1
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Smirnov VV, Drozd VS, Patra CK, Hussein Z, Rybalko DS, Kozlova AV, Nour MAY, Zemerova TP, Kolosova OS, Kalnin AY, El-Deeb AA. Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs. Analyst 2024; 149:1947-1957. [PMID: 38385166 DOI: 10.1039/d3an02178e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.
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Affiliation(s)
- Viktor V Smirnov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Valerya S Drozd
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Christina K Patra
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Daria S Rybalko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Tatiana P Zemerova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Olga S Kolosova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Faculty of Industrial Drug Technology, Saint Petersburg State Chemical and Pharmaceutical University, 14, lit. A, st. Professor Popov, 197022, St. Petersburg, Russian Federation
| | - Arseniy Y Kalnin
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Institute of Chemistry, Saint Petersburg University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
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2
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Zeng M, Sarker B, Rondthaler SN, Vu V, Andrews LB. Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape. ACS Synth Biol 2024; 13:568-589. [PMID: 38206199 DOI: 10.1021/acssynbio.3c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.
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Affiliation(s)
- Min Zeng
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen N Rondthaler
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Vanessa Vu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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3
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Zeng M, Sarker B, Howitz N, Shah I, Andrews LB. Synthetic Homoserine Lactone Sensors for Gram-Positive Bacillus subtilis Using LuxR-Type Regulators. ACS Synth Biol 2024; 13:282-299. [PMID: 38079538 PMCID: PMC10805106 DOI: 10.1021/acssynbio.3c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 01/23/2024]
Abstract
A universal biochemical signal for bacterial cell-cell communication could facilitate programming dynamic responses in diverse bacterial consortia. However, the classical quorum sensing paradigm is that Gram-negative and Gram-positive bacteria generally communicate via homoserine lactones (HSLs) or oligopeptide molecular signals, respectively, to elicit population responses. Here, we create synthetic HSL sensors for Gram-positive Bacillus subtilis 168 using allosteric LuxR-type regulators (RpaR, LuxR, RhlR, and CinR) and synthetic promoters. Promoters were combinatorially designed from different sequence elements (-35, -16, -10, and transcriptional start regions). We quantified the effects of these combinatorial promoters on sensor activity and determined how regulator expression affects its activation, achieving up to 293-fold activation. Using the statistical design of experiments, we identified significant effects of promoter regions and pairwise interactions on sensor activity, which helped to understand the sequence-function relationships for synthetic promoter design. We present the first known set of functional HSL sensors (≥20-fold dynamic range) in B. subtilis for four different HSL chemical signals: p-coumaroyl-HSL, 3-oxohexanoyl-HSL, n-butyryl-HSL, and n-(3-hydroxytetradecanoyl)-HSL. This set of synthetic HSL sensors for a Gram-positive bacterium can pave the way for designable interspecies communication within microbial consortia.
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Affiliation(s)
- Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
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4
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Kim J, de Lorenzo V, Goñi‐Moreno Á. Pressure-dependent growth controls 3D architecture of Pseudomonas putida microcolonies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:708-715. [PMID: 37231623 PMCID: PMC10667634 DOI: 10.1111/1758-2229.13182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Colony formation is key to many ecological and biotechnological processes. In its early stages, colony formation involves the concourse of a number of physical and biological parameters for generation of a distinct 3D structure-the specific influence of which remains unclear. We focused on a thus far neglected aspect of the process, specifically the consequences of the differential pressure experienced by cells in the middle of a colony versus that endured by bacteria located in the growing periphery. This feature was characterized experimentally in the soil bacterium Pseudomonas putida. Using an agent-based model we recreated the growth of microcolonies in a scenario in which pressure was the only parameter affecting proliferation of cells. Simulations exposed that, due to constant collisions with other growing bacteria, cells have virtually no free space to move sideways, thereby delaying growth and boosting chances of overlapping on top of each other. This scenario was tested experimentally on agar surfaces. Comparison between experiments and simulations suggested that the inside/outside differential pressure determines growth, both timewise and in terms of spatial directions, eventually moulding colony shape. We thus argue that-at least in the case studied-mere physical pressure of growing cells suffices to explain key dynamics of colony formation.
