]
Abstract
Several strategies, including inducer addition and biosensor use, have been developed for dynamical regulation. However, the toxicity, cost, and inflexibility of existing strategies have created a demand for superior technology. In this study, we designed an optogenetic dual-switch system and applied it to increase polyhydroxybutyrate (PHB) production. First, an optimized chromatic acclimation sensor/regulator (RBS10–CcaS#10–CcaR) system (comprising an optimized ribosomal binding site (RBS), light sensory protein CcaS, and response regulator CcaR) was selected for a wide sensing range of approximately 10-fold between green-light activation and red-light repression. The RBS10–CcaS#10–CcaR system was combined with a blue light-activated YF1–FixJ–PhlF system (containing histidine kinase YF1, response regulator FixJ, and repressor PhlF) engineered with reduced crosstalk. Finally, the optogenetic dual-switch system was used to rewire the metabolic flux for PHB production by regulating the sequences and intervals of the citrate synthase gene (gltA) and PHB synthesis gene (phbCAB) expression. Consequently, the strain RBS34, which has high gltA expression and a time lag of 3 h, achieved the highest PHB content of 16.6 wt%, which was approximately 3-fold that of F34 (expressed at 0 h). The results indicate that the optogenetic dual-switch system was verified as a practical and convenient tool for increasing PHB production.
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Affiliation(s)
- Sumeng Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Yue Luo
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Wei Jiang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Xiaomeng Li
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Correspondence: (Q.Q.); (Q.L.)
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, China; (S.W.); (Y.L.); (W.J.); (X.L.)
- Correspondence: (Q.Q.); (Q.L.)
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26
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Yang H, Du S, Ye Z, Wang X, Yan Z, Lian C, Bao C, Zhu L. A system for artificial light signal transduction via molecular translocation in a lipid membrane. Chem Sci 2022; 13:2487-2494. [PMID: 35310493 PMCID: PMC8864706 DOI: 10.1039/d1sc06671d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
Abstract
Light signal transduction pathways are central components of the mechanisms that regulate plant development, in which photoreceptors receive light and participate in light signal transduction. Chemical systems can be designed...
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Affiliation(s)
- Huiting Yang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Shengjie Du
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Zhicheng Ye
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Xuebin Wang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Zexin Yan
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Cheng Lian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Chunyan Bao
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology Shanghai 200237 China
| | - Linyong Zhu
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology Shanghai 200237 China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology Shanghai 200237 China
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27
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Lindner F, Diepold A. Optogenetics in bacteria - applications and opportunities. FEMS Microbiol Rev 2021; 46:6427354. [PMID: 34791201 PMCID: PMC8892541 DOI: 10.1093/femsre/fuab055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Optogenetics holds the promise of controlling biological processes with superb temporal and spatial resolution at minimal perturbation. Although many of the light-reactive proteins used in optogenetic systems are derived from prokaryotes, applications were largely limited to eukaryotes for a long time. In recent years, however, an increasing number of microbiologists use optogenetics as a powerful new tool to study and control key aspects of bacterial biology in a fast and often reversible manner. After a brief discussion of optogenetic principles, this review provides an overview of the rapidly growing number of optogenetic applications in bacteria, with a particular focus on studies venturing beyond transcriptional control. To guide future experiments, we highlight helpful tools, provide considerations for successful application of optogenetics in bacterial systems, and identify particular opportunities and challenges that arise when applying these approaches in bacteria.
