101
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Abstract
Constructing genetic logic circuits is an application of synthetic biology in which parts of the DNA of a living cell are engineered to perform a dedicated Boolean function triggered by an appropriate concentration of certain proteins or by different genetic components. These logic circuits work in a manner similar to electronic logic circuits, but they are much more stochastic and hence much harder to characterize. In this article, we introduce an approach to analyze the threshold value and timing of genetic logic circuits. We show how this approach can be used to analyze the timing behavior of single and cascaded genetic logic circuits. We further analyze the timing sensitivity of circuits by varying the degradation rates and concentrations. Our approach can be used not only to characterize the timing behavior but also to analyze the timing constraints of cascaded genetic logic circuits, a capability that we believe will be important for design automation in synthetic biology.
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Affiliation(s)
- Hasan Baig
- Department of Applied
Mathematics
and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jan Madsen
- Department of Applied
Mathematics
and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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102
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Zeng G, Li H, Wei Y, Xuan W, Zhang R, Breden LE, Wang W, Liang FS. Engineering Iron Responses in Mammalian Cells by Signal-Induced Protein Proximity. ACS Synth Biol 2017; 6:921-927. [PMID: 28221778 DOI: 10.1021/acssynbio.6b00255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A new synthetic biology engineering strategy integrating chemical reactivity sensing and small molecule induced protein dimerization has been developed to generate artificial Fe2+ signaling circuitry to control tailored cellular events in mammalian cells. The dual function probe ABA-FE18 (Fe2+-sensing and protein dimerization) derived from ABA was developed and used to control gene activation, signal transduction, and cytoskeletal remodeling in response to Fe2+. This technology was utilized to design signal circuitry incorporating "AND" and "OR" biologic gates that enables mammalian cells to translate different combinations of Fe2+ and H2O2 signals into predefined biological outputs.
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Affiliation(s)
- Guihua Zeng
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Huanqiu Li
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
- Department
of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, P. R. China
| | - Yongyi Wei
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Weimin Xuan
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Roushu Zhang
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Larisa E. Breden
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Wei Wang
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
| | - Fu-Sen Liang
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131, United States
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103
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Xue S, Yin J, Shao J, Yu Y, Yang L, Wang Y, Xie M, Fussenegger M, Ye H. A Synthetic-Biology-Inspired Therapeutic Strategy for Targeting and Treating Hepatogenous Diabetes. Mol Ther 2017; 25:443-455. [PMID: 28153094 DOI: 10.1016/j.ymthe.2016.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
Hepatogenous diabetes is a complex disease that is typified by the simultaneous presence of type 2 diabetes and many forms of liver disease. The chief pathogenic determinant in this pathophysiological network is insulin resistance (IR), an asymptomatic disease state in which impaired insulin signaling in target tissues initiates a variety of organ dysfunctions. However, pharmacotherapies targeting IR remain limited and are generally inapplicable for liver disease patients. Oleanolic acid (OA) is a plant-derived triterpenoid that is frequently used in Chinese medicine as a safe but slow-acting treatment in many liver disorders. Here, we utilized the congruent pharmacological activities of OA and glucagon-like-peptide 1 (GLP-1) in relieving IR and improving liver and pancreas functions and used a synthetic-biology-inspired design principle to engineer a therapeutic gene circuit that enables a concerted action of both drugs. In particular, OA-triggered short human GLP-1 (shGLP-1) expression in hepatogenous diabetic mice rapidly and simultaneously attenuated many disease-specific metabolic failures, whereas OA or shGLP-1 monotherapy failed to achieve corresponding therapeutic effects. Collectively, this work shows that rationally engineered synthetic gene circuits are capable of treating multifactorial diseases in a synergistic manner by multiplexing the targeting efficacies of single therapeutics.
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Affiliation(s)
- Shuai Xue
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jiawei Shao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yuanhuan Yu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Linfeng Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yidan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Mingqi Xie
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
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104
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Ostrov N, Jimenez M, Billerbeck S, Brisbois J, Matragrano J, Ager A, Cornish VW. A modular yeast biosensor for low-cost point-of-care pathogen detection. SCIENCE ADVANCES 2017; 3:e1603221. [PMID: 28782007 PMCID: PMC5489263 DOI: 10.1126/sciadv.1603221] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/15/2017] [Indexed: 05/16/2023]
Abstract
The availability of simple, specific, and inexpensive on-site detection methods is of key importance for deployment of pathogen surveillance networks. We developed a nontechnical and highly specific colorimetric assay for detection of pathogen-derived peptides based on Saccharomyces cerevisiae-a genetically tractable model organism and household product. Integrating G protein-coupled receptors with a visible, reagent-free lycopene readout, we demonstrate differential detection of major human, plant, and food fungal pathogens with nanomolar sensitivity. We further optimized a one-step rapid dipstick prototype that can be used in complex samples, including blood, urine, and soil. This modular biosensor can be economically produced at large scale, is not reliant on cold-chain storage, can be detected without additional equipment, and is thus a compelling platform scalable to global surveillance of pathogens.
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Affiliation(s)
- Nili Ostrov
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Miguel Jimenez
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Sonja Billerbeck
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - James Brisbois
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Joseph Matragrano
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Alastair Ager
- Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
- Institute for Global Health and Development, Queen Margaret University, Edinburgh, UK
| | - Virginia W. Cornish
- Department of Chemistry, Columbia University, New York, NY 10027, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Corresponding author.
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105
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Gomez-Cabrero D, Tegnér J. Iterative Systems Biology for Medicine – Time for advancing from network signatures to mechanistic equations. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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106
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Gilad AA, Shapiro MG. Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging. Mol Imaging Biol 2017; 19:373-378. [PMID: 28213833 PMCID: PMC6058969 DOI: 10.1007/s11307-017-1062-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.
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Affiliation(s)
- Assaf A Gilad
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA.
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Heritage Medical Research Institute, California Institute of Technology, Pasadena, CA, USA.