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Affiliation(s)
- Juhyun Kim
- School of Life ScienceBK21 FOUR KNU Creative BioResearch Group Kyungpook National UniversityDaeguRepublic of Korea
| | - Víctor de Lorenzo
- Systems Biology DepartmentCentro Nacional de Biotecnología (CNB‐CSIC)Cantoblanco‐MadridSpain
| | - Ángel Goñi‐Moreno
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)‐Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC)MadridSpain
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5
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Marken JP, Murray RM. Addressable and adaptable intercellular communication via DNA messaging. Nat Commun 2023; 14:2358. [PMID: 37095088 PMCID: PMC10126159 DOI: 10.1038/s41467-023-37788-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
Engineered consortia are a major research focus for synthetic biologists because they can implement sophisticated behaviors inaccessible to single-strain systems. However, this functional capacity is constrained by their constituent strains' ability to engage in complex communication. DNA messaging, by enabling information-rich channel-decoupled communication, is a promising candidate architecture for implementing complex communication. But its major advantage, its messages' dynamic mutability, is still unexplored. We develop a framework for addressable and adaptable DNA messaging that leverages all three of these advantages and implement it using plasmid conjugation in E. coli. Our system can bias the transfer of messages to targeted receiver strains by 100- to 1000-fold, and their recipient lists can be dynamically updated in situ to control the flow of information through the population. This work lays the foundation for future developments that further utilize the unique advantages of DNA messaging to engineer previously-inaccessible levels of complexity into biological systems.
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Affiliation(s)
- John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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6
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Canadell D, Ortiz-Vaquerizas N, Mogas-Diez S, de Nadal E, Macia J, Posas F. Implementing re-configurable biological computation with distributed multicellular consortia. Nucleic Acids Res 2022; 50:12578-12595. [PMID: 36454021 PMCID: PMC9757037 DOI: 10.1093/nar/gkac1120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/30/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
The use of synthetic biological circuits to deal with numerous biological challenges has been proposed in several studies, but its implementation is still remote. A major problem encountered is the complexity of the cellular engineering needed to achieve complex biological circuits and the lack of general-purpose biological systems. The generation of re-programmable circuits can increase circuit flexibility and the scalability of complex cell-based computing devices. Here we present a new architecture to produce reprogrammable biological circuits that allow the development of a variety of different functions with minimal cell engineering. We demonstrate the feasibility of creating several circuits using only a small set of engineered cells, which can be externally reprogrammed to implement simple logics in response to specific inputs. In this regard, depending on the computation needs, a device composed of a number of defined cells can generate a variety of circuits without the need of further cell engineering or rearrangements. In addition, the inclusion of a memory module in the circuits strongly improved the digital response of the devices. The reprogrammability of biological circuits is an intrinsic capacity that is not provided in electronics and it may be used as a tool to solve complex biological problems.
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Affiliation(s)
- David Canadell
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain,Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Nicolás Ortiz-Vaquerizas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain,Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Sira Mogas-Diez
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain,Synthetic Biology for Biomedical Applications Group, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eulàlia de Nadal
- Correspondence may also be addressed to Eulàlia de Nadal. Tel: +34 93 40 39895;
| | - Javier Macia
- Correspondence may also be addressed to Javier Macia. Tel: +34 93 316 05 39;
| | - Francesc Posas
- To whom correspondence should be addressed. Tel: +34 93 40 37110;
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7
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Calibrating spatiotemporal models of microbial communities to microscopy data: A review. PLoS Comput Biol 2022; 18:e1010533. [PMID: 36227846 PMCID: PMC9560168 DOI: 10.1371/journal.pcbi.1010533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Spatiotemporal models that account for heterogeneity within microbial communities rely on single-cell data for calibration and validation. Such data, commonly collected via microscopy and flow cytometry, have been made more accessible by recent advances in microfluidics platforms and data processing pipelines. However, validating models against such data poses significant challenges. Validation practices vary widely between modelling studies; systematic and rigorous methods have not been widely adopted. Similar challenges are faced by the (macrobial) ecology community, in which systematic calibration approaches are often employed to improve quantitative predictions from computational models. Here, we review single-cell observation techniques that are being applied to study microbial communities and the calibration strategies that are being employed for accompanying spatiotemporal models. To facilitate future calibration efforts, we have compiled a list of summary statistics relevant for quantifying spatiotemporal patterns in microbial communities. Finally, we highlight some recently developed techniques that hold promise for improved model calibration, including algorithmic guidance of summary statistic selection and machine learning approaches for efficient model simulation.
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8
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Moškon M, Mraz M. Programmable evolution of computing circuits in cellular populations. Neural Comput Appl 2022. [DOI: 10.1007/s00521-022-07532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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Gallup O, Ming H, Ellis T. Ten future challenges for synthetic biology. ENGINEERING BIOLOGY 2021; 5:51-59. [PMID: 36968258 PMCID: PMC9996719 DOI: 10.1049/enb2.12011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
After 2 decades of growth and success, synthetic biology has now become a mature field that is driving significant innovation in the bioeconomy and pushing the boundaries of the biomedical sciences and biotechnology. So what comes next? In this article, 10 technological advances are discussed that are expected and hoped to come from the next generation of research and investment in synthetic biology; from ambitious projects to make synthetic life, cell simulators and custom genomes, through to new methods of engineering biology that use automation, deep learning and control of evolution. The non-exhaustive list is meant to inspire those joining the field and looks forward to how synthetic biology may evolve over the coming decades.
