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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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Masaeli E, Marquette C. Direct-Write Bioprinting Approach to Construct Multilayer Cellular Tissues. Front Bioeng Biotechnol 2020; 7:478. [PMID: 32039181 PMCID: PMC6985038 DOI: 10.3389/fbioe.2019.00478] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/23/2019] [Indexed: 12/20/2022] Open
Abstract
As a cellular-assembly technique, bioprinting has been extensively used in tissue engineering and regenerative medicine to construct hydrogel-based three-dimensional (3D) tissue-like models with prescribed geometry. Here, we introduced a unique direct-write bioprinting strategy to fabricate a bilayer flat tissue in a hydrogel-free approach. A printed retina pigmented epithelium layer (RPE) was applied as living biopaper for positioning a fibroblast layer without using any hydrogel in bioink. We adjusted the number of cells in the inkjet droplets in order to obtain a uniform printed cell layer and demonstrated the formation of a bilayer construct through confocal imaging. Since our printing system introduced low levels of shear stress to the cells, it did not have a negative effect on cell survival, although cell viability was generally lower than that of control group over 1 week post-printing. In conclusion, our novel direct-write bioprinting approach to spatiotemporally position different cellular layers may represent an efficient tool to develop living constructs especially for regeneration of complex flat tissues.
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Affiliation(s)
- Elahe Masaeli
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.,3d.FAB, Univ Lyon, Université Lyon1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, Bat. Lederer, Villeurbanne, France
| | - Christophe Marquette
- 3d.FAB, Univ Lyon, Université Lyon1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, Bat. Lederer, Villeurbanne, France
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3
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Zhou X, Franklin RA, Adler M, Jacox JB, Bailis W, Shyer JA, Flavell RA, Mayo A, Alon U, Medzhitov R. Circuit Design Features of a Stable Two-Cell System. Cell 2018; 172:744-757.e17. [PMID: 29398113 PMCID: PMC7377352 DOI: 10.1016/j.cell.2018.01.015] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/06/2017] [Accepted: 01/08/2018] [Indexed: 12/14/2022]
Abstract
Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit with specific properties that ensure homeostasis. Here, we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations. Analytical screening of all possible two-cell circuit topologies revealed the circuit features sufficient for stability, including environmental constraint and negative-feedback regulation. Moreover, we found that cell-cell contact is essential for the stability of the macrophage-fibroblast circuit. These findings illustrate principles of cell circuit design and provide a quantitative perspective on cell interactions.
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Affiliation(s)
- Xu Zhou
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ruth A Franklin
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Miri Adler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Jeremy B Jacox
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Will Bailis
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Justin A Shyer
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard A Flavell
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Ruslan Medzhitov
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA.
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4
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Amyloid single-cell cytotoxicity assays by nanomotion detection. Cell Death Discov 2017; 3:17053. [PMID: 28845298 PMCID: PMC5564330 DOI: 10.1038/cddiscovery.2017.53] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/06/2017] [Accepted: 06/30/2017] [Indexed: 11/18/2022] Open
Abstract
Cells are extremely complex systems able to actively modify their metabolism and behavior in response to environmental conditions and stimuli such as pathogenic agents or drugs. The comprehension of these responses is central to understand the molecular bases of human pathologies, including amyloid misfolding diseases. Conventional bulk biological assays are limited by intrinsic cellular heterogeneity in gene, protein and metabolite expression, and can investigate only indirectly cellular reactions in non-physiological conditions. Here we employ a label-free nanomotion sensor to study single neuroblastoma cells exposed to extracellular monomeric and amyloid α-synuclein species in real-time and in physiological conditions. Combining this technique with fluorescence microscopy, we demonstrate multispecies cooperative cytotoxic effect of amyloids and aggregate-induced loss of cellular membrane integrity. Notably, the method can study cellular reactions and cytotoxicity an order of magnitude faster, and using 100-fold smaller volume of reagents when compared to conventional bulk analyses. This rapidity and sensitivity will allow testing novel pharmacological approaches to stop or delay a wide range of human diseases.
