1
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Rojas V, Larrondo LF. Coupling Cell Communication and Optogenetics: Implementation of a Light-Inducible Intercellular System in Yeast. ACS Synth Biol 2023; 12:71-82. [PMID: 36534043 PMCID: PMC9872819 DOI: 10.1021/acssynbio.2c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 12/23/2022]
Abstract
Cell communication is a widespread mechanism in biology, allowing the transmission of information about environmental conditions. In order to understand how cell communication modulates relevant biological processes such as survival, division, differentiation, and apoptosis, different synthetic systems based on chemical induction have been successfully developed. In this work, we coupled cell communication and optogenetics in the budding yeast Saccharomyces cerevisiae. Our approach is based on two strains connected by the light-dependent production of α-factor pheromone in one cell type, which induces gene expression in the other type. After the individual characterization of the different variants of both strains, the optogenetic intercellular system was evaluated by combining the cells under contrasting illumination conditions. Using luciferase as a reporter gene, specific co-cultures at a 1:1 ratio displayed activation of the response upon constant blue light, which was not observed for the same cell mixtures grown in darkness. Then, the system was assessed at several dark/blue-light transitions, where the response level varies depending on the moment in which illumination was delivered. Furthermore, we observed that the amplitude of response can be tuned by modifying the initial ratio between both strains. Finally, the two-population system showed higher fold inductions in comparison with autonomous strains. Altogether, these results demonstrated that external light information is propagated through a diffusible signaling molecule to modulate gene expression in a synthetic system involving microbial cells, which will pave the road for studies allowing optogenetic control of population-level dynamics.
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Affiliation(s)
- Vicente Rojas
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Luis F. Larrondo
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
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2
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The Evolution of Complex Muscle Cell In Vitro Models to Study Pathomechanisms and Drug Development of Neuromuscular Disease. Cells 2022; 11:cells11071233. [PMID: 35406795 PMCID: PMC8997482 DOI: 10.3390/cells11071233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 12/04/2022] Open
Abstract
Many neuromuscular disease entities possess a significant disease burden and therapeutic options remain limited. Innovative human preclinical models may help to uncover relevant disease mechanisms and enhance the translation of therapeutic findings to strengthen neuromuscular disease precision medicine. By concentrating on idiopathic inflammatory muscle disorders, we summarize the recent evolution of the novel in vitro models to study disease mechanisms and therapeutic strategies. A particular focus is laid on the integration and simulation of multicellular interactions of muscle tissue in disease phenotypes in vitro. Finally, the requirements of a neuromuscular disease drug development workflow are discussed with a particular emphasis on cell sources, co-culture systems (including organoids), functionality, and throughput.
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3
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Barros MT, Doan P, Kandhavelu M, Jennings B, Balasubramaniam S. Engineering calcium signaling of astrocytes for neural-molecular computing logic gates. Sci Rep 2021; 11:595. [PMID: 33436729 PMCID: PMC7803753 DOI: 10.1038/s41598-020-79891-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/24/2020] [Indexed: 11/22/2022] Open
Abstract
This paper proposes the use of astrocytes to realize Boolean logic gates, through manipulation of the threshold of \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {Ca}^{2+}$$\end{document}Ca2+ ion flows between the cells based on the input signals. Through wet-lab experiments that engineer the astrocytes cells with pcDNA3.1-hGPR17 genes as well as chemical compounds, we show that both AND and OR gates can be implemented by controlling \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {Ca}^{2+}$$\end{document}Ca2+ signals that flow through the population. A reinforced learning platform is also presented in the paper to optimize the \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {Ca}^{2+}$$\end{document}Ca2+ activated level and time slot of input signals \documentclass[12pt]{minimal}
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\begin{document}$$T_b$$\end{document}Tb into the gate. This design platform caters for any size and connectivity of the cell population, by taking into consideration the delay and noise produced from the signalling between the cells. To validate the effectiveness of the reinforced learning platform, a \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {Ca}^{2+}$$\end{document}Ca2+ signalling simulator was used to simulate the signalling between the astrocyte cells. The results from the simulation show that an optimum value for both the \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {Ca}^{2+}$$\end{document}Ca2+ activated level and time slot of input signals \documentclass[12pt]{minimal}
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\begin{document}$$T_b$$\end{document}Tb is required to achieve up to 90% accuracy for both the AND and OR gates. Our method can be used as the basis for future Neural–Molecular Computing chips, constructed from engineered astrocyte cells, which can form the basis for a new generation of brain implants.
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Affiliation(s)
- Michael Taynnan Barros
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, UK. .,BioMediTech, Faculty of Medicine and Health Technology, Tampere University, P.O.Box 553, 33101, Tampere, Finland.
| | - Phuong Doan
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, P.O.Box 553, 33101, Tampere, Finland
| | - Meenakshisundaram Kandhavelu
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, P.O.Box 553, 33101, Tampere, Finland
| | - Brendan Jennings
- Telecommunication Software and Systems Group (TSSG), Waterford Institute of Technology (WIT), Waterford, Ireland
| | - Sasitharan Balasubramaniam
- Telecommunication Software and Systems Group (TSSG), Waterford Institute of Technology (WIT), Waterford, Ireland.,FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland
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4
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Miranda JF, Scarinci LD, Ramos LF, Silva CM, Gonçalves LR, de Morais PF, Malaspina O, Moraes KCM. The modulatory effect of triclosan on the reversion of the activated phenotype of LX-2 hepatic stellate cells. J Biochem Mol Toxicol 2019; 34:e22413. [PMID: 31714634 DOI: 10.1002/jbt.22413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 09/12/2019] [Accepted: 10/07/2019] [Indexed: 01/03/2023]
Abstract
Hepatic diseases leading to fibrosis affect millions of individuals worldwide and are a major public health challenge. Although, there have been many advances in understanding hepatic fibrogenesis, an effective therapy remains elusive. Studies focus primarily on activation of the hepatic stellate cells (HSCs), the principal fibrogenic cells in the liver; however, fewer numbers of studies have examined molecular mechanisms that deactivate HSC, controlling the profibrogenic phenotype. In the present study, we evaluated cellular and molecular actions of the chemical triclosan (TCS) in reverting activated HSCs to a quiesced phenotype. We demonstrated that the inhibition of the enzyme fatty acid synthase by TCS in activated HSCs promotes survival of the cells and triggers cellular and molecular changes that promote cellular phenotypic reversion, offering potentially new therapeutic directions.