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107
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Heidari R, Shaw DM, Elger BS. CRISPR and the Rebirth of Synthetic Biology. SCIENCE AND ENGINEERING ETHICS 2017; 23:351-363. [PMID: 27325413 DOI: 10.1007/s11948-016-9768-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/25/2016] [Indexed: 06/06/2023]
Abstract
Emergence of novel genome engineering technologies such as clustered regularly interspaced short palindromic repeat (CRISPR) has refocused attention on unresolved ethical complications of synthetic biology. Biosecurity concerns, deontological issues and human right aspects of genome editing have been the subject of in-depth debate; however, a lack of transparent regulatory guidelines, outdated governance codes, inefficient time-consuming clinical trial pathways and frequent misunderstanding of the scientific potential of cutting-edge technologies have created substantial obstacles to translational research in this area. While a precautionary principle should be applied at all stages of genome engineering research, the stigma of germline editing, synthesis of new life forms and unrealistic presentation of current technologies should not arrest the transition of new therapeutic, diagnostic or preventive tools from research to clinic. We provide a brief review on the present regulation of CRISPR and discuss the translational aspect of genome engineering research and patient autonomy with respect to the "right to try" potential novel non-germline gene therapies.
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Affiliation(s)
- Raheleh Heidari
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland
| | - David Martin Shaw
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland
| | - Bernice Simone Elger
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland.
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108
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Rakic M, Wienand I, Shaw D, Nast R, Elger BS. Autonomy and Fear of Synthetic Biology: How Can Patients' Autonomy Be Enhanced in the Field of Synthetic Biology? A Qualitative Study with Stable Patients. SCIENCE AND ENGINEERING ETHICS 2017; 23:375-388. [PMID: 27138379 DOI: 10.1007/s11948-016-9786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
We analyzed stable patients' views regarding synthetic biology in general, the medical application of synthetic biology, and their potential participation in trials of synthetic biology in particular. The aim of the study was to find out whether patients' views and preferences change after receiving more detailed information about synthetic biology and its clinical applications. The qualitative study was carried out with a purposive sample of 36 stable patients, who suffered from diabetes or gout. Interviews were transcribed verbatim, translated and fully anonymized. Thematic analysis was applied in order to examine stable patients' attitudes towards synthetic biology, its medical application, and their participation in trials. When patients were asked about synthetic biology in general, most of them were anxious that something uncontrollable could be created. After a concrete example of possible future treatment options, patients started to see synthetic biology in a more positive way. Our study constitutes an important first empirical insight into stable patients' views on synthetic biology and into the kind of fears triggered by the term "synthetic biology." Our results show that clear and concrete information can change patients' initial negative feelings towards synthetic biology. Information should thus be transmitted with great accuracy and transparency in order to reduce irrational fears of patients and to minimize the risk that researchers present facts too positively for the purposes of persuading patients to participate in clinical trials. Potential participants need to be adequately informed in order to be able to autonomously decide whether to participate in human subject research involving synthetic biology.
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Affiliation(s)
- Milenko Rakic
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland.
| | - Isabelle Wienand
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
| | - David Shaw
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
| | - Rebecca Nast
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
| | - Bernice S Elger
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
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109
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Evolution of a split RNA polymerase as a versatile biosensor platform. Nat Chem Biol 2017; 13:432-438. [PMID: 28192413 DOI: 10.1038/nchembio.2299] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
Abstract
Biosensors that transduce target chemical and biochemical inputs into genetic outputs are essential for bioengineering and synthetic biology. Current biosensor design strategies are often limited by a low signal-to-noise ratio, the extensive optimization required for each new input, and poor performance in mammalian cells. Here we report the development of a proximity-dependent split RNA polymerase (RNAP) as a general platform for biosensor engineering. After discovering that interactions between fused proteins modulate the assembly of a split T7 RNAP, we optimized the split RNAP components for protein-protein interaction detection by phage-assisted continuous evolution (PACE). We then applied the resulting activity-responsive RNAP (AR) system to create biosensors that can be activated by light and small molecules, demonstrating the 'plug-and-play' nature of the platform. Finally, we validated that ARs can interrogate multidimensional protein-protein interactions and trigger RNA nanostructure production, protein synthesis, and gene knockdown in mammalian systems, illustrating the versatility of ARs in synthetic biology applications.
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110
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Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation. Mol Ther 2017; 25:102-119. [PMID: 28129106 DOI: 10.1016/j.ymthe.2016.10.005] [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] [Received: 05/27/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 12/20/2022] Open
Abstract
Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a "thresholder" to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.
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Affiliation(s)
- Anže Smole
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Urban Bezeljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simon Horvat
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia; Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia.
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111
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Agustí A. Predicting the future from the past. Eur Respir J 2017; 49:49/1/1601854. [DOI: 10.1183/13993003.01854-2016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 12/20/2022]
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112
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Abstract
By using tools from synthetic biology, sophisticated genetic devices can be assembled to reprogram mammalian cell activities. Here, we demonstrate that a self-adjusting synthetic gene circuit can be designed to sense and reverse the insulin-resistance syndrome in different mouse models. By functionally rewiring the mitogen-activated protein kinase (MAPK) signalling pathway to produce MAPK-mediated activation of the hybrid transcription factor TetR-ELK1, we assembled a synthetic insulin-sensitive transcription-control device that self-sufficiently distinguished between physiological and increased blood insulin levels and correspondingly fine-tuned the reversible expression of therapeutic transgenes from synthetic TetR-ELK1-specific promoters. In acute experimental hyperinsulinemia, the synthetic insulin-sensing designer circuit reversed the insulin-resistance syndrome by coordinating expression of the insulin-sensitizing compound adiponectin. Engineering synthetic gene circuits to sense pathologic markers and coordinate the expression of therapeutic transgenes may provide opportunities for future gene- and cell-based treatments of multifactorial metabolic disorders.
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113
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Kong W, Blanchard AE, Liao C, Lu T. Engineering robust and tunable spatial structures with synthetic gene circuits. Nucleic Acids Res 2016; 45:1005-1014. [PMID: 27899571 PMCID: PMC5314756 DOI: 10.1093/nar/gkw1045] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/30/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
Controllable spatial patterning is a major goal for the engineering of biological systems. Recently, synthetic gene circuits have become promising tools to achieve the goal; however, they need to possess both functional robustness and tunability in order to facilitate future applications. Here we show that, by harnessing the dual signaling and antibiotic features of nisin, simple synthetic circuits can direct Lactococcus lactis populations to form programmed spatial band-pass structures that do not require fine-tuning and are robust against environmental and cellular context perturbations. Although robust, the patterns are highly tunable, with their band widths specified by the external nisin gradient and cellular nisin immunity. Additionally, the circuits can direct cells to consistently generate designed patterns, even when the gradient is driven by structured nisin-producing bacteria and the patterning cells are composed of multiple species. A mathematical model successfully reproduces all of the observed patterns. Furthermore, the circuits allow us to establish predictable structures of synthetic communities and controllable arrays of cellular stripes and spots in space. This study offers new synthetic biology tools to program spatial structures. It also demonstrates that a deep mining of natural functionalities of living systems is a valuable route to build circuit robustness and tunability.