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Affiliation(s)
- Olivia Gallup
- Department of BioengineeringImperial College LondonLondonUK
| | - Hia Ming
- Department of BioengineeringImperial College LondonLondonUK
| | - Tom Ellis
- Department of BioengineeringImperial College LondonLondonUK
- Imperial College Centre for Synthetic BiologyImperial College LondonLondonUK
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10
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Moškon M, Komac R, Zimic N, Mraz M. Distributed biological computation: from oscillators, logic gates and switches to a multicellular processor and neural computing applications. Neural Comput Appl 2021. [DOI: 10.1007/s00521-021-05711-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Burmeister A, Akhtar Q, Hollmann L, Tenhaef N, Hilgers F, Hogenkamp F, Sokolowsky S, Marienhagen J, Noack S, Kohlheyer D, Grünberger A. (Optochemical) Control of Synthetic Microbial Coculture Interactions on a Microcolony Level. ACS Synth Biol 2021; 10:1308-1319. [PMID: 34075749 DOI: 10.1021/acssynbio.0c00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic microbial cocultures carry enormous potential for applied biotechnology and are increasingly the subject of fundamental research. So far, most cocultures have been designed and characterized based on bulk cultivations without considering the potentially highly heterogeneous and diverse single-cell behavior. However, an in-depth understanding of cocultures including their interacting single cells is indispensable for the development of novel cultivation approaches and control of cocultures. We present the development, validation, and experimental characterization of an optochemically controllable bacterial coculture on a microcolony level consisting of two Corynebacterium glutamicum strains. Our coculture combines an l-lysine auxotrophic strain together with a l-lysine-producing variant carrying the genetically IPTG-mediated induction of l-lysine production. We implemented two control approaches utilizing IPTG as inducer molecule. First, unmodified IPTG was supplemented to the culture enabling a medium-based control of the production of l-lysine, which serves as the main interacting component. Second, optochemical control was successfully performed by utilizing photocaged IPTG activated by appropriate illumination. Both control strategies were validated studying cellular growth on a microcolony level. The novel microfluidic single-cell cultivation strategies applied in this work can serve as a blueprint to validate cellular control strategies of synthetic mono- and cocultures with single-cell resolution at defined environmental conditions.
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Affiliation(s)
- Alina Burmeister
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, 33615 Bielefeld, Germany
| | - Qiratt Akhtar
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lina Hollmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Fabian Hogenkamp
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Sascha Sokolowsky
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Aachener Verfahrenstechnik (AVT-MSB), RWTH Aachen University, 52074 Aachen, Germany
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12
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Ortiz Y, Carrión J, Lahoz-Beltrá R, Gutiérrez M. A Framework for Implementing Metaheuristic Algorithms Using Intercellular Communication. Front Bioeng Biotechnol 2021; 9:660148. [PMID: 34041231 PMCID: PMC8141851 DOI: 10.3389/fbioe.2021.660148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Metaheuristics (MH) are Artificial Intelligence procedures that frequently rely on evolution. MH approximate difficult problem solutions, but are computationally costly as they explore large solution spaces. This work pursues to lay the foundations of general mappings for implementing MH using Synthetic Biology constructs in cell colonies. Two advantages of this approach are: harnessing large scale parallelism capability of cell colonies and, using existing cell processes to implement basic dynamics defined in computational versions. We propose a framework that maps MH elements to synthetic circuits in growing cell colonies to replicate MH behavior in cell colonies. Cell-cell communication mechanisms such as quorum sensing (QS), bacterial conjugation, and environmental signals map to evolution operators in MH techniques to adapt to growing colonies. As a proof-of-concept, we implemented the workflow associated to the framework: automated MH simulation generators for the gro simulator and two classes of algorithms (Simple Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits. Implementation tests show that synthetic counterparts mimicking MH are automatically produced, but also that cell colony parallelism speeds up the execution in terms of generations. Furthermore, we show an example of how our framework is extended by implementing a different computational model: The Cellular Automaton.