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Affiliation(s)
- Florian Lindner
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.,SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
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28
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Camsund D, Jaramillo A, Lindblad P. Engineering of a Promoter Repressed by a Light-Regulated Transcription Factor in Escherichia coli. BIODESIGN RESEARCH 2021; 2021:9857418. [PMID: 37849950 PMCID: PMC10521638 DOI: 10.34133/2021/9857418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/23/2021] [Indexed: 10/19/2023] Open
Abstract
Light-regulated gene expression systems allow controlling gene expression in space and time with high accuracy. Contrary to previous synthetic light sensors that incorporate two-component systems which require localization at the plasma membrane, soluble one-component repression systems provide several advantageous characteristics. Firstly, they are soluble and able to diffuse across the cytoplasm. Secondly, they are smaller and of lower complexity, enabling less taxing expression and optimization of fewer parts. Thirdly, repression through steric hindrance is a widespread regulation mechanism that does not require specific interaction with host factors, potentially enabling implementation in different organisms. Herein, we present the design of the synthetic promoter PEL that in combination with the light-regulated dimer EL222 constitutes a one-component repression system. Inspired by previously engineered synthetic promoters and the Escherichia coli lacZYA promoter, we designed PEL with two EL222 operators positioned to hinder RNA polymerase binding when EL222 is bound. PEL is repressed by EL222 under conditions of white light with a light-regulated repression ratio of five. Further, alternating conditions of darkness and light in cycles as short as one hour showed that repression is reversible. The design of the PEL-EL222 system herein presented could aid the design and implementation of analogous one-component optogenetic repression systems. Finally, we compare the PEL-EL222 system with similar systems and suggest general improvements that could optimize and extend the functionality of EL222-based as well as other one-component repression systems.
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Affiliation(s)
- Daniel Camsund
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
- Molecular Systems Biology, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, UK
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Institute for Integrative Systems Biology (I2SysBio), CSIC – Universitat de València, 46980 Paterna, Spain
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
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29
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Naseri G, Prause K, Hamdo HH, Arenz C. Artificial Transcription Factors for Tuneable Gene Expression in Pichia pastoris. Front Bioeng Biotechnol 2021; 9:676900. [PMID: 34434924 PMCID: PMC8381338 DOI: 10.3389/fbioe.2021.676900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
The non-conventional yeast Pichia pastoris (syn. Komagataella phaffii) has become a powerful eukaryotic expression platform for biopharmaceutical and biotechnological applications on both laboratory and industrial scales. Despite the fundamental role that artificial transcription factors (ATFs) play in the orthogonal control of gene expression in synthetic biology, a limited number of ATFs are available for P. pastoris. To establish orthogonal regulators for use in P. pastoris, we characterized ATFs derived from Arabidopsis TFs. The plant-derived ATFs contain the binding domain of TFs from the plant Arabidopsis thaliana, in combination with the activation domains of yeast GAL4 and plant EDLL and a synthetic promoter harboring the cognate cis-regulatory motifs. Chromosomally integrated ATFs and their binding sites (ATF/BSs) resulted in a wide spectrum of inducible transcriptional outputs in P. pastoris, ranging from as low as 1- to as high as ∼63-fold induction with only small growth defects. We demonstrated the application of ATF/BSs by generating P. pastoris cells that produce β-carotene. Notably, the productivity of β-carotene in P. pastoris was ∼4.8-fold higher than that in S. cerevisiae, reaching ∼59% of the β-carotene productivity obtained in a S. cerevisiae strain optimized for the production of the β-carotene precursor, farnesyl diphosphate, by rewiring the endogenous metabolic pathways using plant-derived ATF/BSs. Our data suggest that plant-derived regulators have a high degree of transferability from S. cerevisiae to P. pastoris. The plant-derived ATFs, together with their cognate binding sites, powerfully increase the repertoire of transcriptional regulatory modules for the tuning of protein expression levels required in metabolic engineering or synthetic biology in P. pastoris.