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Affiliation(s)
- Juliana F Miranda
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
| | - Letícia D Scarinci
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
| | - Letícia F Ramos
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
| | - Caio M Silva
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
| | - Letícia R Gonçalves
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
| | - Priscila F de Morais
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
| | - Osmar Malaspina
- Instituto de Biociências, Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
| | - Karen C M Moraes
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Rio Claro, São Paulo, Brazil
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5
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Alnahhas RN, Winkle JJ, Hirning AJ, Karamched B, Ott W, Josić K, Bennett MR. Spatiotemporal Dynamics of Synthetic Microbial Consortia in Microfluidic Devices. ACS Synth Biol 2019; 8:2051-2058. [PMID: 31361464 PMCID: PMC6754295 DOI: 10.1021/acssynbio.9b00146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Synthetic microbial consortia consist of two or more engineered strains that grow together and share the same resources. When intercellular signaling pathways are included in the engineered strains, close proximity of the microbes can generate complex dynamic behaviors that are difficult to obtain using a single strain. However, when a consortium is not cultured in a well-mixed environment the constituent strains passively compete for space as they grow and divide, complicating cell-cell signaling. Here, we explore the temporal dynamics of the spatial distribution of consortia cocultured in microfluidic devices. To do this, we grew two different strains of Escherichia coli in microfluidic devices with cell-trapping regions (traps) of several different designs. We found that the size of the traps is a critical determinant of spatiotemporal dynamics. In small traps, cells can easily signal one another, but the relative proportion of each strain within the trap can fluctuate wildly. In large traps, the relative ratio of strains is stabilized, but intercellular signaling can be hindered by distances between cells. This presents a trade-off between the trap size and the effectiveness of intercellular signaling, which can be mitigated by increasing the initial seeding of cells in larger traps. We also built a mathematical model, which suggests that increasing the number of seed cells can also increase the strain ratio variability due to an increased number of strain interfaces in the trap. These results help elucidate the complex behaviors of synthetic microbial consortia in microfluidic traps and provide a means of analysis to help remedy the spatial heterogeneity inherent to different trap types.
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Affiliation(s)
- Razan N Alnahhas
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - James J Winkle
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Andrew J Hirning
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Bhargav Karamched
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - William Ott
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - Krešimir Josić
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
- Department of Biology and Biochemistry , University of Houston , Houston , Texas 77004 , United States
| | - Matthew R Bennett
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Bioengineering , Rice University , Houston , Texas 77005 , United States
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6
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Liu Y, Charpin-El Hamri G, Ye H, Fussenegger M. A synthetic free fatty acid-regulated transgene switch in mammalian cells and mice. Nucleic Acids Res 2019; 46:9864-9874. [PMID: 30219861 PMCID: PMC6182168 DOI: 10.1093/nar/gky805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023] Open
Abstract
Trigger-inducible transgene expression systems are utilized in biopharmaceutical manufacturing and also to enable controlled release of therapeutic agents in vivo. We considered that free fatty acids (FFAs), which are dietary components, signaling molecules and important biomarkers, would be attractive candidates as triggers for novel transgene switches with many potential applications, e.g. in future gene- and cell-based therapies. To develop such a switch, we rewired the signal pathway of human G-protein coupled receptor 40 to a chimeric promoter triggering gene expression through an increase of intracellular calcium concentration. This synthetic gene switch is responsive to physiologically relevant FFA concentrations in different mammalian cell types grown in culture or in a bioreactor, or implanted into mice. Animal recipients of microencapsulated sensor cells containing this switch exhibited significant transgene induction following consumption of dietary fat (such as Swiss cheese) or under hyperlipidaemic conditions, including obesity, diabetes and lipodystrophy.
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Affiliation(s)
- Ying Liu
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El Hamri
- Département Génie Biologique, Université Claude Bernard 1, 43 Boulevard du 11 Novembre 1918, F-69100 Villeurbanne, France
| | - Haifeng Ye
- 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
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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7
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Wang T, Dunlop MJ. Controlling and exploiting cell-to-cell variation in metabolic engineering. Curr Opin Biotechnol 2018; 57:10-16. [PMID: 30261323 DOI: 10.1016/j.copbio.2018.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/16/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022]
Abstract
Individual cells within a population can display diverse phenotypes due to differences in their local environment, genetic variation, and stochastic expression of genes. Understanding this cell-to-cell variation is important for metabolic engineering applications because variability can impact production. For instance, recent studies have shown that production can be highly heterogeneous among engineered cells, and strategies that manage this diversity improve yields of biosynthetic products. These results suggest the potential of controlling variation as a novel approach towards improving performance of engineered cells. In this review, we focus on identifying the origins of cell-to-cell variation in metabolic engineering applications and discuss recent developments on strategies that can be employed to diminish, accept, or even exploit cell-to-cell variation.
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Affiliation(s)
- Tiebin Wang
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA.
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8
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Abstract
Metabolic pathways are often engineered in single microbial populations. However, the introduction of heterologous circuits into the host can create a substantial metabolic burden that limits the overall productivity of the system. This limitation could be overcome by metabolic division of labor (DOL), whereby distinct populations perform different steps in a metabolic pathway, reducing the burden each population will experience. While conceptually appealing, the conditions when DOL is advantageous have not been rigorously established. Here, we have analyzed 24 common architectures of metabolic pathways in which DOL can be implemented. Our analysis reveals general criteria defining the conditions that favor DOL, accounting for the burden or benefit of the pathway activity on the host populations as well as the transport and turnover of enzymes and intermediate metabolites. These criteria can help guide engineering of metabolic pathways and have implications for understanding evolution of natural microbial communities.