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Affiliation(s)
- Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew E Blanchard
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chen Liao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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114
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Zhang Y, Wang J, Cheng H, Sun Y, Liu M, Wu Z, Pei R. Conditional control of suicide gene expression in tumor cells with theophylline-responsive ribozyme. Gene Ther 2016; 24:84-91. [DOI: 10.1038/gt.2016.78] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/06/2016] [Accepted: 11/11/2016] [Indexed: 12/18/2022]
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115
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Krishnamurthy M, Moore RT, Rajamani S, Panchal RG. Bacterial genome engineering and synthetic biology: combating pathogens. BMC Microbiol 2016; 16:258. [PMID: 27814687 PMCID: PMC5097395 DOI: 10.1186/s12866-016-0876-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of MDR pathogenic bacteria. According to recent reports by the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC), there is an unprecedented increase in the occurrence of MDR infections worldwide. The rise in these infections has generated an economic strain worldwide, prompting the WHO to endorse a global action plan to improve awareness and understanding of antimicrobial resistance. This health crisis necessitates an immediate action to target the underlying mechanisms of drug resistance in bacteria. RESEARCH The advent of new bacterial genome engineering and synthetic biology (SB) tools is providing promising diagnostic and treatment plans to monitor and treat widespread recalcitrant bacterial infections. Key advances in genetic engineering approaches can successfully aid in targeting and editing pathogenic bacterial genomes for understanding and mitigating drug resistance mechanisms. In this review, we discuss the application of specific genome engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats (CRISPR), and bacterial cell-cell signaling mechanisms for pathogen targeting. The utility of these tools in developing antibacterial strategies such as novel antibiotic production, phage therapy, diagnostics and vaccine production to name a few, are also highlighted. CONCLUSIONS The prevalent use of antibiotics and the spread of MDR bacteria raise the prospect of a post-antibiotic era, which underscores the need for developing novel therapeutics to target MDR pathogens. The development of enabling SB technologies offers promising solutions to deliver safe and effective antibacterial therapies.
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Affiliation(s)
- Malathy Krishnamurthy
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Richard T. Moore
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Sathish Rajamani
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Rekha G. Panchal
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
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116
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Tang ZF, McMillen DR. Design principles for the analysis and construction of robustly homeostatic biological networks. J Theor Biol 2016; 408:274-289. [DOI: 10.1016/j.jtbi.2016.06.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 06/22/2016] [Accepted: 06/28/2016] [Indexed: 01/09/2023]
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117
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Braff D, Shis D, Collins JJ. Synthetic biology platform technologies for antimicrobial applications. Adv Drug Deliv Rev 2016; 105:35-43. [PMID: 27089812 DOI: 10.1016/j.addr.2016.04.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/08/2016] [Accepted: 04/06/2016] [Indexed: 12/11/2022]
Abstract
The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels.
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Affiliation(s)
- Dana Braff
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - David Shis
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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118
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Wagner HJ, Sprenger A, Rebmann B, Weber W. Upgrading biomaterials with synthetic biological modules for advanced medical applications. Adv Drug Deliv Rev 2016; 105:77-95. [PMID: 27179764 DOI: 10.1016/j.addr.2016.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/02/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
One key aspect of synthetic biology is the development and characterization of modular biological building blocks that can be assembled to construct integrated cell-based circuits performing computational functions. Likewise, the idea of extracting biological modules from the cellular context has led to the development of in vitro operating systems. This principle has attracted substantial interest to extend the repertoire of functional materials by connecting them with modules derived from synthetic biology. In this respect, synthetic biological switches and sensors, as well as biological targeting or structure modules, have been employed to upgrade functions of polymers and solid inorganic material. The resulting systems hold great promise for a variety of applications in diagnosis, tissue engineering, and drug delivery. This review reflects on the most recent developments and critically discusses challenges concerning in vivo functionality and tolerance that must be addressed to allow the future translation of such synthetic biology-upgraded materials from the bench to the bedside.
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119
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Menezes AA, Montague MG, Cumbers J, Hogan JA, Arkin AP. Grand challenges in space synthetic biology. J R Soc Interface 2016; 12:20150803. [PMID: 26631337 PMCID: PMC4707852 DOI: 10.1098/rsif.2015.0803] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth.
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Affiliation(s)
- Amor A Menezes
- California Institute for Quantitative Biosciences, University of California, 2151 Berkeley Way, Berkeley, CA 94704-5230, USA
| | - Michael G Montague
- Applications of Vital Knowledge, 113 Chestnut Hill Way, Frederick, MD 21702, USA
| | - John Cumbers
- NASA Ames Space Portal, NASA Ames Research Center, MS 555-2, Moffett Field, CA 94035, USA
| | - John A Hogan
- Bioengineering Branch, NASA Ames Research Center, MS 239-15, Moffett Field, CA 94035, USA
| | - Adam P Arkin
- California Institute for Quantitative Biosciences, University of California, 2151 Berkeley Way, Berkeley, CA 94704-5230, USA E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS955-512 L, Berkeley, CA 94720, USA Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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120
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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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121
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Din MO, Danino T, Prindle A, Skalak M, Selimkhanov J, Allen K, Julio E, Atolia E, Tsimring LS, Bhatia SN, Hasty J. Synchronized cycles of bacterial lysis for in vivo delivery. Nature 2016; 536:81-85. [PMID: 27437587 PMCID: PMC5048415 DOI: 10.1038/nature18930] [Citation(s) in RCA: 387] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/13/2016] [Indexed: 12/29/2022]
Abstract
The pervasive view of bacteria as strictly pathogenic has given way to an appreciation of the widespread prevalence of beneficial microbes within the human body1–3. Given this milieu, it is perhaps inevitable that some bacteria would evolve to preferentially grow in environments that harbor disease and thus provide a natural platform for the development of engineered therapies4–6. Such therapies could benefit from bacteria that are programmed to limit bacterial growth while continually producing and releasing cytotoxic agents in situ7–10. Here, we engineer a clinically relevant bacterium to lyse synchronously at a threshold population density and to release genetically encoded cargo. Following quorum lysis, a small number of surviving bacteria reseed the growing population, thus leading to pulsatile delivery cycles. We use microfluidic devices to characterize the engineered lysis strain and we demonstrate its potential as a drug delivery platform via co-culture with human cancer cells in vitro. As a proof of principle, we track the bacterial population dynamics in ectopic syngeneic colorectal tumors in mice. The lysis strain exhibits pulsatile population dynamics in vivo, with mean bacterial luminescence that remained two orders of magnitude lower than an unmodified strain. Finally, guided by previous findings that certain bacteria can enhance the efficacy of standard therapies11, we orally administer the lysis strain, alone or in combination with a clinical chemotherapeutic, to a syngeneic transplantation model of hepatic colorectal metastases. We find that the combination of both circuit-engineered bacteria and chemotherapy leads to a notable reduction of tumor activity along with a marked survival benefit over either therapy alone. Our approach establishes a methodology for leveraging the tools of synthetic biology to exploit the natural propensity for certain bacteria to colonize disease sites.
