51
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Riangrungroj P, Polizzi KM. BeQuIK (Biosensor Engineered Quorum Induced Killing): designer bacteria for destroying recalcitrant biofilms. Microb Biotechnol 2019; 13:311-314. [PMID: 31328393 PMCID: PMC7017806 DOI: 10.1111/1751-7915.13465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
- Pinpunya Riangrungroj
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Karen M Polizzi
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK
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52
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Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation. PLoS Biol 2019; 17:e3000250. [PMID: 31095567 PMCID: PMC6522007 DOI: 10.1371/journal.pbio.3000250] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/12/2019] [Indexed: 01/12/2023] Open
Abstract
Rapid point-of-care resistance diagnostics (POC-RD) are a key tool in the fight against antibiotic resistance. By tailoring drug choice to infection genotype, doctors can improve treatment efficacy while limiting costs of inappropriate antibiotic prescription. Here, we combine epidemiological theory and data to assess the potential of resistance diagnostics (RD) innovations in a public health context, as a means to limit or even reverse selection for antibiotic resistance. POC-RD can be used to impose a nonbiological fitness cost on resistant strains by enabling diagnostic-informed treatment and targeted interventions that reduce resistant strains' opportunities for transmission. We assess this diagnostic-imposed fitness cost in the context of a spectrum of bacterial population biologies and find that POC-RD have a greater potential against obligate pathogens than opportunistic pathogens already subject to selection under "bystander" antibiotic exposure during asymptomatic carriage (e.g., the pneumococcus). We close by generalizing the notion of RD-informed strategies to incorporate carriage surveillance information and illustrate that coupling transmission-control interventions to the discovery of resistant strains in carriage can potentially select against resistance in a broad range of opportunistic pathogens.
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53
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Healy CP, Deans TL. Genetic circuits to engineer tissues with alternative functions. J Biol Eng 2019; 13:39. [PMID: 31073328 PMCID: PMC6500048 DOI: 10.1186/s13036-019-0170-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/17/2019] [Indexed: 12/23/2022] Open
Abstract
Persistent and complex problems arising with respect to human physiology and pathology have led to intense investigation into therapies and tools that permit more targeted outcomes and biomimetic responses to pathological conditions. A primary goal in mammalian synthetic biology is to build genetic circuits that exert fine control over cell behavior for next-generation biomedical applications. In pursuit of this, synthetic biologists have engineered cells endowed with genetic circuits with sensor that are capable of reacting to a variety of stimuli and responding with targeted behavior. Here, we highlight how synthetic biology approaches are being used to program cells with novel functions for therapeutic applications, and how they can be used in stem cells to improve differentiation outcomes. These approaches open the possibilities for engineering synthetic tissues for employing personalized medicine and to develop next-generation biomedical therapies.
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Affiliation(s)
- C P Healy
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
| | - T L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
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54
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Virgile C, Hauk P, Wu HC, Bentley WE. Plasmid-encoded protein attenuates Escherichia coli swimming velocity and cell growth, not reprogrammed regulatory functions. Biotechnol Prog 2019; 35:e2778. [PMID: 30666816 PMCID: PMC10711804 DOI: 10.1002/btpr.2778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 12/17/2023]
Abstract
In addition to engineering new pathways for synthesis, synthetic biologists rewire cells to carry out "programmable" functions, an example being the creation of wound-healing probiotics. Engineering regulatory circuits and synthetic machinery, however, can be deleterious to cell function, particularly if the "metabolic burden" is significant. Here, a synthetic regulatory circuit previously constructed to direct Escherichia coli to swim toward hydrogen peroxide, a signal of wound generation, was shown to work even with coexpression of antibiotic resistance genes and genes associated with lactose utilization. We found, however, that cotransformation with a second vector constitutively expressing GFP (as a marker) and additionally conferring resistance to kanamycin and tetracycline resulted in slower velocity (Δ~6 μm/s) and dramatically reduced growth rate (Δ > 50%). The additional vector did not, however, alter the run-and-tumble ratio or directional characteristics of H2 O2 -dependent motility. The main impact of this additional burden was limited to slowing cell velocity and growth, suggesting that reprogrammed cell motility by minimally altering native regulatory circuits can be maintained even when extraneous burden is placed on the host cell. © 2019 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2778, 2019.