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9
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A triple co-culture method to investigate the effect of macrophages and fibroblasts on myoblast proliferation and migration. Biotechniques 2018; 64:52-58. [PMID: 29571282 DOI: 10.2144/btn-2017-0100] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/11/2018] [Indexed: 11/23/2022] Open
Abstract
The communication between nonmyogenic cells, such as macrophages and fibroblasts, and myoblasts is crucial for successful skeletal muscle repair. In vitro co-culture methods can be used to increase our understanding of these cellular interactions; however, current protocols are restricted to two, often physically separate, cell populations. Here, we demonstrate a novel, inexpensive in vitro triple co-culture method that facilitates the co-culture of at least three cell populations with some degree of cell-cell contact. Using this method, we determined the effect of macrophages and fibroblasts on myoblast proliferation and migration. A significant increase in myoblast proliferation and migration was observed following co-culture with either macrophages or fibroblasts. However, triple co-culture of macrophages, fibroblasts, and myoblasts revealed that the presence of macrophages prevented fibroblasts from maintaining this positive effect on myoblast migration. Macrophages, on the other hand, continued to promote myoblast proliferation whether in the presence of fibroblasts or not. Our triple co-culture system highlights the significance of multicellular communication in regulating myoblast proliferation and migration and emphasizes the importance of more complex co-culture systems when investigating myogenesis in vitro.
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10
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Dolinšek J, Goldschmidt F, Johnson DR. Synthetic microbial ecology and the dynamic interplay between microbial genotypes. FEMS Microbiol Rev 2018; 40:961-979. [PMID: 28201744 DOI: 10.1093/femsre/fuw024] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/27/2016] [Accepted: 07/04/2016] [Indexed: 01/27/2023] Open
Abstract
Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.
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Affiliation(s)
- Jan Dolinšek
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Felix Goldschmidt
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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11
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Liu Y, Li J, Tschirhart T, Terrell JL, Kim E, Tsao C, Kelly DL, Bentley WE, Payne GF. Connecting Biology to Electronics: Molecular Communication via Redox Modality. Adv Healthc Mater 2017; 6. [PMID: 29045017 DOI: 10.1002/adhm.201700789] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/18/2017] [Indexed: 12/13/2022]
Abstract
Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues.
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Affiliation(s)
- Yi Liu
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Jinyang Li
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Tanya Tschirhart
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Jessica L. Terrell
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Chen‐Yu Tsao
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Deanna L. Kelly
- Maryland Psychiatric Research Center University of Maryland School of Medicine Baltimore MD 21228 USA
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
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12
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Liu Y, Tsao C, Kim E, Tschirhart T, Terrell JL, Bentley WE, Payne GF. Using a Redox Modality to Connect Synthetic Biology to Electronics: Hydrogel-Based Chemo-Electro Signal Transduction for Molecular Communication. Adv Healthc Mater 2017; 6. [PMID: 27863177 DOI: 10.1002/adhm.201600908] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/15/2016] [Indexed: 01/08/2023]
Abstract
A hydrogel-based dual film coating is electrofabricated for transducing bio-relevant chemical information into electronical output. The outer film has a synthetic biology construct that recognizes an external molecular signal and transduces this input into the expression of an enzyme that converts redox-inactive substrate into a redox-active intermediate, which is detected through an amplification mechanism of the inner redox-capacitor film.
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Affiliation(s)
- Yi Liu
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
| | - Chen‐Yu Tsao
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
| | - Tanya Tschirhart
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Jessica L. Terrell
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD 20742 USA
- Fischell Department of Bioengineering University of Maryland College Park MD 20742 USA
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13
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Zargar A, Quan DN, Abutaleb N, Choi E, Terrell JL, Payne GF, Bentley WE. Constructing "quantized quorums" to guide emergent phenotypes through quorum quenching capsules. Biotechnol Bioeng 2016; 114:407-415. [PMID: 27543759 DOI: 10.1002/bit.26080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022]
Abstract
Microbial cells have for many years been engineered to facilitate efficient production of biologics, chemicals, and other compounds. As the "metabolic" burden of synthetic genetic components can impair cell performance, microbial consortia are being developed to piece together specialized subpopulations that collectively produce desired products. Their use, however, has been limited by the inability to control their composition and function. One approach to leverage advantages of the division of labor within consortia is to link microbial subpopulations together through quorum sensing (QS) molecules. Previously, we directed the assembly of "quantized quorums," microbial subpopulations that are parsed through QS activation, by the exogenous addition of QS signal molecules to QS synthase mutants. In this work, we develop a more facile and general platform for creating "quantized quorums." Moreover, the methodology is not restricted to QS-mutant populations. We constructed quorum quenching capsules that partition QS-mediated phenotypes into discrete subpopulations. This compartmentalization guides QS subpopulations in a dose-dependent manner, parsing cell populations into activated or deactivated groups. The capsular "devices" consist of polyelectrolyte alginate-chitosan beads that encapsulate high-efficiency (HE) "controller cells" that, in turn, provide rapid uptake of the QS signal molecule AI-2 from culture fluids. In this methodology, instead of adding AI-2 to parse QS-mutants into subpopulations, we engineered cells to encapsulate them into compartments, and they serve to deplete AI-2 from wild-type populations. These encapsulated bacteria therefore, provide orthogonal control of population composition while allowing only minimal interaction with the product-producing cell population or consortia. We envision that compartmentalized control of QS should have applications in both metabolic engineering and human disease. Biotechnol. Bioeng. 2017;114: 407-415. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Amin Zargar
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - David N Quan
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Nadia Abutaleb
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Erica Choi
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Jessica L Terrell
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
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14
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Abstract
The enabling technologies of synthetic biology are opening up new opportunities for engineering and enhancement of mammalian cells. This will stimulate diverse applications in many life science sectors such as regenerative medicine, development of biosensing cell lines, therapeutic protein production, and generation of new synthetic genetic regulatory circuits. Harnessing the full potential of these new engineering-based approaches requires the design and assembly of large DNA constructs-potentially up to chromosome scale-and the effective delivery of these large DNA payloads to the host cell. Random integration of large transgenes, encoding therapeutic proteins or genetic circuits into host chromosomes, has several drawbacks such as risks of insertional mutagenesis, lack of control over transgene copy-number and position-specific effects; these can compromise the intended functioning of genetic circuits. The development of a system orthogonal to the endogenous genome is therefore beneficial. Mammalian artificial chromosomes (MACs) are functional, add-on chromosomal elements, which behave as normal chromosomes-being replicating and portioned to daughter cells at each cell division. They are deployed as useful gene expression vectors as they remain independent from the host genome. MACs are maintained as a single-copy and can accommodate multiple gene expression cassettes of, in theory, unlimited DNA size (MACs up to 10 megabases have been constructed). MACs therefore enabled control over ectopic gene expression and represent an excellent platform to rapidly prototype and characterize novel synthetic gene circuits without recourse to engineering the host genome. This review describes the obstacles synthetic biologists face when working with mammalian systems and how the development of improved MACs can overcome these-particularly given the spectacular advances in DNA synthesis and assembly that are fuelling this research area.