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Affiliation(s)
- M Omar Din
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Tal Danino
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA
| | - Arthur Prindle
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Matt Skalak
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jangir Selimkhanov
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Kaitlin Allen
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA
| | - Ellixis Julio
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Eta Atolia
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, California, USA
| | - Sangeeta N Bhatia
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA.,Broad Institute of Harvard and MIT, Cambridge, MA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA.,Electrical Engineering and Computer Science and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,BioCircuits Institute, University of California, San Diego, La Jolla, California, USA.,Molecular Biology Section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA
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122
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Del Vecchio D, Dy AJ, Qian Y. Control theory meets synthetic biology. J R Soc Interface 2016; 13:rsif.2016.0380. [PMID: 27440256 DOI: 10.1098/rsif.2016.0380] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022] Open
Abstract
The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology.
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Affiliation(s)
- Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron J Dy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yili Qian
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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123
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Preston MA, Pimentel B, Bermejo-Rodríguez C, Dionne I, Turnbull A, de la Cueva-Méndez G. Repurposing a Prokaryotic Toxin-Antitoxin System for the Selective Killing of Oncogenically Stressed Human Cells. ACS Synth Biol 2016; 5:540-6. [PMID: 26230535 DOI: 10.1021/acssynbio.5b00096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prokaryotes express intracellular toxins that pass unnoticed to carrying cells until coexpressed antitoxin partners are degraded in response to stress. Although not evolved to function in eukaryotes, one of these toxins, Kid, induces apoptosis in mammalian cells, an effect that is neutralized by its cognate antitoxin, Kis. Here we engineered this toxin-antitoxin pair to create a synthetic system that becomes active in human cells suffering a specific oncogenic stress. Inspired by the way Kid becomes active in bacterial cells, we produced a Kis variant that is selectively degraded in human cells expressing oncoprotein E6. The resulting toxin-antitoxin system functions autonomously in human cells, distinguishing those that suffer the oncogenic insult, which are killed by Kid, from those that do not, which remain protected by Kis. Our results provide a framework for developing personalized anticancer strategies avoiding off-target effects, a challenge that has been hardly tractable by other means thus far.
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Affiliation(s)
- Mark A. Preston
- MRC Cancer Cell Unit. Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, U.K
| | - Belén Pimentel
- MRC Cancer Cell Unit. Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, U.K
| | | | - Isabelle Dionne
- MRC Cancer Cell Unit. Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, U.K
| | - Alice Turnbull
- MRC Cancer Cell Unit. Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, U.K
| | - Guillermo de la Cueva-Méndez
- MRC Cancer Cell Unit. Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, U.K
- Andalusian Centre for Nanomedicine and Biotechnology (BIONAND), Parque Tecnológico de Andalucı́a, C/Severo Ochoa 35, 29590 Campanillas, Málaga, Spain
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124
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Harder D, Hirschi S, Ucurum Z, Goers R, Meier W, Müller DJ, Fotiadis D. Engineering a Chemical Switch into the Light-driven Proton Pump Proteorhodopsin by Cysteine Mutagenesis and Thiol Modification. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Harder
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
| | - Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
| | - Roland Goers
- Department of Chemistry; University of Basel; 4056 Basel Switzerland
- Department of Biosystems Science and Engineering; ETH Zürich; 4058 Basel Switzerland
| | - Wolfgang Meier
- Department of Chemistry; University of Basel; 4056 Basel Switzerland
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering; ETH Zürich; 4058 Basel Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
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125
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Harder D, Hirschi S, Ucurum Z, Goers R, Meier W, Müller DJ, Fotiadis D. Engineering a Chemical Switch into the Light-driven Proton Pump Proteorhodopsin by Cysteine Mutagenesis and Thiol Modification. Angew Chem Int Ed Engl 2016; 55:8846-9. [PMID: 27294681 DOI: 10.1002/anie.201601537] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/27/2016] [Indexed: 12/20/2022]
Abstract
For applications in synthetic biology, for example, the bottom-up assembly of biomolecular nanofactories, modules of specific and controllable functionalities are essential. Of fundamental importance in such systems are energizing modules, which are able to establish an electrochemical gradient across a vesicular membrane as an energy source for powering other modules. Light-driven proton pumps like proteorhodopsin (PR) are excellent candidates for efficient energy conversion. We have extended the versatility of PR by implementing an on/off switch based on reversible chemical modification of a site-specifically introduced cysteine residue. The position of this cysteine residue in PR was identified by structure-based cysteine mutagenesis combined with a proton-pumping assay using E. coli cells overexpressing PR and PR proteoliposomes. The identified PR mutant represents the first light-driven proton pump that can be chemically switched on/off depending on the requirements of the molecular system.
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Affiliation(s)
- Daniel Harder
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Roland Goers
- Department of Chemistry, University of Basel, 4056, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland.
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126
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Abstract
The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli.
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127
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Nielsen AAK, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA. Genetic circuit design automation. Science 2016; 352:aac7341. [PMID: 27034378 DOI: 10.1126/science.aac7341] [Citation(s) in RCA: 576] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/21/2016] [Indexed: 12/12/2022]
Abstract
Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits forEscherichia coli(880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization.
