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Urrios A, Gonzalez-Flo E, Canadell D, de Nadal E, Macia J, Posas F. Plug-and-Play Multicellular Circuits with Time-Dependent Dynamic Responses. ACS Synth Biol 2018; 7:1095-1104. [PMID: 29584406 DOI: 10.1021/acssynbio.7b00463] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic biology studies aim to develop cellular devices for biomedical applications. These devices, based on living instead of electronic or electromechanic technology, might provide alternative treatments for a wide range of diseases. However, the feasibility of these devices depends, in many cases, on complex genetic circuits that must fulfill physiological requirements. In this work, we explored the potential of multicellular architectures to act as an alternative to complex circuits for implementation of new devices. As a proof of concept, we developed specific circuits for insulin or glucagon production in response to different glucose levels. Here, we show that fundamental features, such as circuit's affinity or sensitivity, are dependent on the specific configuration of the multicellular consortia, providing a method for tuning these properties without genetic engineering. As an example, we have designed and built circuits with an incoherent feed-forward loop architecture (FFL) that can be easily adjusted to generate single pulse responses. Our results might serve as a blueprint for future development of cellular devices for glycemia regulation in diabetic patients.
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Urrios A, Macia J, Manzoni R, Conde N, Bonforti A, de Nadal E, Posas F, Solé R. A Synthetic Multicellular Memory Device. ACS Synth Biol 2016; 5:862-73. [PMID: 27439436 DOI: 10.1021/acssynbio.5b00252] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Changing environments pose a challenge to living organisms. Cells need to gather and process incoming information, adapting to changes in predictable ways. This requires in particular the presence of memory, which allows different internal states to be stored. Biological memory can be stored by switches that retain information on past and present events. Synthetic biologists have implemented a number of memory devices for biological applications, mostly in single cells. It has been shown that the use of multicellular consortia provides interesting advantages to implement biological circuits. Here we show how to build a synthetic biological memory switch using an eukaryotic consortium. We engineered yeast cells that can communicate and retain memory of changes in the extracellular environment. These cells were able to produce and secrete a pheromone and sense a different pheromone following NOT logic. When the two strains were cocultured, they behaved as a double-negative-feedback motif with memory. In addition, we showed that memory can be effectively changed by the use of external inputs. Further optimization of these modules and addition of other cells could lead to new multicellular circuits that exhibit memory over a broad range of biological inputs.
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Affiliation(s)
| | | | | | | | - Adriano Bonforti
- Centre per a la Innovació de la Diabetis Infantil Sant Joan de Déu (CIDI), E-08950 Esplugues de Llobregat, Barcelona, Spain
| | | | | | - Ricard Solé
- Santa Fe Institute, Santa Fe, New Mexico 87501, United States
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Sardanyés J, Bonforti A, Conde N, Solé R, Macia J. Computational implementation of a tunable multicellular memory circuit for engineered eukaryotic consortia. Front Physiol 2015; 6:281. [PMID: 26500559 PMCID: PMC4598587 DOI: 10.3389/fphys.2015.00281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/22/2015] [Indexed: 11/25/2022] Open
Abstract
Cells are complex machines capable of processing information by means of an entangled network of molecular interactions. A crucial component of these decision-making systems is the presence of memory and this is also a specially relevant target of engineered synthetic systems. A classic example of memory devices is a 1-bit memory element known as the flip-flop. Such system can be in principle designed using a single-cell implementation, but a direct mapping between standard circuit design and a living circuit can be cumbersome. Here we present a novel computational implementation of a 1-bit memory device using a reliable multicellular design able to behave as a set-reset flip-flop that could be implemented in yeast cells. The dynamics of the proposed synthetic circuit is investigated with a mathematical model using biologically-meaningful parameters. The circuit is shown to behave as a flip-flop in a wide range of parameter values. The repression strength for the NOT logics is shown to be crucial to obtain a good flip-flop signal. Our model also shows that the circuit can be externally tuned to achieve different memory states and dynamics, such as persistent and transient memory. We have characterized the parameter domains for robust memory storage and retrieval as well as the corresponding time response dynamics.
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Affiliation(s)
- Josep Sardanyés
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra Barcelona, Spain ; Institut de Biologia Evolutiva, CSIC-UPF Barcelona, Spain
| | - Adriano Bonforti
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra Barcelona, Spain ; Institut de Biologia Evolutiva, CSIC-UPF Barcelona, Spain
| | - Nuria Conde
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra Barcelona, Spain ; Institut de Biologia Evolutiva, CSIC-UPF Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra Barcelona, Spain ; Institut de Biologia Evolutiva, CSIC-UPF Barcelona, Spain ; Santa Fe Institute Santa Fe, NM, USA
| | - Javier Macia
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra Barcelona, Spain ; Institut de Biologia Evolutiva, CSIC-UPF Barcelona, Spain
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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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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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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: 342] [Impact Index Per Article: 34.2] [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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Singh V. Recent advances and opportunities in synthetic logic gates engineering in living cells. SYSTEMS AND SYNTHETIC BIOLOGY 2014; 8:271-82. [PMID: 26396651 DOI: 10.1007/s11693-014-9154-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 08/09/2014] [Accepted: 08/23/2014] [Indexed: 01/03/2023]
Abstract
Recently, a number of synthetic biologic gates including AND, OR, NOR, NOT, XOR and NAND have been engineered and characterized in a wide range of hosts. The hope in the emerging synthetic biology community is to construct an inventory of well-characterized parts and install distinct gene and circuit behaviours that are externally controllable. Though the field is still growing and major successes are yet to emerge, the payoffs are predicted to be significant. In this review, we highlight specific examples of logic gates engineering with applications towards fundamental understanding of network complexity and generating a novel socially useful applications.
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Affiliation(s)
- Vijai Singh
- Department of Biotechnology, Invertis University, Bareilly- Lucknow National Highway-24, Bareilly, 243123 India ; Synthetic Biology Laboratory, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulju-gun, Ulsan, 689-798 Republic of Korea
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Moe-Behrens GH. The biological microprocessor, or how to build a computer with biological parts. Comput Struct Biotechnol J 2013; 7:e201304003. [PMID: 24688733 PMCID: PMC3962179 DOI: 10.5936/csbj.201304003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 01/21/2023] Open
Abstract
Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.
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