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Affiliation(s)
- Andrea Martella
- School of Biological Sciences, The University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF, U.K
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, The University of Edinburgh , Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, EH16 4UU, U.K
| | - Junbiao Dai
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yizhi Cai
- School of Biological Sciences, The University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF, U.K
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15
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Quorum-sensing in yeast and its potential in wine making. Appl Microbiol Biotechnol 2016; 100:7841-52. [DOI: 10.1007/s00253-016-7758-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 10/21/2022]
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16
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Marchand N, Collins CH. Synthetic Quorum Sensing and Cell-Cell Communication in Gram-Positive Bacillus megaterium. ACS Synth Biol 2016. [PMID: 26203497 DOI: 10.1021/acssynbio.5b00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The components of natural quorum-sensing (QS) systems can be used to engineer synthetic communication systems that regulate gene expression in response to chemical signals. We have used the machinery from the peptide-based agr QS system from Staphylococcus aureus to engineer a synthetic QS system in Bacillus megaterium to enable autoinduction of a target gene at high cell densities. Growth and gene expression from these synthetic QS cells were characterized in both complex and minimal media. We also split the signal production and sensing components between two strains of B. megaterium to produce sender and receiver cells and characterized the resulting communication in liquid media and on semisolid agar. The system described in this work represents the first synthetic QS and cell-cell communication system that has been engineered to function in a Gram-positive host, and it has the potential to enable the generation of dynamic gene regulatory networks in B. megaterium and other Gram-positive organisms.
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Affiliation(s)
- Nicholas Marchand
- Department of Chemical and Biological Engineering, ‡Center for Biotechnology
and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Cynthia H. Collins
- Department of Chemical and Biological Engineering, ‡Center for Biotechnology
and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
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17
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Jayaraman P, Devarajan K, Chua TK, Zhang H, Gunawan E, Poh CL. Blue light-mediated transcriptional activation and repression of gene expression in bacteria. Nucleic Acids Res 2016; 44:6994-7005. [PMID: 27353329 PMCID: PMC5001607 DOI: 10.1093/nar/gkw548] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/06/2016] [Indexed: 11/14/2022] Open
Abstract
Light-regulated modules offer unprecedented new ways to control cellular behavior in precise spatial and temporal resolution. The availability of such tools may dramatically accelerate the progression of synthetic biology applications. Nonetheless, current optogenetic toolbox of prokaryotes has potential issues such as lack of rapid and switchable control, less portable, low dynamic expression and limited parts. To address these shortcomings, we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222. We demonstrated that by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely. We show that both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light. In addition, the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model. We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal. Overall, our modular approach layers a transformative platform for next-generation light-controllable synthetic biology systems in prokaryotes.
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Affiliation(s)
- Premkumar Jayaraman
- Department of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
| | - Kavya Devarajan
- School of Electrical and Electronics Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Tze Kwang Chua
- Department of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
| | - Hanzhong Zhang
- Department of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
| | - Erry Gunawan
- School of Electrical and Electronics Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Chueh Loo Poh
- Department of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
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18
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Reetz MT. What are the Limitations of Enzymes in Synthetic Organic Chemistry? CHEM REC 2016; 16:2449-2459. [DOI: 10.1002/tcr.201600040] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Manfred T. Reetz
- Fachbereich Chemie (15) Philipps-Universität Marburg Hans-Meerwein Straße; 35032 Marburg Germany
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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19
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Zhang H, Wang X. Modular co-culture engineering, a new approach for metabolic engineering. Metab Eng 2016; 37:114-121. [PMID: 27242132 DOI: 10.1016/j.ymben.2016.05.007] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA.
| | - Xiaonan Wang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA
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20
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Woloszynek S, Pastor S, Mell JC, Nandi N, Sokhansanj B, Rosen GL. Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:67-124. [PMID: 27017007 DOI: 10.1016/bs.ircmb.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.
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Affiliation(s)
- S Woloszynek
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America
| | - S Pastor
- Department of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - J C Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - N Nandi
- Division of Gastroenterology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - B Sokhansanj
- McKool Smith Hennigan, P. C., Redwood Shores, CA, United States of America
| | - G L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America.
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21
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Affiliation(s)
- Brian P Teague
- Department of Biological Engineering and Department of Electrical Engineering and Computer Science, NE47-223, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Ron Weiss
- Department of Biological Engineering and Department of Electrical Engineering and Computer Science, NE47-223, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.
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22
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Abstract
The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.
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Affiliation(s)
- Songzi Kou
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Danhui Cheng
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fei Sun
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - I-Ming Hsing
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong. and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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23
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Martínez I, Mohamed MES, Rozas D, García JL, Díaz E. Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds. Metab Eng 2016; 35:46-54. [PMID: 26802977 DOI: 10.1016/j.ymben.2016.01.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/27/2015] [Accepted: 01/11/2016] [Indexed: 01/04/2023]
Abstract
The 4S pathway is the most studied bioprocess for the removal of the recalcitrant sulfur of aromatic heterocycles present in fuels. It consists of three sequential functional units, encoded by the dszABCD genes, through which the model compound dibenzothiophene (DBT) is transformed into the sulfur-free 2-hydroxybiphenyl (2HBP) molecule. In this work, a set of synthetic dsz cassettes were implanted in Pseudomonas putida KT2440, a model bacterial "chassis" for metabolic engineering studies. The complete dszB1A1C1-D1 cassette behaved as an attractive alternative - to the previously constructed recombinant dsz cassettes - for the conversion of DBT into 2HBP. Refactoring the 4S pathway by the use of synthetic dsz modules encoding individual 4S pathway reactions revealed unanticipated traits, e.g., the 4S intermediate 2HBP-sulfinate (HBPS) behaves as an inhibitor of the Dsz monooxygenases, and once secreted from the cells it cannot be further taken up. That issue should be addressed for the rational design of more efficient biocatalysts for DBT bioconversions. In this sense, the construction of synthetic bacterial consortia to compartmentalize the 4S pathway into different cell factories for individual optimization was shown to enhance the conversion of DBT into 2HBP, overcome the inhibition of the Dsz enzymes by the 4S intermediates, and enable efficient production of unattainable high added value intermediates, e.g., HBPS, that are difficult to obtain using the current monocultures.