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Affiliation(s)
- Gita Naseri
- Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Kevin Prause
- Institute of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Housam Haj Hamdo
- Institute of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Christoph Arenz
- Institute of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
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30
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Alex Wong CF, van Vliet L, Bhujbal SV, Guo C, Sletmoen M, Stokke BT, Hollfelder F, Lale R. A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalized Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution. ACS Synth Biol 2021; 10:1882-1894. [PMID: 34260196 PMCID: PMC8383311 DOI: 10.1021/acssynbio.1c00084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Water-in-oil emulsion
droplets are an attractive format for ultrahigh-throughput
screening in functional metagenomics and directed evolution applications
that allow libraries with more than 107 members to be characterized
in a day. Single library members are compartmentalized in droplets
that are generated in microfluidic devices and tested for the presence
of target biocatalysts. The target proteins can be produced intracellularly,
for example, in bacterial hosts in-droplet cell lysis is therefore
necessary to allow the enzymes to encounter the substrate to initiate
an activity assay. Here, we present a titratable lysis-on-demand (LoD)
system enabling the control of the cell lysis rate in Escherichia
coli. We demonstrate that the rate of cell lysis can be controlled
by adjusting the externally added inducer concentration. This LoD
system is evaluated both at the population level (by optical density
measurements) and at the single-cell level (on single-cell arrays
and in alginate microbeads). Additionally, we validate the LoD system
by droplet screening of a phosphotriesterase expressed from E. coli, with cell lysis triggered by inducer concentrations
in the μM range. The LoD system yields sufficient release of
the intracellularly produced enzymes to bring about a detectable quantity
of product (measured by fluorescence in flow cytometry of double emulsions),
while leaving viable cells for the downstream recovery of the genetic
material.
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Affiliation(s)
- Che Fai Alex Wong
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Liisa van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Swapnil Vilas Bhujbal
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Chengzhi Guo
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marit Sletmoen
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Bjørn Torger Stokke
- Department of Physics, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Rahmi Lale
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
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31
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Engineering AraC to make it responsive to light instead of arabinose. Nat Chem Biol 2021; 17:817-827. [PMID: 33903769 DOI: 10.1038/s41589-021-00787-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023]
Abstract
The L-arabinose-responsive AraC and its cognate PBAD promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology and synthetic biology. Here, we change the sensing capability of AraC from L-arabinose to blue light, making its dimerization and the resulting PBAD activation light-inducible. We engineer an entire family of blue light-inducible AraC dimers in Escherichia coli (BLADE) to control gene expression in space and time. We show that BLADE can be used with pre-existing L-arabinose-responsive plasmids and strains, enabling optogenetic experiments without the need to clone. Furthermore, we apply BLADE to control, with light, the catabolism of L-arabinose, thus externally steering bacterial growth with a simple transformation step. Our work establishes BLADE as a highly practical and effective optogenetic tool with plug-and-play functionality-features that we hope will accelerate the broader adoption of optogenetics and the realization of its vast potential in microbiology, synthetic biology and biotechnology.
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32
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Dietler J, Schubert R, Krafft TGA, Meiler S, Kainrath S, Richter F, Schweimer K, Weyand M, Janovjak H, Möglich A. A Light-Oxygen-Voltage Receptor Integrates Light and Temperature. J Mol Biol 2021; 433:167107. [PMID: 34146595 DOI: 10.1016/j.jmb.2021.167107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Sensory photoreceptors enable organisms to adjust their physiology, behavior, and development in response to light, generally with spatiotemporal acuity and reversibility. These traits underlie the use of photoreceptors as genetically encoded actuators to alter by light the state and properties of heterologous organisms. Subsumed as optogenetics, pertinent approaches enable regulating diverse cellular processes, not least gene expression. Here, we controlled the widely used Tet repressor by coupling to light-oxygen-voltage (LOV) modules that either homodimerize or dissociate under blue light. Repression could thus be elevated or relieved, and consequently protein expression was modulated by light. Strikingly, the homodimeric RsLOV module from Rhodobacter sphaeroides not only dissociated under light but intrinsically reacted to temperature. The limited light responses of wild-type RsLOV at 37 °C were enhanced in two variants that exhibited closely similar photochemistry and structure. One variant improved the weak homodimerization affinity of 40 µM by two-fold and thus also bestowed light sensitivity on a receptor tyrosine kinase. Certain photoreceptors, exemplified by RsLOV, can evidently moonlight as temperature sensors which immediately bears on their application in optogenetics and biotechnology. Properly accounted for, the temperature sensitivity can be leveraged for the construction of signal-responsive cellular circuits.
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Affiliation(s)
- Julia Dietler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Roman Schubert
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Tobias G A Krafft
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Simone Meiler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Stephanie Kainrath
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Florian Richter
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Kristian Schweimer
- Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany
| | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany; Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany; Bayreuth Center for Biochemistry & Molecular Biology, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany.