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Affiliation(s)
- Alec A K Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bryan S Der
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Biological Design Center, Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Jonghyeon Shin
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Prashant Vaidyanathan
- Biological Design Center, Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Vanya Paralanov
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20817, USA
| | - Elizabeth A Strychalski
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20817, USA
| | - David Ross
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20817, USA
| | - Douglas Densmore
- Biological Design Center, Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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128
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Courbet A, Endy D, Renard E, Molina F, Bonnet J. Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates. Sci Transl Med 2016; 7:289ra83. [PMID: 26019219 DOI: 10.1126/scitranslmed.aaa3601] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Whole-cell biosensors have several advantages for the detection of biological substances and have proven to be useful analytical tools. However, several hurdles have limited whole-cell biosensor application in the clinic, primarily their unreliable operation in complex media and low signal-to-noise ratio. We report that bacterial biosensors with genetically encoded digital amplifying genetic switches can detect clinically relevant biomarkers in human urine and serum. These bactosensors perform signal digitization and amplification, multiplexed signal processing with the use of Boolean logic gates, and data storage. In addition, we provide a framework with which to quantify whole-cell biosensor robustness in clinical samples together with a method for easily reprogramming the sensor module for distinct medical detection agendas. Last, we demonstrate that bactosensors can be used to detect pathological glycosuria in urine from diabetic patients. These next-generation whole-cell biosensors with improved computing and amplification capacity could meet clinical requirements and should enable new approaches for medical diagnosis.
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Affiliation(s)
- Alexis Courbet
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France
| | - Drew Endy
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Eric Renard
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France. Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Department of Endocrinology, Diabetes, Nutrition, Montpellier University Hospital; INSERM 1411 Clinical Investigation Center; Institute of Functional Genomics, CNRS UMR 5203, INSERM U661, University of Montpellier, 34090 Montpellier, France. Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Franck Molina
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France.
| | - Jérôme Bonnet
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France. Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Department of Endocrinology, Diabetes, Nutrition, Montpellier University Hospital; INSERM 1411 Clinical Investigation Center; Institute of Functional Genomics, CNRS UMR 5203, INSERM U661, University of Montpellier, 34090 Montpellier, France. Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France.
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129
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Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG. Synthetic and systems biology for microbial production of commodity chemicals. NPJ Syst Biol Appl 2016; 2:16009. [PMID: 28725470 PMCID: PMC5516863 DOI: 10.1038/npjsba.2016.9] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 01/08/2023] Open
Abstract
The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.
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Affiliation(s)
- Victor Chubukov
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Héctor García Martín
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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130
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Kanakov O, Laptyeva T, Tsimring L, Ivanchenko M. Spatiotemporal dynamics of distributed synthetic genetic circuits. PHYSICA D. NONLINEAR PHENOMENA 2016; 318-319:116-123. [PMID: 26955203 PMCID: PMC4778264 DOI: 10.1016/j.physd.2015.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We propose and study models of two distributed synthetic gene circuits, toggle-switch and oscillator, each split between two cell strains and coupled via quorum-sensing signals. The distributed toggle switch relies on mutual repression of the two strains, and oscillator is comprised of two strains, one of which acts as an activator for another that in turn acts as a repressor. Distributed toggle switch can exhibit mobile fronts, switching the system from the weaker to the stronger spatially homogeneous state. The circuit can also act as a biosensor, with the switching front dynamics determined by the properties of an external signal. Distributed oscillator system displays another biosensor functionality: oscillations emerge once a small amount of one cell strain appears amid the other, present in abundance. Distribution of synthetic gene circuits among multiple strains allows one to reduce crosstalk among different parts of the overall system and also decrease the energetic burden of the synthetic circuit per cell, which may allow for enhanced functionality and viability of engineered cells.
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Affiliation(s)
- Oleg Kanakov
- Lobachevsky State University of Nizhniy Novgorod, Prospekt Gagarina 23, 603950 Nizhniy Novgorod, Russia
| | - Tetyana Laptyeva
- Lobachevsky State University of Nizhniy Novgorod, Prospekt Gagarina 23, 603950 Nizhniy Novgorod, Russia
| | - Lev Tsimring
- BioCircuits Institute, University of California – San Diego, La Jolla, CA 92093-0328, USA
| | - Mikhail Ivanchenko
- Lobachevsky State University of Nizhniy Novgorod, Prospekt Gagarina 23, 603950 Nizhniy Novgorod, Russia
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131
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Abstract
The human gut microbiota plays a major role in the development and maintenance of good health. Many recent studies have attempted to define links between microbiota residents, their function and the development of colorectal cancer (CRC). Gut microbiota drive the development of inflammation within the colon and such inflammation is implicated in colonic neoplastic development. Although the precise mechanisms through which the microbiota is involved in cancer development remain elusive, the message is clear: the microbiota contributes to cancer risk by influencing a number of key host processes. It is also recognized that we have the ability to influence the role of the gut microbiota by considering our nutritional intake. We have always known that 'we are what we eat' but it is also true that 'they (our gut microbiota) are what we eat'. We therefore have a huge opportunity to positively influence our health through microbial manipulation. There is now a clear need to move past defining the constituents of the gastrointestinal microbiota and to focus more on understanding the functional capabilities of the resident microbial community and how this impacts on host health. One such emerging concept is the development of microbial biofilms which can form in the gut in conjunction with CRC tissue. By better understanding of the interaction between the host and its resident microbiota, in the context of health and cancer development, we will open new therapeutic and diagnostic opportunities for reducing the CRC global health burden.
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Affiliation(s)
- Georgina L Hold
- School of Medicine and Dentistry, Aberdeen University, Aberdeen, UK
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132
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Bracho OR, Manchery C, Haskell EC, Blanar CA, Smith RP. Circumvention of Learning Increases Intoxication Efficacy of Nematicidal Engineered Bacteria. ACS Synth Biol 2016; 5:241-9. [PMID: 26692340 DOI: 10.1021/acssynbio.5b00192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Synthetic biology holds promise to engineer systems to treat diseases. One critical, yet underexplored, facet of designing such systems is the interplay between the system and the pathogen. Understanding this interplay may be critical to increasing efficacy and overcoming resistance against the system. Using the principles of synthetic biology, we engineer a strain of Escherichia coli to attract and intoxicate the nematode Caenorhabditis elegans. Our bacteria are engineered with a toxin module, which intoxicates the nematode upon ingestion, and an attraction module, which serves to attract and increase the feeding rate of the nematodes. When independently implemented, these modules successfully intoxicate and attract the worms, respectively. However, in combination, the efficacy of our bacteria is significantly reduced due to aversive associative learning in C. elegans. Guided by mathematical modeling, we dynamically regulate module induction to increase intoxication by circumventing learning. Our results detail the creation of a novel nematicidal bacterium that may have application against nematodes, unravel unique constraints on circuit dynamics that are governed by C. elegans physiology, and add to the growing list of design and implementation considerations associated with synthetic biology.