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Affiliation(s)
- Igor Martínez
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | | | - Daniel Rozas
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - José Luis García
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
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24
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Kolar K, Wischhusen HM, Müller K, Karlsson M, Weber W, Zurbriggen MD. A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication. BMC SYSTEMS BIOLOGY 2015; 9:97. [PMID: 26714638 PMCID: PMC4696150 DOI: 10.1186/s12918-015-0252-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 12/15/2015] [Indexed: 02/05/2023]
Abstract
Background Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to engineer well-defined systems that allow the convenient study and manipulation of intercellular communication networks. Results Here, we present the first mammalian synthetic network for reciprocal cell-cell communication to compute the border between a sender/receiver and a processing cell population. The two populations communicate via L-tryptophan and interleukin-4 to highlight the population border by the production of a fluorescent protein. The sharpness of that visualized edge can be adjusted by modulating key parameters of the network. Conclusions We anticipate that this network will on the one hand be a useful tool to gain deeper insights into the mechanisms of tissue formation in nature and will on the other hand contribute to our ability to engineer artificial tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0252-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Kolar
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany
| | - Hanna M Wischhusen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: DMK GmbH, Head of Quality Assurance, DE-26939, Ovelgönne, Germany
| | - Konrad Müller
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Novartis Pharma AG, Biologics Process R&D, CH-4002, Basel, Switzerland
| | - Maria Karlsson
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Respiratory, Inflammation and Autoimmunity (RIA) iMED, AstraZeneca, SE-431 83, Mölndal, Sweden
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, DE-79104, Freiburg, Germany
| | - Matias D Zurbriggen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany. .,Present address: Institute of Synthetic Biology and Cluster of Excellence on Plant Science (CEPLAS), University of Düsseldorf, DE-40225, Düsseldorf, Germany.
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25
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Terrell JL, Wu HC, Tsao CY, Barber NB, Servinsky MD, Payne GF, Bentley WE. Nano-guided cell networks as conveyors of molecular communication. Nat Commun 2015; 6:8500. [PMID: 26455828 PMCID: PMC4633717 DOI: 10.1038/ncomms9500] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 08/28/2015] [Indexed: 01/06/2023] Open
Abstract
Advances in nanotechnology have provided unprecedented physical means to sample molecular space. Living cells provide additional capability in that they identify molecules within complex environments and actuate function. We have merged cells with nanotechnology for an integrated molecular processing network. Here we show that an engineered cell consortium autonomously generates feedback to chemical cues. Moreover, abiotic components are readily assembled onto cells, enabling amplified and 'binned' responses. Specifically, engineered cell populations are triggered by a quorum sensing (QS) signal molecule, autoinducer-2, to express surface-displayed fusions consisting of a fluorescent marker and an affinity peptide. The latter provides means for attaching magnetic nanoparticles to fluorescently activated subpopulations for coalescence into colour-indexed output. The resultant nano-guided cell network assesses QS activity and conveys molecular information as a 'bio-litmus' in a manner read by simple optical means.
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Affiliation(s)
- Jessica L Terrell
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Hsuan-Chen Wu
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Chen-Yu Tsao
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Nathan B Barber
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA
| | - Matthew D Servinsky
- U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20783, USA
| | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
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26
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Zargar A, Payne GF, Bentley WE. A 'bioproduction breadboard': programming, assembling, and actuating cellular networks. Curr Opin Biotechnol 2015; 36:154-60. [PMID: 26342587 DOI: 10.1016/j.copbio.2015.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/07/2015] [Accepted: 08/14/2015] [Indexed: 10/23/2022]
Abstract
With advances in synthetic biology and biofabrication, cellular networks can be functionalized and connected with unprecedented sophistication. We describe a platform for the creation of a 'bioproduction breadboard'. This would consist of physically isolated product-producing cell populations, product capture devices, and other unit operations that function as programmed in place, using unique, orthogonal inputs. For product synthesis, customized cell populations would be connected through standardized, generic inputs allowing 'plug and play' functionality and primary, user-mediated regulation. In addition, through autonomous pathway redirection and balancing, the cells themselves would provide secondary, self-directed regulation to optimize bioproduction. By leveraging specialization and division of labor, we envision diverse cell populations linked to create new pathway designs.
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Affiliation(s)
- Amin Zargar
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, MD 20742, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, MD 20742, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, College Park, MD 20742, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
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27
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Affiliation(s)
- Kristin Hagen
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Margret Engelhard
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Georg Toepfer
- Center for Literary and Cultural Research Berlin, Berlin, Germany
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28
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Artificial cell-cell communication as an emerging tool in synthetic biology applications. J Biol Eng 2015; 9:13. [PMID: 26265937 PMCID: PMC4531478 DOI: 10.1186/s13036-015-0011-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/25/2015] [Indexed: 01/14/2023] Open
Abstract
Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication modes offer the possibility to control the behavior of an entire community by modifying the performance of individual cells in specific ways. Synthetic biology, i.e., the implementation of artificial functions within biological systems, is a promising approach towards the engineering of sophisticated, autonomous devices based on specifically functionalized cells. With the growing complexity of the functions performed by such systems, both the risk of circuit crosstalk and the metabolic burden resulting from the expression of numerous foreign genes are increasing. Therefore, systems based on a single type of cells are no longer feasible. Synthetic biology approaches with multiple subpopulations of specifically functionalized cells, wired by artificial cell-cell communication systems, provide an attractive and powerful alternative. Here we review recent applications of synthetic cell-cell communication systems with a specific focus on recent advances with fungal hosts.