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33
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Recent advances in tuning the expression and regulation of genes for constructing microbial cell factories. Biotechnol Adv 2021; 50:107767. [PMID: 33974979 DOI: 10.1016/j.biotechadv.2021.107767] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022]
Abstract
To overcome environmental problems caused by the use of fossil resources, microbial cell factories have become a promising technique for the sustainable and eco-friendly development of valuable products from renewable resources. Constructing microbial cell factories with high titers, yields, and productivity requires a balance between growth and production; to this end, tuning gene expression and regulation is necessary to optimise and precisely control complicated metabolic fluxes. In this article, we review the current trends and advances in tuning gene expression and regulation and consider their engineering at each of the three stages of gene regulation: genomic, mRNA, and protein. In particular, the technological approaches utilised in a diverse range of genetic-engineering-based tools for the construction of microbial cell factories are reviewed and representative applications of these strategies are presented. Finally, the prospects for strategies and systems for tuning gene expression and regulation are discussed.
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34
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Oh TJ, Fan H, Skeeters SS, Zhang K. Steering Molecular Activity with Optogenetics: Recent Advances and Perspectives. Adv Biol (Weinh) 2021; 5:e2000180. [PMID: 34028216 PMCID: PMC8218620 DOI: 10.1002/adbi.202000180] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/14/2020] [Indexed: 12/24/2022]
Abstract
Optogenetics utilizes photosensitive proteins to manipulate the localization and interaction of molecules in living cells. Because light can be rapidly switched and conveniently confined to the sub-micrometer scale, optogenetics allows for controlling cellular events with an unprecedented resolution in time and space. The past decade has witnessed an enormous progress in the field of optogenetics within the biological sciences. The ever-increasing amount of optogenetic tools, however, can overwhelm the selection of appropriate optogenetic strategies. Considering that each optogenetic tool may have a distinct mode of action, a comparative analysis of the current optogenetic toolbox can promote the further use of optogenetics, especially by researchers new to this field. This review provides such a compilation that highlights the spatiotemporal accuracy of current optogenetic systems. Recent advances of optogenetics in live cells and animal models are summarized, the emerging work that interlinks optogenetics with other research fields is presented, and exciting clinical and industrial efforts to employ optogenetic strategy toward disease intervention are reported.
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Affiliation(s)
- Teak-Jung Oh
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Huaxun Fan
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Savanna S Skeeters
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Kai Zhang
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
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35
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Forlani G, Di Ventura B. A light way for nuclear cell biologists. J Biochem 2021; 169:273-286. [PMID: 33245128 PMCID: PMC8053400 DOI: 10.1093/jb/mvaa139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleus is a very complex organelle present in eukaryotic cells. Having the crucial task to safeguard, organize and manage the genetic information, it must tightly control its molecular constituents, its shape and its internal architecture at any given time. Despite our vast knowledge of nuclear cell biology, much is yet to be unravelled. For instance, only recently we came to appreciate the existence of a dynamic nuclear cytoskeleton made of actin filaments that regulates processes such as gene expression, DNA repair and nuclear expansion. This suggests further exciting discoveries ahead of us. Modern cell biologists embrace a new methodology relying on precise perturbations of cellular processes that require a reversible, highly spatially confinable, rapid, inexpensive and tunEable external stimulus: light. In this review, we discuss how optogenetics, the state-of-the-art technology that uses genetically encoded light-sensitive proteins to steer biological processes, can be adopted to specifically investigate nuclear cell biology.