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Affiliation(s)
- Olena R. Bracho
- Department
of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33314, United States
| | - Cyril Manchery
- Department
of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33314, United States
| | - Evan C. Haskell
- Department
of Mathematics, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33314, United States
| | - Christopher A. Blanar
- Department
of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33314, United States
| | - Robert P. Smith
- Department
of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33314, United States
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133
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Kis Z, Pereira HS, Homma T, Pedrigi RM, Krams R. Mammalian synthetic biology: emerging medical applications. J R Soc Interface 2016; 12:rsif.2014.1000. [PMID: 25808341 DOI: 10.1098/rsif.2014.1000] [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] Open
Abstract
In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON-OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes.
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Affiliation(s)
- Zoltán Kis
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Takayuki Homma
- Department of Bioengineering, Imperial College London, London, UK
| | - Ryan M Pedrigi
- Department of Bioengineering, Imperial College London, London, UK
| | - Rob Krams
- Department of Bioengineering, Imperial College London, London, UK
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134
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Kong W, Kapuganti VS, Lu T. A gene network engineering platform for lactic acid bacteria. Nucleic Acids Res 2016; 44:e37. [PMID: 26503255 PMCID: PMC4770204 DOI: 10.1093/nar/gkv1093] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 11/28/2022] Open
Abstract
Recent developments in synthetic biology have positioned lactic acid bacteria (LAB) as a major class of cellular chassis for applications. To achieve the full potential of LAB, one fundamental prerequisite is the capacity for rapid engineering of complex gene networks, such as natural biosynthetic pathways and multicomponent synthetic circuits, into which cellular functions are encoded. Here, we present a synthetic biology platform for rapid construction and optimization of large-scale gene networks in LAB. The platform involves a copy-controlled shuttle for hosting target networks and two associated strategies that enable efficient genetic editing and phenotypic validation. By using a nisin biosynthesis pathway and its variants as examples, we demonstrated multiplex, continuous editing of small DNA parts, such as ribosome-binding sites, as well as efficient manipulation of large building blocks such as genes and operons. To showcase the platform, we applied it to expand the phenotypic diversity of the nisin pathway by quickly generating a library of 63 pathway variants. We further demonstrated its utility by altering the regulatory topology of the nisin pathway for constitutive bacteriocin biosynthesis. This work demonstrates the feasibility of rapid and advanced engineering of gene networks in LAB, fostering their applications in biomedicine and other areas.
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Affiliation(s)
- Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Venkata S Kapuganti
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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135
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Huang S, Lee AJ, Tsoi R, Wu F, Zhang Y, Leong KW, You L. Coupling spatial segregation with synthetic circuits to control bacterial survival. Mol Syst Biol 2016; 12:859. [PMID: 26925805 PMCID: PMC4770385 DOI: 10.15252/msb.20156567] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Engineered bacteria have great potential for medical and environmental applications. Fulfilling this potential requires controllability over engineered behaviors and scalability of the engineered systems. Here, we present a platform technology, microbial swarmbot, which employs spatial arrangement to control the growth dynamics of engineered bacteria. As a proof of principle, we demonstrated a safeguard strategy to prevent unintended bacterial proliferation. In particular, we adopted several synthetic gene circuits to program collective survival in Escherichia coli: the engineered bacteria could only survive when present at sufficiently high population densities. When encapsulated by permeable membranes, these bacteria can sense the local environment and respond accordingly. The cells inside the microbial swarmbot capsules will survive due to their high densities. Those escaping from a capsule, however, will be killed due to a decrease in their densities. We demonstrate that this design concept is modular and readily generalizable. Our work lays the foundation for engineering integrated and programmable control of hybrid biological–material systems for diverse applications.
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Affiliation(s)
- Shuqiang Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Anna Jisu Lee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ryan Tsoi
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ying Zhang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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136
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Manzoni R, Urrios A, Velazquez-Garcia S, de Nadal E, Posas F. Synthetic biology: insights into biological computation. Integr Biol (Camb) 2016; 8:518-32. [DOI: 10.1039/c5ib00274e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology.
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Affiliation(s)
- Romilde Manzoni
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Arturo Urrios
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Silvia Velazquez-Garcia
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Francesc Posas
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
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137
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Ullah E, Aeron S, Hassoun S. gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:122-134. [PMID: 26886737 DOI: 10.1109/tcbb.2015.2430344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Computational methods to engineer cellular metabolism promise to play a critical role in producing pharmaceutical, repairing defective genes, destroying cancer cells, and generating biofuels. Elementary Flux Mode (EFM) analysis is one such powerful technique that has elucidated cell growth and regulation, predicted product yield, and analyzed network robustness. EFM analysis, however, is a computationally daunting task because it requires the enumeration of all independent and stoichiometrically balanced pathways within a cellular network. We present in this paper an EFM enumeration algorithm, termed graphical EFM or gEFM. The algorithm is based on graph traversal, an approach previously assumed unsuitable for enumerating EFMs. The approach is derived from a pathway synthesis method proposed by Mavrovouniotis et al. The algorithm is described and proved correct. We apply gEFM to several networks and report runtimes in comparison with other EFM computation tools. We show how gEFM benefits from network compression. Like other EFM computational techniques, gEFM is sensitive to constraint ordering; however, we are able to demonstrate that knowledge of the underlying network structure leads to better constraint ordering. gEFM is shown to be competitive with state-of-the-art EFM computational techniques for several networks, but less so for networks with a larger number of EFMs.
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138
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Verseux CN, Paulino-Lima IG, Baqué M, Billi D, Rothschild LJ. Synthetic Biology for Space Exploration: Promises and Societal Implications. ETHICS OF SCIENCE AND TECHNOLOGY ASSESSMENT 2016. [DOI: 10.1007/978-3-319-21088-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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139
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Synthetic biology’s multiple dimensions of benefits and risks: implications for governance and policies. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-658-10988-2_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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140
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Lindsay RJ, Kershaw MJ, Pawlowska BJ, Talbot NJ, Gudelj I. Harbouring public good mutants within a pathogen population can increase both fitness and virulence. eLife 2016; 5:e18678. [PMID: 28029337 PMCID: PMC5193496 DOI: 10.7554/elife.18678] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/14/2016] [Indexed: 01/27/2023] Open
Abstract
Existing theory, empirical, clinical and field research all predict that reducing the virulence of individuals within a pathogen population will reduce the overall virulence, rendering disease less severe. Here, we show that this seemingly successful disease management strategy can fail with devastating consequences for infected hosts. We deploy cooperation theory and a novel synthetic system involving the rice blast fungus Magnaporthe oryzae. In vivo infections of rice demonstrate that M. oryzae virulence is enhanced, quite paradoxically, when a public good mutant is present in a population of high-virulence pathogens. We reason that during infection, the fungus engages in multiple cooperative acts to exploit host resources. We establish a multi-trait cooperation model which suggests that the observed failure of the virulence reduction strategy is caused by the interference between different social traits. Multi-trait cooperative interactions are widespread, so we caution against the indiscriminant application of anti-virulence therapy as a disease-management strategy.