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Affiliation(s)
- Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, College Park, MD 20742
- Fischell Department of Bioengineering, Room 3122, Jeong H. Kim Engineering Building (Bldg. #225), University of Maryland, College Park, MD 20742
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, College Park, MD 20742
- Fischell Department of Bioengineering, Room 3122, Jeong H. Kim Engineering Building (Bldg. #225), University of Maryland, College Park, MD 20742
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, College Park, MD 20742
- Fischell Department of Bioengineering, Room 3122, Jeong H. Kim Engineering Building (Bldg. #225), University of Maryland, College Park, MD 20742
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55
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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56
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Wan X, Volpetti F, Petrova E, French C, Maerkl SJ, Wang B. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals. Nat Chem Biol 2019; 15:540-548. [PMID: 30911179 DOI: 10.1038/s41589-019-0244-3] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/11/2019] [Indexed: 11/09/2022]
Abstract
Cell-based biosensors have great potential to detect various toxic and pathogenic contaminants in aqueous environments. However, frequently they cannot meet practical requirements due to insufficient sensing performance. To address this issue, we investigated a modular, cascaded signal amplifying methodology. We first tuned intracellular sensory receptor densities to increase sensitivity, and then engineered multi-layered transcriptional amplifiers to sequentially boost output expression level. We demonstrated these strategies by engineering ultrasensitive bacterial sensors for arsenic and mercury, and improved detection limit and output up to 5,000-fold and 750-fold, respectively. Coupled by leakage regulation approaches, we developed an encapsulated microbial sensor cell array for low-cost, portable and precise field monitoring, where the analyte can be readily quantified via displaying an easy-to-interpret volume bar-like pattern. The ultrasensitive signal amplifying methodology along with the background regulation and the sensing platform will be widely applicable to many other cell-based sensors, paving the way for their real-world applications.
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Affiliation(s)
- Xinyi Wan
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Francesca Volpetti
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Ekaterina Petrova
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Chris French
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK. .,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK.
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57
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Cao X, Hamilton JJ, Venturelli OS. Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. Biochemistry 2019; 58:94-107. [PMID: 30457843 PMCID: PMC6733022 DOI: 10.1021/acs.biochem.8b01006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbiomes impact nearly every environment on Earth by modulating the molecular composition of the environment. Temporally changing environmental stimuli and spatial organization are major variables shaping the structure and function of microbiomes. The web of interactions among members of these communities and between the organisms and the environment dictates microbiome functions. Microbial interactions are major drivers of microbiomes and are modulated by spatiotemporal parameters. A mechanistic and quantitative understanding of ecological, molecular, and environmental forces shaping microbiomes could inform strategies to control microbiome dynamics and functions. Major challenges for harnessing the potential of microbiomes for diverse applications include the development of predictive modeling frameworks and tools for precise manipulation of microbiome behaviors.
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Affiliation(s)
| | | | - Ophelia S. Venturelli
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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58
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Abstract
Measuring biological data across time and space is critical for understanding complex biological processes and for various biosurveillance applications. However, such data are often inaccessible or difficult to directly obtain. Less invasive, more robust and higher-throughput biological recording tools are needed to profile cells and their environments. DNA-based cellular recording is an emerging and powerful framework for tracking intracellular and extracellular biological events over time across living cells and populations. Here, we review and assess DNA recorders that utilize CRISPR nucleases, integrases and base-editing strategies, as well as recombinase and polymerase-based methods. Quantitative characterization, modelling and evaluation of these DNA-recording modalities can guide their design and implementation for specific application areas.