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Affiliation(s)
- Yerko Ortiz
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
| | - Javier Carrión
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
| | - Rafael Lahoz-Beltrá
- Department of Biodiversity, Ecology and Evolution (Biomathematics), Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - Martín Gutiérrez
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
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13
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Moškon M, Pušnik Ž, Zimic N, Mraz M. Field-programmable biological circuits and configurable (bio)logic blocks for distributed biological computing. Comput Biol Med 2020; 128:104109. [PMID: 33221638 DOI: 10.1016/j.compbiomed.2020.104109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022]
Abstract
Synthetic biology applications often require engineered computing structures, which can be programmed to process the information in a given way. However, programming of these structures usually requires significant amount of trial-and-error genetic engineering. This process is to some degree analogous to the design of application-specific integrated circuits (ASIC) in the domain of digital electronic circuits, which often require complex and time-consuming workflows to obtain a desired response. We describe a design of programmable biological circuits that can be configured without additional genetic engineering. Their configuration can be changed in vivo, i.e. during the execution of their biological program, simply with an introduction of programming inputs. These, e.g., increase the degradation rates of selected proteins that store the current configuration of the circuit. Programming can be thus performed in the field as in the case of field-programmable gate array (FPGA) circuits, which present an attractive alternative of ASICs in digital electronics. We describe a basic programmable unit, which we denote configurable (bio)logical block (CBLB) inspired by the architecture of configurable logic blocks (CLBs), basic functional units within the FPGA circuits. The design of a CBLB is based on distributed cellular computing modules, which makes its biological implementation easier to achieve. We establish a computational model of a CBLB and analyse its response with a given set of biologically feasible parameter values. Furthermore, we show that the proposed CBLB design exhibits correct behaviour for a vast range of kinetic parameter values, different population ratios, and as well preserves this response in stochastic simulations.
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Affiliation(s)
- Miha Moškon
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
| | - Žiga Pušnik
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Nikolaj Zimic
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Mraz
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
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14
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Brown B, Bartley B, Beal J, Bird JE, Goñi-Moreno Á, McLaughlin JA, Mısırlı G, Roehner N, Skelton DJ, Poh CL, Ofiteru ID, James K, Wipat A. Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL). ACS Synth Biol 2020; 9:2410-2417. [PMID: 32786354 DOI: 10.1021/acssynbio.0c00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.
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Affiliation(s)
- Bradley Brown
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Bryan Bartley
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Jasmine E. Bird
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Ángel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, United Kingdom
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politénica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcon, Madrid, Spain
| | | | - Göksel Mısırlı
- School of Computing and Mathematics, Keele University, Newcastle ST5 5BG, United Kingdom
| | - Nicholas Roehner
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - David James Skelton
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, United Kingdom
| | - Chueh Loo Poh
- Department of Biomedical Engineering and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Irina Dana Ofiteru
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Katherine James
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, United Kingdom
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15
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Al-Radhawi MA, Tran AP, Ernst EA, Chen T, Voigt CA, Sontag ED. Distributed Implementation of Boolean Functions by Transcriptional Synthetic Circuits. ACS Synth Biol 2020; 9:2172-2187. [PMID: 32589837 DOI: 10.1021/acssynbio.0c00228] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Starting in the early 2000s, sophisticated technologies have been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in order to achieve greater computational power has been hampered by many constraints, including repressor toxicity and the lack of large sets of mutually orthogonal repressors. As a consequence, a typical circuit contains no more than roughly seven repressor-based gates per cell. A possible way around this scalability problem is to distribute the computation among multiple cell types, each of which implements a small subcircuit, which communicate among themselves using diffusible small molecules (DSMs). Examples of DSMs are those employed by quorum sensing systems in bacteria. This paper focuses on systematic ways to implement this distributed approach, in the context of the evaluation of arbitrary Boolean functions. The unique characteristics of genetic circuits and the properties of DSMs require the development of new Boolean synthesis methods, distinct from those classically used in electronic circuit design. In this work, we propose a fast algorithm to synthesize distributed realizations for any Boolean function, under constraints on the number of gates per cell and the number of orthogonal DSMs. The method is based on an exact synthesis algorithm to find the minimal circuit per cell, which in turn allows us to build an extensive database of Boolean functions up to a given number of inputs. For concreteness, we will specifically focus on circuits of up to 4 inputs, which might represent, for example, two chemical inducers and two light inputs at different frequencies. Our method shows that, with a constraint of no more than seven gates per cell, the use of a single DSM increases the total number of realizable circuits by at least 7.58-fold compared to centralized computation. Moreover, when allowing two DSM's, one can realize 99.995% of all possible 4-input Boolean functions, still with at most 7 gates per cell. The methodology introduced here can be readily adapted to complement recent genetic circuit design automation software. A toolbox that uses the proposed algorithm was created and made available at https://github.com/sontaglab/DBC/.
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Affiliation(s)
- M. Ali Al-Radhawi
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Anh Phong Tran
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Elizabeth A. Ernst
- Department of Mathematics, Statistics, and Computer Science, Macalester College, Saint Paul, Minnesota 55105, United States
| | - Tianchi Chen
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Christopher A. Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eduardo D. Sontag
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts 02115, United States
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16
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Karkaria BD, Treloar NJ, Barnes CP, Fedorec AJH. From Microbial Communities to Distributed Computing Systems. Front Bioeng Biotechnol 2020; 8:834. [PMID: 32793576 PMCID: PMC7387671 DOI: 10.3389/fbioe.2020.00834] [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: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.