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29
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Synthetic biology expands chemical control of microorganisms. Curr Opin Chem Biol 2015; 28:20-8. [PMID: 26056951 DOI: 10.1016/j.cbpa.2015.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/30/2015] [Accepted: 05/15/2015] [Indexed: 01/21/2023]
Abstract
The tools of synthetic biology allow researchers to change the ways engineered organisms respond to chemical stimuli. Decades of basic biology research and new efforts in computational protein and RNA design have led to the development of small molecule sensors that can be used to alter organism function. These new functions leap beyond the natural propensities of the engineered organisms. They can range from simple fluorescence or growth reporting to pathogen killing, and can involve metabolic coordination among multiple cells or organisms. Herein, we discuss how synthetic biology alters microorganisms' responses to chemical stimuli resulting in the development of microbes as toxicity sensors, disease treatments, and chemical factories.
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30
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Wang H, Ye H, Xie M, Daoud El-Baba M, Fussenegger M. Cosmetics-triggered percutaneous remote control of transgene expression in mice. Nucleic Acids Res 2015; 43:e91. [PMID: 25943548 PMCID: PMC4538802 DOI: 10.1093/nar/gkv326] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/31/2015] [Indexed: 12/24/2022] Open
Abstract
Synthetic biology has significantly advanced the rational design of trigger-inducible gene switches that program cellular behavior in a reliable and predictable manner. Capitalizing on genetic componentry, including the repressor PmeR and its cognate operator OPmeR, that has evolved in Pseudomonas syringae pathovar tomato DC3000 to sense and resist plant-defence metabolites of the paraben class, we have designed a set of inducible and repressible mammalian transcription-control devices that could dose-dependently fine-tune transgene expression in mammalian cells and mice in response to paraben derivatives. With an over 60-years track record as licensed preservatives in the cosmetics industry, paraben derivatives have become a commonplace ingredient of most skin-care products including shower gels, cleansing toners and hand creams. As parabens can rapidly reach the bloodstream of mice following topical application, we used this feature to percutaneously program transgene expression of subcutaneous designer cell implants using off-the-shelf commercial paraben-containing skin-care cosmetics. The combination of non-invasive, transdermal and orthogonal trigger-inducible remote control of transgene expression may provide novel opportunities for dynamic interventions in future gene and cell-based therapies.
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Affiliation(s)
- Hui Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Haifeng Ye
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, 200241 Shanghai, China
| | - Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Marie Daoud El-Baba
- Département Génie Biologique, Institut Universitaire de Technologie, F-69622 Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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31
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Liu H, Lu T. Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered Escherichia coli. Metab Eng 2015; 29:135-141. [DOI: 10.1016/j.ymben.2015.03.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
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32
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Liu Y, Wu HC, Chhuan M, Terrell JL, Tsao CY, Bentley WE, Payne GF. Functionalizing Soft Matter for Molecular Communication. ACS Biomater Sci Eng 2015; 1:320-328. [PMID: 26501127 PMCID: PMC4603720 DOI: 10.1021/ab500160e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/26/2015] [Indexed: 11/28/2022]
Abstract
![]()
The
information age was enabled by advances in microfabrication
and communication theory that allowed information to be processed
by electrons and transmitted by electromagnetic radiation. Despite
immense capabilities, microelectronics has limited abilities to access
and participate in the molecular-based communication that characterizes
our biological world. Here, we use biological materials and methods
to create components and fabricate devices to perform simple molecular
communication functions based on bacterial quorum sensing (QS). Components
were created by protein engineering to generate a multidomain fusion
protein capable of sending a molecular QS signal, and by synthetic
biology to engineer E. coli to receive and report
this QS signal. The device matrix was formed using stimuli-responsive
hydrogel-forming biopolymers (alginate and gelatin). Assembly of the
components within the device matrix was achieved by physically entrapping
the cell-based components, and covalently conjugating the protein-based
components using the enzyme microbial transglutaminase. We demonstrate
simple devices that can send or receive a molecular QS signal to/from
the surrounding medium, and a two-component device in which one component
generates the signal (i.e., issues a command) that is acted upon by
the second component. These studies illustrate the broad potential
of biofabrication to generate molecular communication devices.
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Affiliation(s)
- Yi Liu
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Hsuan-Chen Wu
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Melanie Chhuan
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Jessica L Terrell
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
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33
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Heng BC, Aubel D, Fussenegger M. Prosthetic gene networks as an alternative to standard pharmacotherapies for metabolic disorders. Curr Opin Biotechnol 2015; 35:37-45. [PMID: 25679308 DOI: 10.1016/j.copbio.2015.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/28/2015] [Accepted: 01/28/2015] [Indexed: 12/19/2022]
Abstract
Synthetic biology makes inroads into clinical therapy with the debut of closed-loop prosthetic gene networks specifically designed to treat human diseases. Prosthetic networks are synthetic sensor/effector devices that could functionally integrate and interface with host metabolism to monitor disease states and coordinate appropriate therapeutic responses in a self-sufficient, timely and automatic manner. Prosthetic networks hold particular promise for the current global epidemic of closely interrelated metabolic disorders encompassing obesity, type 2 diabetes, hypertension and hyperlipidaemia, which arise from the unhealthy lifestyle and dietary factors in the modern urbanised world. This review will critically examine the various attempts at constructing prosthetic gene networks for the treatment of these metabolic disorders, as well as provide insight into future developments in the field.
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Affiliation(s)
- Boon Chin Heng
- Department of Biological Sciences, Sunway University, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia; Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Boulevard du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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34
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Barcena Menendez D, Senthivel VR, Isalan M. Sender-receiver systems and applying information theory for quantitative synthetic biology. Curr Opin Biotechnol 2015; 31:101-7. [PMID: 25282688 PMCID: PMC4332572 DOI: 10.1016/j.copbio.2014.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 12/31/2022]
Abstract
Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning.
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Affiliation(s)
- Diego Barcena Menendez
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Vivek Raj Senthivel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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35
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DiSCUS: A Simulation Platform for Conjugation Computing. UNCONVENTIONAL COMPUTATION AND NATURAL COMPUTATION 2015. [DOI: 10.1007/978-3-319-21819-9_13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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Goers L, Freemont P, Polizzi KM. Co-culture systems and technologies: taking synthetic biology to the next level. J R Soc Interface 2014; 11:rsif.2014.0065. [PMID: 24829281 DOI: 10.1098/rsif.2014.0065] [Citation(s) in RCA: 343] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions.