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Affiliation(s)
- Ravi U Sheth
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
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59
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Pedrolli DB, Ribeiro NV, Squizato PN, de Jesus VN, Cozetto DA. Engineering Microbial Living Therapeutics: The Synthetic Biology Toolbox. Trends Biotechnol 2018; 37:100-115. [PMID: 30318171 DOI: 10.1016/j.tibtech.2018.09.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/31/2022]
Abstract
Microbes can be engineered to act like living therapeutics designed to perform specific actions in the human body. From fighting and preventing infections to eliminating tumors and treating metabolic disorders, engineered living systems are the next generation of therapeutics. In recent years, synthetic biologists have greatly expanded the genetic toolbox for microbial living therapeutics, adding sensors, regulators, memory circuits, delivery devices, and kill switches. These advances have paved the way for successful engineering of fully functional living therapeutics, with sensing, production, and biocontainment devices. However, some important tools are still missing from the box. In this review, we cover the most recent biological parts and approaches developed and describe the missing tools needed to build robust living therapeutics.
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Affiliation(s)
- Danielle B Pedrolli
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017.
| | - Nathan V Ribeiro
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Patrick N Squizato
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Victor N de Jesus
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Daniel A Cozetto
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
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60
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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61
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McKay R, Ghodasra M, Schardt J, Quan D, Pottash AE, Shang W, Jay SM, Payne GF, Chang MW, March JC, Bentley WE. A platform of genetically engineered bacteria as vehicles for localized delivery of therapeutics: Toward applications for Crohn's disease. Bioeng Transl Med 2018; 3:209-221. [PMID: 30377661 PMCID: PMC6195910 DOI: 10.1002/btm2.10113] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/22/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022] Open
Abstract
For therapies targeting diseases of the gastrointestinal tract, we and others envision probiotic bacteria that synthesize and excrete biotherapeutics at disease sites. Toward this goal, we have engineered commensal E. coli that selectively synthesize and secrete a model biotherapeutic in the presence of nitric oxide (NO), an intestinal biomarker for Crohn's disease (CD). This is accomplished by co‐expressing the pore forming protein TolAIII with the biologic, granulocyte macrophage‐colony stimulating factor (GM‐CSF). We have additionally engineered these bacteria to accumulate at sites of elevated NO by engineering their motility circuits and controlling pseudotaxis. Importantly, because we have focused on in vitro test beds, motility and biotherapeutics production are spatiotemporally characterized. Together, the targeted recognition, synthesis, and biomolecule delivery comprises a “smart” probiotics platform that may have utility in the treatment of CD. Further, this platform could be modified to accommodate other pursuits by swapping the promoter and therapeutic gene to reflect other disease biomarkers and treatments, respectively.
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Affiliation(s)
- Ryan McKay
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Monil Ghodasra
- Fischell Dept. of Bioengineering University of Maryland College Park MD
| | - John Schardt
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health Bethesda MD
| | - David Quan
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Alex Eli Pottash
- Fischell Dept. of Bioengineering University of Maryland College Park MD
| | - Wu Shang
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Steven M Jay
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health Bethesda MD.,Marlene and Stewart Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine Baltimore MD.,Program in Molecular and Cellular Biology University of Maryland College Park MD
| | - Gregory F Payne
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Matthew Wook Chang
- Dept. of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation, Life Sciences Institute National University of Singapore Singapore
| | - John C March
- Dept. of Biological and Environmental Engineering Cornell University Ithaca NY
| | - William E Bentley
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
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62
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Storm DW, Braga LH, Cooper CS. Continuous Antibiotic Prophylaxis in Pediatric Urology. Urol Clin North Am 2018; 45:525-538. [PMID: 30316308 DOI: 10.1016/j.ucl.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Continuous antibiotic prophylaxis (CAP) for urinary tract infection prevention in children with vesicoureteral reflux, hydronephrosis, and hydroureteronephrosis is reviewed. A more selective use of CAP is advocated based on a review of known individual risk factors in each of these conditions that subsequently helps identify the children most likely to benefit from CAP. Both short-term and potential long-term side effects of CAP are reviewed, including the impact of prophylactic antibiotics on bacterial resistance and the microbiome. Alternatives to continuous antibiotic prophylaxis including Vaccinium macrocarpon (Cranberry), probiotics, and vaccines are reviewed.