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Affiliation(s)
- Behzad D. Karkaria
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Alex J. H. Fedorec
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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17
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Abstract
Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the “genetic circuit” metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits the types of computation that may be engineered inside the cell, and fails to exploit the rich and diverse functionality available in natural living systems. We propose the notion of “cellular supremacy” to focus attention on domains in which biocomputing might offer superior performance over traditional computers. We consider potential pathways toward cellular supremacy, and suggest application areas in which it may be found. Synthetic biology uses cells as its computing substrate, often based on the genetic circuit concept. In this Perspective, the authors argue that existing synthetic biology approaches based on classical models of computation limit the potential of biocomputing, and propose that living organisms have under-exploited capabilities.
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18
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Guzmán-Herrador DL, Llosa M. The secret life of conjugative relaxases. Plasmid 2019; 104:102415. [PMID: 31103521 DOI: 10.1016/j.plasmid.2019.102415] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/17/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
Conjugative relaxases are well-characterized proteins responsible for the site- and strand-specific endonucleolytic cleavage and strand transfer reactions taking place at the start and end of the conjugative DNA transfer process. Most of the relaxases characterized biochemically and structurally belong to the HUH family of endonucleases. However, an increasing number of new families of relaxases are revealing a variety of protein folds and catalytic alternatives to accomplish conjugative DNA processing. Relaxases show high specificity for their cognate target DNA sequences, but several recent reports underscore the importance of their activity on secondary targets, leading to widespread mobilization of plasmids containing an oriT-like sequence. Some relaxases perform other functions associated with their nicking and strand transfer ability, such as catalyzing site-specific recombination or initiation of plasmid replication. They perform these roles in the absence of conjugation, and the validation of these functions in several systems strongly suggest that they are not mere artifactual laboratory observations. Other unexpected roles recently assigned to relaxases include controlling plasmid copy number and promoting retrotransposition. Their capacity to mediate promiscuous mobilization and genetic reorganizations can be exploited for a number of imaginative biotechnological applications. Overall, there is increasing evidence that conjugative relaxases are not only key enzymes for horizontal gene transfer, but may have been adapted to perform other roles which contribute to prokaryotic genetic plasticity. Relaxed target specificity may be key to this versatility.
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Affiliation(s)
- Dolores Lucía Guzmán-Herrador
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain.
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19
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Goñi-Moreno A, de la Cruz F, Rodríguez-Patón A, Amos M. Dynamical Task Switching in Cellular Computers. Life (Basel) 2019; 9:E14. [PMID: 30691149 PMCID: PMC6463194 DOI: 10.3390/life9010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/23/2018] [Accepted: 01/23/2019] [Indexed: 01/24/2023] Open
Abstract
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discuss the potential for future work in this area.
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Affiliation(s)
- Angel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle Upon Tyne NE4 5TG, UK.
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, 39011 Santander, Spain.
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, 28660 Madrid, Spain.
| | - Martyn Amos
- Department of Computer and Information Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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20
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Dalchau N, Szép G, Hernansaiz-Ballesteros R, Barnes CP, Cardelli L, Phillips A, Csikász-Nagy A. Computing with biological switches and clocks. NATURAL COMPUTING 2018; 17:761-779. [PMID: 30524215 PMCID: PMC6244770 DOI: 10.1007/s11047-018-9686-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The complex dynamics of biological systems is primarily driven by molecular interactions that underpin the regulatory networks of cells. These networks typically contain positive and negative feedback loops, which are responsible for switch-like and oscillatory dynamics, respectively. Many computing systems rely on switches and clocks as computational modules. While the combination of such modules in biological systems leads to a variety of dynamical behaviours, it is also driving development of new computing algorithms. Here we present a historical perspective on computation by biological systems, with a focus on switches and clocks, and discuss parallels between biology and computing. We also outline our vision for the future of biological computing.
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Affiliation(s)
| | | | | | | | - Luca Cardelli
- Microsoft Research, Cambridge, UK
- University of Oxford, Oxford, UK
| | | | - Attila Csikász-Nagy
- King’s College London, London, UK
- Pázmány Péter Catholic University, Budapest, Hungary
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21
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Guiziou S, Ulliana F, Moreau V, Leclere M, Bonnet J. An Automated Design Framework for Multicellular Recombinase Logic. ACS Synth Biol 2018; 7:1406-1412. [PMID: 29641183 PMCID: PMC5962929 DOI: 10.1021/acssynbio.8b00016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Tools
to systematically reprogram cellular behavior are crucial
to address pressing challenges in manufacturing, environment, or healthcare.