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Affiliation(s)
- Lisa Goers
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Paul Freemont
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Karen M Polizzi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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37
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Dorado-Morales P, Iglesias A, Zafrilla G, Valero A, Torres A, Miravet-Verde S, de Loma J, Mañas M, Ruiz A, Corman A, Morales LJ, Peretó J, Vilanova C, Porcar M. Engineering bacteria to form a biofilm and induce clumping in Caenorhabditis elegans. ACS Synth Biol 2014; 3:941-3. [PMID: 24933529 DOI: 10.1021/sb4001883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria are needed for a vast range of biotechnological processes, which they carry out either as pure cultures or in association with other bacteria and/or fungi. The potential of bacteria as biofactories is hampered, though, by their limited mobility in solid or semisolid media such as agricultural or domestic waste. This work represents an attempt toward overcoming this limitation by associating bacterial biotechnological properties with the transport ability of the nematode Caenorhabditis elegans. We report here biofilm formation on C. elegans by engineered Escherichia coli expressing a Xhenorhabdus nematophila adhesion operon and induction of nematode social feeding behavior (clumping) through an E. coli-mediated iRNA blocking on the expression of FLP-21, a neuropeptide involved in worm solitary behavior.
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Affiliation(s)
- Pedro Dorado-Morales
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Alba Iglesias
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Guillermo Zafrilla
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Alejandro Valero
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Alejandro Torres
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Samuel Miravet-Verde
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Jessica de Loma
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Marina Mañas
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Antonio Ruiz
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Alba Corman
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Lucas J. Morales
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Juli Peretó
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
- Departament
de Bioquímica i Biologia Molecular, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Cristina Vilanova
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
| | - Manuel Porcar
- Institut
Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, Valencia, Spain
- Fundació General de la Universitat de València, 46980 Paterna, Valencia, Spain
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38
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A yeast pheromone-based inter-species communication system. Appl Microbiol Biotechnol 2014; 99:1299-308. [PMID: 25331280 DOI: 10.1007/s00253-014-6133-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
We report on a pheromone-based inter-species communication system, allowing for a controlled cell-cell communication between the two species Saccharomyces cerevisiae and Schizosaccharomyces pombe as a proof of principle. It exploits the mating response pathways of the two yeast species employing the pheromones, α- or P-factor, as signaling molecules. The authentic and chimeric pheromone-encoding genes were engineered to code for the P-factor in S. cerevisiae and the α-factor in S. pombe. Upon transformation of the respective constructs, cells were enabled to express the mating pheromone of the opposite species. The supernatant of cultures of S. pombe cells expressing α-factor were able to induce a G1 arrest in the cell cycle, a change in morphology to the typical shmoo effect and expression driven by the pheromone-responsive FIG1 promoter in S. cerevisiae. The supernatant of cultures of S. cerevisiae cells expressing P-factor similarly induced cell cycle arrest in G1, an alteration in morphology typical for mating as well as the activation of the pheromone-responsive promoters of the rep1 and sxa2 genes in a pheromone-hypersensitive reporter strain of S. pombe. Apparently, both heterologous pheromones were correctly processed and secreted in an active form by the cells of the other species. Our data clearly show that the species-specific pheromone systems of yeast species can be exploited for a controlled inter-species communication.
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39
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Xie M, Ye H, Hamri GCE, Fussenegger M. Antagonistic control of a dual-input mammalian gene switch by food additives. Nucleic Acids Res 2014; 42:e116. [PMID: 25030908 PMCID: PMC4132709 DOI: 10.1093/nar/gku545] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology has significantly advanced the design of mammalian trigger-inducible transgene-control devices that are able to programme complex cellular behaviour. Fruit-based benzoate derivatives licensed as food additives, such as flavours (e.g. vanillate) and preservatives (e.g. benzoate), are a particularly attractive class of trigger compounds for orthogonal mammalian transgene control devices because of their innocuousness, physiological compatibility and simple oral administration. Capitalizing on the genetic componentry of the soil bacterium Comamonas testosteroni, which has evolved to catabolize a variety of aromatic compounds, we have designed different mammalian gene expression systems that could be induced and repressed by the food additives benzoate and vanillate. When implanting designer cells engineered for gene switch-driven expression of the human placental secreted alkaline phosphatase (SEAP) into mice, blood SEAP levels of treated animals directly correlated with a benzoate-enriched drinking programme. Additionally, the benzoate-/vanillate-responsive device was compatible with other transgene control systems and could be assembled into higher-order control networks providing expression dynamics reminiscent of a lap-timing stopwatch. Designer gene switches using licensed food additives as trigger compounds to achieve antagonistic dual-input expression profiles and provide novel control topologies and regulation dynamics may advance future gene- and cell-based therapies.
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Affiliation(s)
- Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Haifeng Ye
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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40
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Song H, Ding MZ, Jia XQ, Ma Q, Yuan YJ. Synthetic microbial consortia: from systematic analysis to construction and applications. Chem Soc Rev 2014; 43:6954-81. [PMID: 25017039 DOI: 10.1039/c4cs00114a] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.
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Affiliation(s)
- Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, and Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China.
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41
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Ye H, Fussenegger M. Synthetic therapeutic gene circuits in mammalian cells. FEBS Lett 2014; 588:2537-44. [PMID: 24844435 DOI: 10.1016/j.febslet.2014.05.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 05/05/2014] [Indexed: 12/19/2022]
Abstract
In the emerging field of synthetic biology, scientists are focusing on designing and creating functional devices, systems, and organisms with novel functions by engineering and assembling standardised biological building blocks. The progress of synthetic biology has significantly advanced the design of functional gene networks that can reprogram metabolic activities in mammalian cells and provide new therapeutic opportunities for future gene- and cell-based therapies. In this review, we describe the most recent advances in synthetic mammalian gene networks designed for biomedical applications, including how these synthetic therapeutic gene circuits can be assembled to control signalling networks and applied to treat metabolic disorders, cancer, and immune diseases. We conclude by discussing the various challenges and future prospects of using synthetic mammalian gene networks for disease therapy.