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Affiliation(s)
- Douglas W Storm
- Department of Urology, University of Iowa, Carver College of Medicine, 200 Hawkins Drive, 3RCP, Iowa City, IA 5224, USA
| | - Luis H Braga
- Department of Surgery, Division of Urology, Mcmaster University, McMaster Children's Hospital, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Christopher S Cooper
- Department of Urology, University of Iowa, Carver College of Medicine, 200 Hawkins Drive, 3RCP, Iowa City, IA 5224, USA.
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63
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Pouvreau B, Vanhercke T, Singh S. From plant metabolic engineering to plant synthetic biology: The evolution of the design/build/test/learn cycle. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:3-12. [PMID: 29907306 DOI: 10.1016/j.plantsci.2018.03.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/19/2018] [Accepted: 03/28/2018] [Indexed: 05/21/2023]
Abstract
Genetic improvement of crops started since the dawn of agriculture and has continuously evolved in parallel with emerging technological innovations. The use of genome engineering in crop improvement has already revolutionised modern agriculture in less than thirty years. Plant metabolic engineering is still at a development stage and faces several challenges, in particular with the time necessary to develop plant based solutions to bio-industrial demands. However the recent success of several metabolic engineering approaches applied to major crops are encouraging and the emerging field of plant synthetic biology offers new opportunities. Some pioneering studies have demonstrated that synthetic genetic circuits or orthogonal metabolic pathways can be introduced into plants to achieve a desired function. The combination of metabolic engineering and synthetic biology is expected to significantly accelerate crop improvement. A defining aspect of both fields is the design/build/test/learn cycle, or the use of iterative rounds of testing modifications to refine hypotheses and develop best solutions. Several technological and technical improvements are now available to make a better use of each design, build, test, and learn components of the cycle. All these advances should facilitate the rapid development of a wide variety of bio-products for a world in need of sustainable solutions.
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Affiliation(s)
- Benjamin Pouvreau
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia.
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia
| | - Surinder Singh
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia
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64
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Hwang IY, Lee HL, Huang JG, Lim YY, Yew WS, Lee YS, Chang MW. Engineering microbes for targeted strikes against human pathogens. Cell Mol Life Sci 2018; 75:2719-2733. [PMID: 29736607 PMCID: PMC11105496 DOI: 10.1007/s00018-018-2827-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/06/2018] [Accepted: 04/23/2018] [Indexed: 12/24/2022]
Abstract
Lack of pathogen specificity in antimicrobial therapy causes non-discriminant microbial cell killing that disrupts the microflora present. As a result, potentially helpful microbial cells are killed along with the pathogen, altering the biodiversity and dynamic interactions within the population. Moreover, the unwarranted exposure of antibiotics to microbes increases the likelihood of developing resistance and perpetuates the emergence of multidrug resistance. Synthetic biology offers an alternative solution where specificity can be conferred to reduce the non-specific, non-targeted activity of currently available antibiotics, and instead provides targeted therapy against specific pathogens and minimising collateral damage to the host's inherent microbiota. With a greater understanding of the microbiome and the available genetic engineering tools for microbial cells, it is possible to devise antimicrobial strategies for novel antimicrobial therapy that are able to precisely and selectively remove infectious pathogens. Herein, we review the strategies developed by unlocking some of the natural mechanisms used by the microbes and how these may be utilised in targeted antimicrobial therapy, with the promise of reducing the current global bane of multidrug antimicrobial resistance.
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Affiliation(s)
- In Young Hwang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Hui Ling Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - James Guoxian Huang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Yvonne Yijuan Lim
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
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65
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McKay R, Hauk P, Quan D, Bentley WE. Development of Cell-Based Sentinels for Nitric Oxide: Ensuring Marker Expression and Unimodality. ACS Synth Biol 2018; 7:1694-1701. [PMID: 29975512 PMCID: PMC7025431 DOI: 10.1021/acssynbio.8b00146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We generated "sentinel" bacteria that respond to the biomarker nitric oxide (NO) and produce a homogeneous and strong fluorescent response. Our dual-plasmid system consists of a signal "relay" vector that employs an NO-responsive promoter that amplifies the native signal (via expression of T7 Polymerase (T7Pol)) to a second vector responsible for GFP expression. Importantly, to achieve an optimal "sentinel" response, we developed strategies that balance the transcriptional load within cells by altering (i) translation and (ii) activity of the T7Pol. Our optimized genetic circuitry was then used to transform commensal E. coli Nissle, as a proof-of-concept toward an ingestible cell-based sensor for Crohn's disease (CD) that, in turn, is marked by elevated levels of intestinal NO. Thus, the "biosensors" demonstrated here may serve as a simple diagnostic tool, contrasting the standard of care including colonoscopies or biopsies.