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Affiliation(s)
| | | | | | | | - Ivana Gudelj
- School of Biosciences, University of Exeter, Exeter, United Kingdom,
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141
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Kolar K, Wischhusen HM, Müller K, Karlsson M, Weber W, Zurbriggen MD. A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication. BMC SYSTEMS BIOLOGY 2015; 9:97. [PMID: 26714638 PMCID: PMC4696150 DOI: 10.1186/s12918-015-0252-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 12/15/2015] [Indexed: 02/05/2023]
Abstract
Background Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to engineer well-defined systems that allow the convenient study and manipulation of intercellular communication networks. Results Here, we present the first mammalian synthetic network for reciprocal cell-cell communication to compute the border between a sender/receiver and a processing cell population. The two populations communicate via L-tryptophan and interleukin-4 to highlight the population border by the production of a fluorescent protein. The sharpness of that visualized edge can be adjusted by modulating key parameters of the network. Conclusions We anticipate that this network will on the one hand be a useful tool to gain deeper insights into the mechanisms of tissue formation in nature and will on the other hand contribute to our ability to engineer artificial tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0252-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Kolar
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany
| | - Hanna M Wischhusen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: DMK GmbH, Head of Quality Assurance, DE-26939, Ovelgönne, Germany
| | - Konrad Müller
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Novartis Pharma AG, Biologics Process R&D, CH-4002, Basel, Switzerland
| | - Maria Karlsson
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Respiratory, Inflammation and Autoimmunity (RIA) iMED, AstraZeneca, SE-431 83, Mölndal, Sweden
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, DE-79104, Freiburg, Germany
| | - Matias D Zurbriggen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany. .,Present address: Institute of Synthetic Biology and Cluster of Excellence on Plant Science (CEPLAS), University of Düsseldorf, DE-40225, Düsseldorf, Germany.
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142
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Pu J, Chronis I, Ahn D, Dickinson BC. A Panel of Protease-Responsive RNA Polymerases Respond to Biochemical Signals by Production of Defined RNA Outputs in Live Cells. J Am Chem Soc 2015; 137:15996-9. [PMID: 26652972 DOI: 10.1021/jacs.5b10290] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA is an attractive biomolecule for biosensing and engineering applications due to its information storage capacity and ability to drive gene expression or knockdown. However, methods to link chemical signals to the production of specific RNAs are lacking. Here, we develop protease-responsive RNA polymerases (PRs) as a strategy to encode multiple specific proteolytic events in defined sequences of RNA in live mammalian cells. This work demonstrates that RNAP-based molecular recording devices can be deployed for multimodal analyses of biochemical activities or to trigger gene circuits using measured signaling events.
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Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ian Chronis
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Daniel Ahn
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
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143
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Schukur L, Geering B, Charpin-El Hamri G, Fussenegger M. Implantable synthetic cytokine converter cells with AND-gate logic treat experimental psoriasis. Sci Transl Med 2015; 7:318ra201. [PMID: 26676608 DOI: 10.1126/scitranslmed.aac4964] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Psoriasis is a chronic inflammatory skin disease characterized by a relapsing-remitting disease course and correlated with increased expression of proinflammatory cytokines, such as tumor necrosis factor (TNF) and interleukin 22 (IL22). Psoriasis is hard to treat because of the unpredictable and asymptomatic flare-up, which limits handling of skin lesions to symptomatic treatment. Synthetic biology-based gene circuits are uniquely suited for the treatment of diseases with complex dynamics, such as psoriasis, because they can autonomously couple the detection of disease biomarkers with the production of therapeutic proteins. We designed a mammalian cell synthetic cytokine converter that quantifies psoriasis-associated TNF and IL22 levels using serially linked receptor-based synthetic signaling cascades, processes the levels of these proinflammatory cytokines with AND-gate logic, and triggers the corresponding expression of therapeutic levels of the anti-inflammatory/psoriatic cytokines IL4 and IL10, which have been shown to be immunomodulatory in patients. Implants of microencapsulated cytokine converter transgenic designer cells were insensitive to simulated bacterial and viral infections as well as psoriatic-unrelated inflammation. The designer cells specifically prevented the onset of psoriatic flares, stopped acute psoriasis, improved psoriatic skin lesions and restored normal skin-tissue morphology in mice. The antipsoriatic designer cells were equally responsive to blood samples from psoriasis patients, suggesting that the synthetic cytokine converter captures the clinically relevant cytokine range. Implanted designer cells that dynamically interface with the patient's metabolism by detecting specific disease metabolites or biomarkers, processing their blood levels with synthetic circuits in real time, and coordinating immediate production and systemic delivery of protein therapeutics may advance personalized gene- and cell-based therapies.
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Affiliation(s)
- Lina Schukur
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Barbara Geering
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | | | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland. Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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144
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Lin J, Liu Y, Zhan Y, Zhuang C, Liu L, Fu X, Xu W, Li J, Chen M, Cai Z, Huang W. Synthetic Tet-inducible small hairpin RNAs targeting hTERT or Bcl-2 inhibit malignant phenotypes of bladder cancer T24 and 5637 cells. Tumour Biol 2015; 37:3115-21. [PMID: 26427661 DOI: 10.1007/s13277-015-4122-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/20/2015] [Indexed: 02/05/2023] Open
Abstract
Small hairpin RNA (shRNA) can inhibit the malignant phenotypes of tumor cell through ribonucleic acid interference (RNAi). However, it is hardly to be regulated and it may induce few phenotypic changes. Here, we build a type of tetracycline (Tet)-inducible vectors which can achieve regulatable expression of shRNA in a time-dependent manner by using synthetic biology approach. In order to prove the effectiveness of this device, we chose hTERT and Bcl-2 as target genes and test the utility of the device on 5637 and T24 cell lines. The experiments show that the Tet-inducible small hairpin RNA can effectively suppress their target genes and generate anti-cancer effects on both 5637 and T24 cell lines. The device we build not only can inhibit proliferation but also can induce apoptosis and suppress migration of the bladder cancer cell lines 5637 and T24. The Tet-inducible small hairpin RNAs may provide a novel strategy for the treatment of human bladder cancer in the future.