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Affiliation(s)
- Giada Forlani
- Spemann Graduate School of Biology and Medicine (SGBM)
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
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Baumschlager A, Khammash M. Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria. Adv Biol (Weinh) 2021; 5:e2000256. [PMID: 34028214 DOI: 10.1002/adbi.202000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Light has become established as a tool not only to visualize and investigate but also to steer biological systems. This review starts by discussing the unique features that make light such an effective control input in biology. It then gives an overview of how light-control came to progress, starting with photoactivatable compounds and leading up to current genetic implementations using optogenetic approaches. The review then zooms in on optogenetics, focusing on photosensitive proteins, which form the basis for optogenetic engineering using synthetic biological approaches. As the regulation of transcription provides a highly versatile means for steering diverse biological functions, the focus of this review then shifts to transcriptional light regulators, which are presented in the biotechnologically highly relevant model organism Escherichia coli.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
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37
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Li T, Chen X, Qian Y, Shao J, Li X, Liu S, Zhu L, Zhao Y, Ye H, Yang Y. A synthetic BRET-based optogenetic device for pulsatile transgene expression enabling glucose homeostasis in mice. Nat Commun 2021; 12:615. [PMID: 33504786 PMCID: PMC7840992 DOI: 10.1038/s41467-021-20913-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/21/2020] [Indexed: 12/26/2022] Open
Abstract
Pulsing cellular dynamics in genetic circuits have been shown to provide critical capabilities to cells in stress response, signaling and development. Despite the fascinating discoveries made in the past few years, the mechanisms and functional capabilities of most pulsing systems remain unclear, and one of the critical challenges is the lack of a technology that allows pulsatile regulation of transgene expression both in vitro and in vivo. Here, we describe the development of a synthetic BRET-based transgene expression (LuminON) system based on a luminescent transcription factor, termed luminGAVPO, by fusing NanoLuc luciferase to the light-switchable transcription factor GAVPO. luminGAVPO allows pulsatile and quantitative activation of transgene expression via both chemogenetic and optogenetic approaches in mammalian cells and mice. Both the pulse amplitude and duration of transgene expression are highly tunable via adjustment of the amount of furimazine. We further demonstrated LuminON-mediated blood-glucose homeostasis in type 1 diabetic mice. We believe that the BRET-based LuminON system with the pulsatile dynamics of transgene expression provides a highly sensitive tool for precise manipulation in biological systems that has strong potential for application in diverse basic biological studies and gene- and cell-based precision therapies in the future.
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Affiliation(s)
- Ting Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yajie Qian
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Jiawei Shao
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Xie Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Shuning Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
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Hartsough LA, Park M, Kotlajich MV, Lazar JT, Han B, Lin CCJ, Musteata E, Gambill L, Wang MC, Tabor JJ. Optogenetic control of gut bacterial metabolism to promote longevity. eLife 2020; 9:56849. [PMID: 33325823 PMCID: PMC7744093 DOI: 10.7554/elife.56849] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Gut microbial metabolism is associated with host longevity. However, because it requires direct manipulation of microbial metabolism in situ, establishing a causal link between these two processes remains challenging. We demonstrate an optogenetic method to control gene expression and metabolite production from bacteria residing in the host gut. We genetically engineer an Escherichia coli strain that secretes colanic acid (CA) under the quantitative control of light. Using this optogenetically-controlled strain to induce CA production directly in the Caenorhabditis elegans gut, we reveal the local effect of CA in protecting intestinal mitochondria from stress-induced hyper-fragmentation. We also demonstrate that the lifespan-extending effect of this strain is positively correlated with the intensity of green light, indicating a dose-dependent CA benefit on the host. Thus, optogenetics can be used to achieve quantitative and temporal control of gut bacterial metabolism in order to reveal its local and systemic effects on host health and aging.
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Affiliation(s)
| | | | | | - John Tyler Lazar
- Department of Chemical and Biomolecular Engineering, Houston, United States
| | - Bing Han
- Huffington Center on Aging, Houston, United States
| | - Chih-Chun J Lin
- Huffington Center on Aging, Houston, United States.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, United States
| | - Elena Musteata
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, United States
| | - Lauren Gambill
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, United States
| | - Meng C Wang
- Huffington Center on Aging, Houston, United States.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Houston, United States
| | - Jeffrey J Tabor
- Department of Bioengineering, Houston, United States.,Systems, Synthetic, and Physical Biology Program, Rice University, Houston, United States.,Department of Biosciences, Houston, United States
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