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Affiliation(s)
- Ryan McKay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - David Quan
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
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66
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Ozdemir T, Fedorec AJ, Danino T, Barnes CP. Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity. Cell Syst 2018; 7:5-16. [DOI: 10.1016/j.cels.2018.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/31/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
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67
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Zúñiga A, Fuente FDL, Federici F, Lionne C, Bônnet J, de Lorenzo V, González B. An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth. ACS Synth Biol 2018; 7:1519-1527. [PMID: 29746094 DOI: 10.1021/acssynbio.8b00002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.
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Affiliation(s)
- Ana Zúñiga
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez—Center of Applied Ecology and Sustainability, Santiago de Chile, 2640, Chile
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Francisco de la Fuente
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez—Center of Applied Ecology and Sustainability, Santiago de Chile, 2640, Chile
- R2B Catalyst, Research Center, Andrés Bello 2299, Santiago, Chile
| | - Fernán Federici
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Corinne Lionne
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Jérome Bônnet
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | | | - Bernardo González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez—Center of Applied Ecology and Sustainability, Santiago de Chile, 2640, Chile
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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69
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Lubkowicz D, Ho CL, Hwang IY, Yew WS, Lee YS, Chang MW. Reprogramming Probiotic Lactobacillus reuteri as a Biosensor for Staphylococcus aureus Derived AIP-I Detection. ACS Synth Biol 2018; 7:1229-1237. [PMID: 29652493 DOI: 10.1021/acssynbio.8b00063] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gram-positive Staphylococcus aureus infection that results in pneumonia, urinary tract infection, and in severe cases, sepsis, has recently been classified as a serious threat to public health. Rapid and cost-effective detection of these infections are costly and time-consuming. Here, we present probiotic lactic acid bacteria engineered to detect autoinducer peptide-I (AIP-I), a quorum sensing molecule produced by Staphylococcus sp. during pathogenesis. We achieved this by adapting the well-characterized agr quorum sensing ( agrQS) from Staphylococcus aureus into Lactobacillus reuteri. The engineered biosensor is able to detect AIP-I levels in the nanomolar to micromolar range. We further investigated the function of the biosensor to detect real-time changes in AIP-I levels to understand the dynamics of Staphylococcus aureus under various strenuous conditions. The developed sensors would be useful for detection of Staphylococcus contamination in hospital settings and for high-throughput drug screening.