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Affiliation(s)
- Junhao Lin
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
- Shantou University Medical College, Shantou, 515041, China.
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Yonghao Zhan
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
- Shantou University Medical College, Shantou, 515041, China
| | - Chengle Zhuang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
- Shantou University Medical College, Shantou, 515041, China
| | - Li Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
- Shantou University Medical College, Shantou, 515041, China
| | - Xing Fu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Wen Xu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jianfa Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
- Shantou University Medical College, Shantou, 515041, China
| | - Mingwei Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Zhiming Cai
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
- Shantou University Medical College, Shantou, 515041, China.
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
- Shantou University Medical College, Shantou, 515041, China.
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145
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Kali A. Human Microbiome Engineering: The Future and Beyond. J Clin Diagn Res 2015; 9:DE01-4. [PMID: 26500908 DOI: 10.7860/jcdr/2015/14946.6570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/10/2015] [Indexed: 12/22/2022]
Abstract
Microbial flora of skin and mucosal surface are vital component of human biology. Current research indicates that this microbial constellation, rather than being inert commensals, has greater implications in health and disease. They play essential role in metabolism, immunity, inflammation, neuro-endocrine regulation and even moderate host response to cancer. Genetic engineering was a major breakthrough in medical research in 1970's and it opened up newer dimensions in vaccinology, large-scale synthesis of bio-molecule and drug development. Engineering human microbiome is a novel concept. Recombinant DNA technology can be employed to modify the genome of critical components of resident microflora to achieve unprecedented goals.
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Affiliation(s)
- Arunava Kali
- Assistant Professor, Department of Microbiology, Mahatma Gandhi Medical College & Research Institute , Pondicherry, India
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146
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Glass L. Dynamical disease: Challenges for nonlinear dynamics and medicine. CHAOS (WOODBURY, N.Y.) 2015; 25:097603. [PMID: 26428556 DOI: 10.1063/1.4915529] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dynamical disease refers to illnesses that are associated with striking changes in the dynamics of some bodily function. There is a large literature in mathematics and physics which proposes mathematical models for the physiological systems and carries out analyses of the properties of these models using nonlinear dynamics concepts involving analyses of the stability and bifurcations of attractors. This paper discusses how these concepts can be applied to medicine.
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Affiliation(s)
- Leon Glass
- Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
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147
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Affiliation(s)
- Kristin Hagen
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Margret Engelhard
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Georg Toepfer
- Center for Literary and Cultural Research Berlin, Berlin, Germany
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148
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Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun 2015; 6:7970. [PMID: 26258987 PMCID: PMC4918353 DOI: 10.1038/ncomms8970] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/01/2015] [Indexed: 12/27/2022] Open
Abstract
The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the genome-wide regulatory role of GadEWX is still unknown. Here we comprehensively reconstruct the genome-wide GadEWX transcriptional regulatory network and RpoS involvement in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons consist of 45 genes in 31 transcription units and 28 of these genes were associated with RpoS-binding sites. We demonstrate that GadEWX directly and coherently regulate several proton-generating/consuming enzymes with pairs of negative-feedback loops for pH homeostasis. In addition, GadEWX regulate genes with assorted functions, including molecular chaperones, acid resistance, stress response and other regulatory activities. These results show how GadEWX simultaneously coordinate many cellular processes to produce the overall response of E. coli to acid stress. GadEWX regulons play a critical role in transcription regulation in response to acid stress. By reconstructing genome-wide GadEWX transcriptional network, here the authors show how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress.
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Affiliation(s)
- Sang Woo Seo
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Donghyuk Kim
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Edward J O'Brien
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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149
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Exploring Host-Microbiome Interactions using an in Silico Model of Biomimetic Robots and Engineered Living Cells. Sci Rep 2015; 5:11988. [PMID: 26178309 PMCID: PMC4648426 DOI: 10.1038/srep11988] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 05/29/2015] [Indexed: 12/26/2022] Open
Abstract
The microbiome's underlying dynamics play an important role in regulating the behavior and health of its host. In order to explore the details of these interactions, we created an in silico model of a living microbiome, engineered with synthetic biology, that interfaces with a biomimetic, robotic host. By analytically modeling and computationally simulating engineered gene networks in these commensal communities, we reproduced complex behaviors in the host. We observed that robot movements depended upon programmed biochemical network dynamics within the microbiome. These results illustrate the model's potential utility as a tool for exploring inter-kingdom ecological relationships. These systems could impact fields ranging from synthetic biology and ecology to biophysics and medicine.
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150
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Krom RJ, Bhargava P, Lobritz MA, Collins JJ. Engineered Phagemids for Nonlytic, Targeted Antibacterial Therapies. NANO LETTERS 2015; 15:4808-4813. [PMID: 26044909 DOI: 10.1021/acs.nanolett.5b01943] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The increasing incidence of antibiotic-resistant bacterial infections is creating a global public health threat. Because conventional antibiotic drug discovery has failed to keep pace with the rise of resistance, a growing need exists to develop novel antibacterial methodologies. Replication-competent bacteriophages have been utilized in a limited fashion to treat bacterial infections. However, this approach can result in the release of harmful endotoxins, leading to untoward side effects. Here, we engineer bacterial phagemids to express antimicrobial peptides (AMPs) and protein toxins that disrupt intracellular processes, leading to rapid, nonlytic bacterial death. We show that this approach is highly modular, enabling one to readily alter the number and type of AMPs and toxins encoded by the phagemids. Furthermore, we demonstrate the effectiveness of engineered phagemids in an in vivo murine peritonitis infection model. This work shows that targeted, engineered phagemid therapy can serve as a viable, nonantibiotic means to treat bacterial infections, while avoiding the health issues inherent to lytic and replicative bacteriophage use.
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Affiliation(s)
- Russell J Krom
- †Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- ‡Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- ∥Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- ⊥Department of Molecular and Translational Medicine, Boston University, Boston, Massachusetts 02215, United States
| | - Prerna Bhargava
- †Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- §Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- ∥Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Michael A Lobritz
- †Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- §Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- ∥Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- #Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - James J Collins
- †Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- ‡Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- §Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- ∥Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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