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Affiliation(s)
- Haifeng Ye
- 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; Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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42
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Zafrilla G, Iglesias A, Marín M, Torralba L, Dorado-Morales P, Racero JL, Alcaina JJ, Morales LJ, Martínez L, Collantes M, Gómez L, Vilanova C, Porcar M. Towards light-mediated sensing of bacterial comfort. Lett Appl Microbiol 2014; 59:127-32. [PMID: 24785827 DOI: 10.1111/lam.12255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/25/2014] [Accepted: 03/19/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED Bacterial comfort is central to biotechnological applications. Here, we report the characterization of different sensoring systems, the first step within a broader synthetic biology-inspired light-mediated strategy to determine Escherichia coli perception of environmental factors critical to bacterial performance. We did so by directly 'asking' bacterial cultures with light-encoded questions corresponding to the excitation wavelength of fluorescent proteins placed under the control of environment-sensitive promoters. We built four genetic constructions with fluorescent proteins responding to glucose, temperature, oxygen and nitrogen; and a fifth construction allowing UV-induced expression of heterologous genes. Our engineered strains proved able to give feedback in response to key environmental factors and to express heterologous proteins upon light induction. This light-based dialoguing strategy reported here is the first effort towards developing a human-bacteria interphase with both fundamental and applied implications. SIGNIFICANCE AND IMPACT OF THE STUDY The results we present here are at the core of a larger synthetic biology research effort aiming at establishing a dialogue with bacteria. The framework is to convert the human voice into electric pulses, these into light pulses exciting bacterial fluorescent proteins, and convert light-emission back into electric pulses, which will be finally transformed into synthetic voice messages. We report here the first results of the project, in the form of light-based determination of key parameters for bacterial comfort. The ultimate goal of this strategy is to combine different engineered populations to have a combined feedback from the pool.
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Affiliation(s)
- G Zafrilla
- Universitat de València (Cavanilles Institute of Biodiversity and Evolutionary Biology), Valencia, Spain
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43
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44
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Porcar M, Latorre A, Moya A. What Symbionts Teach us about Modularity. Front Bioeng Biotechnol 2013; 1:14. [PMID: 25023877 PMCID: PMC4090905 DOI: 10.3389/fbioe.2013.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/22/2013] [Indexed: 11/13/2022] Open
Abstract
The main goal of Synthetic Biology (SB) is to apply engineering principles to biotechnology in order to make life easier to engineer. These engineering principles include modularity: decoupling of complex systems into smaller, orthogonal sub-systems that can be used in a range of different applications. The successful use of modules in engineering is expected to be reproduced in synthetic biological systems. But the difficulties experienced up to date with SB approaches question the short-term feasibility of designing life. Considering the “engineerable” nature of life, here we discuss the existence of modularity in natural living systems, particularly in symbiotic interactions, and compare the behavior of such systems, with those of engineered modules. We conclude that not only is modularity present but it is also common among living structures, and that symbioses are a new example of module-like sub-systems having high similarity with modularly designed ones. However, we also detect and stress fundamental differences between man-made and biological modules. Both similarities and differences should be taken into account in order to adapt SB design to biological laws.
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Affiliation(s)
- Manuel Porcar
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Fundació General de la Universitat de València , València , Spain
| | - Amparo Latorre
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - Salud Pública , València , Spain
| | - Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - Salud Pública , València , Spain
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45
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Reetz MT. Biocatalysis in organic chemistry and biotechnology: past, present, and future. J Am Chem Soc 2013; 135:12480-96. [PMID: 23930719 DOI: 10.1021/ja405051f] [Citation(s) in RCA: 522] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of the 20th century, but nevertheless suffered from two major limitations. First, many enzymes were not accessible in large enough quantities for practical applications. The advent of recombinant DNA technology changed this dramatically in the late 1970s. Second, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity and/or insufficient stability under operating conditions. With the development of directed evolution beginning in the 1990s and continuing to the present day, all of these problems can be addressed and generally solved. The present Perspective focuses on these and other developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Included is a discussion of the scope and limitation of cascade reactions using enzyme mixtures in vitro and of metabolic engineering of pathways in cells as factories for the production of simple compounds such as biofuels and complex natural products. Future trends and problems are also highlighted, as is the discussion concerning biocatalysis versus nonbiological catalysis in synthetic organic chemistry. This Perspective does not constitute a comprehensive review, and therefore the author apologizes to those researchers whose work is not specifically treated here.
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Affiliation(s)
- Manfred T Reetz
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg, Germany.
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46
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Du J, Bai W, Song H, Yuan YJ. Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-L-gulonic acid production in Ketogulonigenium vulgare-Bacillus cereus consortium. Metab Eng 2013; 19:50-6. [PMID: 23747604 DOI: 10.1016/j.ymben.2013.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 05/26/2013] [Accepted: 05/30/2013] [Indexed: 11/29/2022]
Abstract
The expression levels of sorbose/sorbosone dehydrogenase genes (sdh and sndh) and the synthesis genes (pqqABCDEN) of the adjoint cofactor pyrroloquinoline quinone (PQQ) were genetically manipulated in Ketogulonigenium vulgare to increase the production of 2-keto-l-gulonic acid (2-KLG), the precursor of vitamin C, in the consortium of K. vulgare and Bacillus cereus. We found that overexpression of sdh-sndh alone in K. vulgare could not significantly enhance the production of 2-KLG, revealing the cofactor PQQ was required for the biosynthesis of 2-KLG. Various expression levels of PQQ were achieved by differential expression of pqqA, pqqABCDE and pqqABCDEN, respectively. The combinatorial expression of sdh/sndh and pqqABCDEN in K. vulgare enabled a 20% increase in the production of 2-KLG (79.1±0.6gl(-1)) than that of the parental K. vulgare (65.9±0.4gl(-1)) in shaking flasks. Our results demonstrated the balanced co-expression of both the key enzymes and the related cofactors was an efficient strategy to increase chemicals' biosynthesis.
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Affiliation(s)
- Jin Du
- Key Laboratory of Systems Bioengineering, Ministry of Education and Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, P.O. Box 6888, Tianjin 300072, PR China
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