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5
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Zucca S, Pasotti L, Politi N, Casanova M, Mazzini G, Cusella De Angelis MG, Magni P. Multi-Faceted Characterization of a Novel LuxR-Repressible Promoter Library for Escherichia coli. PLoS One 2015; 10:e0126264. [PMID: 26010244 PMCID: PMC4444344 DOI: 10.1371/journal.pone.0126264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
The genetic elements regulating the natural quorum sensing (QS) networks of several microorganisms are widely used in synthetic biology to control the behaviour of single cells and engineered bacterial populations via ad-hoc constructed synthetic circuits. A number of novel engineering-inspired biological functions have been implemented and model systems have also been constructed to improve the knowledge on natural QS systems. Synthetic QS-based parts, such as promoters, have been reported in literature, to provide biological components with functions that are not present in nature, like modified induction logic or activation/repression by additional molecules. In this work, a library of promoters that can be repressed by the LuxR protein in presence of the QS autoinducer N-3-oxohexanoyl-L-homoserine lactone (AHL) was reported for Escherichia coli, to expand the toolkit of genetic parts that can be used to engineer novel synthetic QS-based systems. The library was constructed via polymerase chain reaction with highly constrained degenerate oligonucleotides, designed according to the consensus -35 and -10 sequences of a previously reported constitutive promoter library of graded strength, to maximize the probability of obtaining functional clones. All the promoters have a lux box between the -35 and -10 regions, to implement a LuxR-repressible behaviour. Twelve unique library members of graded strength (about 100-fold activity range) were selected to form the final library and they were characterized in several genetic contexts, such as in different plasmids, via different reporter genes, in presence of a LuxR expression cassette in different positions and in response to different AHL concentrations. The new obtained regulatory parts and corresponding data can be exploited by synthetic biologists to implement an artificial AHL-dependent repression of transcription in genetic circuits. The target transcriptional activity can be selected among the available library members to meet the design specifications of the biological system.
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Affiliation(s)
- Susanna Zucca
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | - Lorenzo Pasotti
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | - Nicolò Politi
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | - Michela Casanova
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | | | | | - Paolo Magni
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
- * E-mail:
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Davis RM, Muller RY, Haynes KA. Can the natural diversity of quorum-sensing advance synthetic biology? Front Bioeng Biotechnol 2015; 3:30. [PMID: 25806368 PMCID: PMC4354409 DOI: 10.3389/fbioe.2015.00030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/21/2015] [Indexed: 12/12/2022] Open
Abstract
Quorum-sensing networks enable bacteria to sense and respond to chemical signals produced by neighboring bacteria. They are widespread: over 100 morphologically and genetically distinct species of eubacteria are known to use quorum sensing to control gene expression. This diversity suggests the potential to use natural protein variants to engineer parallel, input-specific, cell-cell communication pathways. However, only three distinct signaling pathways, Lux, Las, and Rhl, have been adapted for and broadly used in engineered systems. The paucity of unique quorum-sensing systems and their propensity for crosstalk limits the usefulness of our current quorum-sensing toolkit. This review discusses the need for more signaling pathways, roadblocks to using multiple pathways in parallel, and strategies for expanding the quorum-sensing toolbox for synthetic biology.
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Affiliation(s)
- René Michele Davis
- Ira A. Fulton School of Biological and Health Systems Engineering, Arizona State University , Tempe, AZ , USA ; Biological Design Graduate Program, Arizona State University , Tempe, AZ , USA
| | - Ryan Yue Muller
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, AZ , USA ; School of Life Sciences, Arizona State University , Tempe, AZ , USA
| | - Karmella Ann Haynes
- Ira A. Fulton School of Biological and Health Systems Engineering, Arizona State University , Tempe, AZ , USA
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7
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Chen AY, Deng Z, Billings AN, Seker UO, Lu MY, Citorik RJ, Zakeri B, Lu TK. Synthesis and patterning of tunable multiscale materials with engineered cells. NATURE MATERIALS 2014; 13:515-23. [PMID: 24658114 PMCID: PMC4063449 DOI: 10.1038/nmat3912] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 02/11/2014] [Indexed: 05/03/2023]
Abstract
Many natural biological systems--such as biofilms, shells and skeletal tissues--are able to assemble multifunctional and environmentally responsive multiscale assemblies of living and non-living components. Here, by using inducible genetic circuits and cellular communication circuits to regulate Escherichia coli curli amyloid production, we show that E. coli cells can organize self-assembling amyloid fibrils across multiple length scales, producing amyloid-based materials that are either externally controllable or undergo autonomous patterning. We also interfaced curli fibrils with inorganic materials, such as gold nanoparticles (AuNPs) and quantum dots (QDs), and used these capabilities to create an environmentally responsive biofilm-based electrical switch, produce gold nanowires and nanorods, co-localize AuNPs with CdTe/CdS QDs to modulate QD fluorescence lifetimes, and nucleate the formation of fluorescent ZnS QDs. This work lays a foundation for synthesizing, patterning, and controlling functional composite materials with engineered cells.
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Affiliation(s)
- Allen Y. Chen
- Biophysics Program, Harvard University, Cambridge, MA
02138, USA
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
- Harvard-MIT Health Sciences and Technology, Institute for
Medical Engineering and Science, 77 Massachusetts Avenue, Cambridge, MA 02139,
USA
| | - Zhengtao Deng
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Amanda N. Billings
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Urartu O.S. Seker
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Michelle Y. Lu
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Robert J. Citorik
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
- MIT Microbiology Program, 77 Massachusetts Avenue,
Cambridge MA 02139, USA
| | - Bijan Zakeri
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Timothy K. Lu
- Biophysics Program, Harvard University, Cambridge, MA
02138, USA
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
- MIT Microbiology Program, 77 Massachusetts Avenue,
Cambridge MA 02139, USA
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