Recombinases can very efficiently encode Boolean and history-dependent
logic in many species, yet current designs are performed on a case-by-case
basis, limiting their scalability and requiring time-consuming optimization.
Here we present an automated workflow for designing recombinase logic
devices executing Boolean functions. Our theoretical framework uses
a reduced library of computational devices distributed into different
cellular subpopulations, which are then composed in various manners
to implement all desired logic functions at the multicellular level.
Our design platform called CALIN (Composable Asynchronous Logic using
Integrase Networks) is broadly accessible via a web
server, taking truth tables as inputs and providing corresponding
DNA designs and sequences as outputs (available at http://synbio.cbs.cnrs.fr/calin). We anticipate that this automated design workflow will streamline
the implementation of Boolean functions in many organisms and for
various applications.
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Affiliation(s)
- Sarah Guiziou
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Federico Ulliana
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Violaine Moreau
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Michel Leclere
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
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22
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Gutiérrez M, Gregorio-Godoy P, Pérez del Pulgar G, Muñoz LE, Sáez S, Rodríguez-Patón A. A New Improved and Extended Version of the Multicell Bacterial Simulator gro. ACS Synth Biol 2017; 6:1496-1508. [PMID: 28438021 DOI: 10.1021/acssynbio.7b00003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits and microbial consortia. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use, and provide new functionalities. The new version of gro is between 1 and 2 orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 105 cells in less than 10 min. A new library, CellEngine, accelerates the resolution of spatial physical interactions between growing and dividing cells by implementing a new shoving algorithm. A genetic library, CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified and easy to compute digital proteins. We also propose a more convenient language specification layer, ProSpec, based on the idea that proteins drive cell behavior. CellNutrient, another library, implements Monod-based growth and nutrient uptake functionalities. The intercellular signaling management was improved and extended in a library called CellSignals. Finally, bacterial conjugation, another local cell-cell communication process, was added to the simulator. To show the versatility and potential outreach of this version of gro, we provide studies and novel examples ranging from synthetic biology to evolutionary microbiology. We believe that the upgrades implemented for gro have made it into a powerful and fast prototyping tool capable of simulating a large variety of systems and synthetic biology designs.
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Affiliation(s)
- Martín Gutiérrez
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Escuela
de Informática y Telecomunicaciones, Universidad Diego Portales, 8370190 Santiago, Chile
| | - Paula Gregorio-Godoy
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Guillermo Pérez del Pulgar
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Luis E. Muñoz
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Sandra Sáez
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfonso Rodríguez-Patón
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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23
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Agent-based modelling in synthetic biology. Essays Biochem 2017; 60:325-336. [PMID: 27903820 PMCID: PMC5264505 DOI: 10.1042/ebc20160037] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/08/2016] [Indexed: 11/17/2022]
Abstract
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions.
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24
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Malwade A, Nguyen A, Sadat-Mousavi P, Ingalls BP. Predictive Modeling of a Batch Filter Mating Process. Front Microbiol 2017; 8:461. [PMID: 28377756 PMCID: PMC5359259 DOI: 10.3389/fmicb.2017.00461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/06/2017] [Indexed: 01/21/2023] Open
Abstract
Quantitative characterizations of horizontal gene transfer are needed to accurately describe gene transfer processes in natural and engineered systems. A number of approaches to the quantitative description of plasmid conjugation have appeared in the literature. In this study, we seek to extend that work, motivated by the question of whether a mathematical model can accurately predict growth and conjugation dynamics in a batch process. We used flow cytometry to make time-point observations of a filter-associated mating between two E. coli strains, and fit ordinary differential equation models to the data. A model comparison analysis identified the model formulation that is best supported by the data. Identifiability analysis revealed that the parameters were estimated with acceptable accuracy. The predictive power of the model was assessed by comparison with test data that demanded extrapolation from the training experiments. This study represents the first attempt to assess the quality of model predictions for plasmid conjugation. Our successful application of this approach lays a foundation for predictive modeling that can be used both in the study of natural plasmid transmission and in model-based design of engineering approaches that employ conjugation, such as plasmid-mediated bioaugmentation.
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Affiliation(s)
- Akshay Malwade
- Department of Applied Mathematics, University of Waterloo Waterloo, ON, Canada
| | - Angel Nguyen
- Department of Applied Mathematics, University of Waterloo Waterloo, ON, Canada
| | | | - Brian P Ingalls
- Department of Applied Mathematics, University of Waterloo Waterloo, ON, Canada
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25
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Goñi-Moreno A, Carcajona M, Kim J, Martínez-García E, Amos M, de Lorenzo V. An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology. ACS Synth Biol 2016; 5:1127-1135. [PMID: 27454551 DOI: 10.1021/acssynbio.6b00029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As synthetic biology moves away from trial and error and embraces more formal processes, workflows have emerged that cover the roadmap from conceptualization of a genetic device to its construction and measurement. This latter aspect (i.e., characterization and measurement of synthetic genetic constructs) has received relatively little attention to date, but it is crucial for their outcome. An end-to-end use case for engineering a simple synthetic device is presented, which is supported by information standards and computational methods and focuses on such characterization/measurement. This workflow captures the main stages of genetic device design and description and offers standardized tools for both population-based measurement and single-cell analysis. To this end, three separate aspects are addressed. First, the specific vector features are discussed. Although device/circuit design has been successfully automated, important structural information is usually overlooked, as in the case of plasmid vectors. The use of the Standard European Vector Architecture (SEVA) is advocated for selecting the optimal carrier of a design and its thorough description in order to unequivocally correlate digital definitions and molecular devices. A digital version of this plasmid format was developed with the Synthetic Biology Open Language (SBOL) along with a software tool that allows users to embed genetic parts in vector cargoes. This enables annotation of a mathematical model of the device's kinetic reactions formatted with the Systems Biology Markup Language (SBML). From that point onward, the experimental results and their in silico counterparts proceed alongside, with constant feedback to preserve consistency between them. A second aspect involves a framework for the calibration of fluorescence-based measurements. One of the most challenging endeavors in standardization, metrology, is tackled by reinterpreting the experimental output in light of simulation results, allowing us to turn arbitrary fluorescence units into relative measurements. Finally, integration of single-cell methods into a framework for multicellular simulation and measurement is addressed, allowing standardized inspection of the interplay between the carrier chassis and the culture conditions.
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Affiliation(s)
- Angel Goñi-Moreno
- Systems
Biology Program, Centro Nacional de Biotecnología, Cantoblanco, 28049 Madrid, Spain
| | - Marta Carcajona
- Systems
Biology Program, Centro Nacional de Biotecnología, Cantoblanco, 28049 Madrid, Spain
| | - Juhyun Kim
- Systems
Biology Program, Centro Nacional de Biotecnología, Cantoblanco, 28049 Madrid, Spain
| | | | - Martyn Amos
- Informatics
Research Centre, Manchester Metropolitan University, Manchester M1 5GD, United Kingdom
| | - Víctor de Lorenzo
- Systems
Biology Program, Centro Nacional de Biotecnología, Cantoblanco, 28049 Madrid, Spain
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26
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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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27
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Kim NH, Lee G, Sherer NA, Martini KM, Goldenfeld N, Kuhlman TE. Real-time transposable element activity in individual live cells. Proc Natl Acad Sci U S A 2016; 113:7278-83. [PMID: 27298350 PMCID: PMC4932956 DOI: 10.1073/pnas.1601833113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The excision and reintegration of transposable elements (TEs) restructure their host genomes, generating cellular diversity involved in evolution, development, and the etiology of human diseases. Our current knowledge of TE behavior primarily results from bulk techniques that generate time and cell ensemble averages, but cannot capture cell-to-cell variation or local environmental and temporal variability. We have developed an experimental system based on the bacterial TE IS608 that uses fluorescent reporters to directly observe single TE excision events in individual cells in real time. We find that TE activity depends upon the TE's orientation in the genome and the amount of transposase protein in the cell. We also find that TE activity is highly variable throughout the lifetime of the cell. Upon entering stationary phase, TE activity increases in cells hereditarily predisposed to TE activity. These direct observations demonstrate that real-time live-cell imaging of evolution at the molecular and individual event level is a powerful tool for the exploration of genome plasticity in stressed cells.
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Affiliation(s)
- Neil H Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Gloria Lee
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Nicholas A Sherer
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - K Michael Martini
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Nigel Goldenfeld
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Institute for Universal Biology NASA Astrobiology Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
| | - Thomas E Kuhlman
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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28
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Better together: engineering and application of microbial symbioses. Curr Opin Biotechnol 2015; 36:40-9. [DOI: 10.1016/j.copbio.2015.08.008] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 12/26/2022]
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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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Ball P. Forging patterns and making waves from biology to geology: a commentary on Turing (1952) 'The chemical basis of morphogenesis'. Philos Trans R Soc Lond B Biol Sci 2015; 373:rsta.2014.0218. [PMID: 25750229 DOI: 10.1098/rsta.2014.0218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2015] [Indexed: 05/21/2023] Open
Abstract
Alan Turing was neither a biologist nor a chemist, and yet the paper he published in 1952, 'The chemical basis of morphogenesis', on the spontaneous formation of patterns in systems undergoing reaction and diffusion of their ingredients has had a substantial impact on both fields, as well as in other areas as disparate as geomorphology and criminology. Motivated by the question of how a spherical embryo becomes a decidedly non-spherical organism such as a human being, Turing devised a mathematical model that explained how random fluctuations can drive the emergence of pattern and structure from initial uniformity. The spontaneous appearance of pattern and form in a system far away from its equilibrium state occurs in many types of natural process, and in some artificial ones too. It is often driven by very general mechanisms, of which Turing's model supplies one of the most versatile. For that reason, these patterns show striking similarities in systems that seem superficially to share nothing in common, such as the stripes of sand ripples and of pigmentation on a zebra skin. New examples of 'Turing patterns' in biology and beyond are still being discovered today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.
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Affiliation(s)
- Philip Ball
- 18 Hillcourt Road, East Dulwich, London SE22 0PE, UK
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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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Abstract
ABSTRACT
The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include
inter alia
origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.
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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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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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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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36
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Clark KB. Basis for a neuronal version of Grover's quantum algorithm. Front Mol Neurosci 2014; 7:29. [PMID: 24860419 PMCID: PMC4029008 DOI: 10.3389/fnmol.2014.00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/31/2014] [Indexed: 11/25/2022] Open
Abstract
Grover's quantum (search) algorithm exploits principles of quantum information theory and computation to surpass the strong Church–Turing limit governing classical computers. The algorithm initializes a search field into superposed N (eigen)states to later execute nonclassical “subroutines” involving unitary phase shifts of measured states and to produce root-rate or quadratic gain in the algorithmic time (O(N1/2)) needed to find some “target” solution m. Akin to this fast technological search algorithm, single eukaryotic cells, such as differentiated neurons, perform natural quadratic speed-up in the search for appropriate store-operated Ca2+ response regulation of, among other processes, protein and lipid biosynthesis, cell energetics, stress responses, cell fate and death, synaptic plasticity, and immunoprotection. Such speed-up in cellular decision making results from spatiotemporal dynamics of networked intracellular Ca2+-induced Ca2+ release and the search (or signaling) velocity of Ca2+ wave propagation. As chemical processes, such as the duration of Ca2+ mobilization, become rate-limiting over interstore distances, Ca2+ waves quadratically decrease interstore-travel time from slow saltatory to fast continuous gradients proportional to the square-root of the classical Ca2+ diffusion coefficient, D1/2, matching the computing efficiency of Grover's quantum algorithm. In this Hypothesis and Theory article, I elaborate on these traits using a fire-diffuse-fire model of store-operated cytosolic Ca2+ signaling valid for glutamatergic neurons. Salient model features corresponding to Grover's quantum algorithm are parameterized to meet requirements for the Oracle Hadamard transform and Grover's iteration. A neuronal version of Grover's quantum algorithm figures to benefit signal coincidence detection and integration, bidirectional synaptic plasticity, and other vital cell functions by rapidly selecting, ordering, and/or counting optional response regulation choices.
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Affiliation(s)
- Kevin B Clark
- Research and Development Service, Veterans Affairs Greater Los Angeles Healthcare System Los Angeles, CA, USA ; Complex Biological Systems Alliance North Andover, MA, USA
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Abstract
Different species inhabit different sensory worlds and thus have evolved diverse means of processing information, learning and memory. In the escalated arms race with host defense, each pathogenic bacterium not only has evolved its individual cellular sensing and behavior, but also collective sensing, interbacterial communication, distributed information processing, joint decision making, dissociative behavior, and the phenotypic and genotypic heterogeneity necessary for epidemiologic success. Moreover, pathogenic populations take advantage of dormancy strategies and rapid evolutionary speed, which allow them to save co-generated intelligent traits in a collective genomic memory. This review discusses how these mechanisms add further levels of complexity to bacterial pathogenicity and transmission, and how mining for these mechanisms could help to develop new anti-infective strategies.
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Affiliation(s)
- Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig Braunschweig, Germany
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Abstract
Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined.
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Affiliation(s)
- Javier Macia
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Barcelona, Spain
- Institut de Biologia Evolutiva, UPF-CSIC, Barcelona, Spain
- * E-mail: (JM); (RS)
| | - Ricard Sole
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Barcelona, Spain
- Institut de Biologia Evolutiva, UPF-CSIC, Barcelona, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail: (JM); (RS)
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Trosset JY, Carbonell P. Synergistic Synthetic Biology: Units in Concert. Front Bioeng Biotechnol 2013; 1:11. [PMID: 25022769 PMCID: PMC4090895 DOI: 10.3389/fbioe.2013.00011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/01/2013] [Indexed: 01/31/2023] Open
Abstract
Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.
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Affiliation(s)
| | - Pablo Carbonell
- BioRetroSynth Laboratory, Institute of Systems and Synthetic Biology, University of Evry-Val d'Essonne , Evry , France ; BioRetroSynth Laboratory, Institute of Systems and Synthetic Biology, CNRS , Evry , France
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