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Affiliation(s)
- David Lubkowicz
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, 119077, Singapore
| | - Chun Loong Ho
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, 119077, Singapore
| | - In Young Hwang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, 119077, Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, 119077, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, 119077, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, 119077, Singapore
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70
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Virgile C, Hauk P, Wu HC, Shang W, Tsao CY, Payne GF, Bentley WE. Engineering bacterial motility towards hydrogen-peroxide. PLoS One 2018; 13:e0196999. [PMID: 29750783 PMCID: PMC5947916 DOI: 10.1371/journal.pone.0196999] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/24/2018] [Indexed: 11/19/2022] Open
Abstract
Synthetic biologists construct innovative genetic/biological systems to treat environmental, energy, and health problems. Many systems employ rewired cells for non-native product synthesis, while a few have employed the rewired cells as 'smart' devices with programmable function. Building on the latter, we developed a genetic construct to control and direct bacterial motility towards hydrogen peroxide, one of the body's immune response signaling molecules. A motivation for this work is the creation of cells that can target and autonomously treat disease, the latter signaled by hydrogen peroxide release. Bacteria naturally move towards a variety of molecular cues (e.g., nutrients) in the process of chemotaxis. In this work, we engineered bacteria to recognize and move towards hydrogen peroxide, a non-native chemoattractant and potential toxin. Our system exploits oxyRS, the native oxidative stress regulon of E. coli. We first demonstrated H2O2-mediated upregulation motility regulator, CheZ. Using transwell assays, we showed a two-fold increase in net motility towards H2O2. Then, using a 2D cell tracking system, we quantified bacterial motility descriptors including velocity, % running (of tumble/run motions), and a dynamic net directionality towards the molecular cue. In CheZ mutants, we found that increased H2O2 concentration (0-200 μM) and induction time resulted in increased running speeds, ultimately reaching the native E. coli wild-type speed of ~22 μm/s with a ~45-65% ratio of running to tumbling. Finally, using a microfluidic device with stable H2O2 gradients, we characterized responses and the potential for "programmed" directionality towards H2O2 in quiescent fluids. Overall, the synthetic biology framework and tracking analysis in this work will provide a framework for investigating controlled motility of E. coli and other 'smart' probiotics for signal-directed treatment.
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Affiliation(s)
- Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Wu Shang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
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71
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Bober JR, Beisel CL, Nair NU. Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications. Annu Rev Biomed Eng 2018. [PMID: 29528686 DOI: 10.1146/annurev-bioeng-062117-121019] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An increasing number of studies have strongly correlated the composition of the human microbiota with many human health conditions and, in several cases, have shown that manipulating the microbiota directly affects health. These insights have generated significant interest in engineering indigenous microbiota community members and nonresident probiotic bacteria as biotic diagnostics and therapeutics that can probe and improve human health. In this review, we discuss recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes, and we provide our perspective on the future potential of these technologies.
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Affiliation(s)
- Josef R Bober
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA;
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA;
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Abstract
Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded in recent times. The capacity for DNA synthesis is increasing and costing less; new tools are being developed for fast, large-scale genetic manipulation; and more tested genetic parts are available for use, as is the knowledge of how to use them effectively. These advances promise to unlock an exciting array of 'smart' bacteria for clinical use but will also challenge scientists to better optimize preclinical testing regimes for early identification and validation of promising strains and strategies. Here, we review recent advances in the development and testing of engineered bacterial diagnostics and therapeutics. We highlight new technologies that will assist the development of more complex, robust and reliable engineered bacteria for future clinical applications, and we discuss approaches to more efficiently evaluate engineered strains throughout their preclinical development.
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73
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Saltepe B, Kehribar EŞ, Su Yirmibeşoğlu SS, Şafak Şeker UÖ. Cellular Biosensors with Engineered Genetic Circuits. ACS Sens 2018; 3:13-26. [PMID: 29168381 DOI: 10.1021/acssensors.7b00728] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An increasing interest in building novel biological devices with designed cellular functionalities has triggered the search of innovative tools for biocomputation. Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits. Whole cell biosensors are widely used biological devices that employ several biocomputation tools to program cells for desired functions. Up to the present date, a wide range of whole-cell biosensors have been designed and implemented for disease theranostics, biomedical applications, and environmental monitoring. In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines. Additionally, we stated the novel applications of biological devices with computing functionalities for diagnosis and therapy of various diseases such as infections, cancer, or metabolic diseases, as well as the detection of environmental pollutants such as heavy metals or organic toxic compounds. Current whole-cell biosensors are innovative alternatives to classical biosensors; however, there is still a need to advance decision making capabilities by developing novel biocomputing devices.
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Affiliation(s)
- Behide Saltepe
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Ebru Şahin Kehribar
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | | | - Urartu Özgür Şafak Şeker
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
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74
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A cheZ-Like Gene in Azorhizobium caulinodans Is a Key Gene in the Control of Chemotaxis and Colonization of the Host Plant. Appl Environ Microbiol 2018; 84:AEM.01827-17. [PMID: 29150498 DOI: 10.1128/aem.01827-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/01/2017] [Indexed: 02/07/2023] Open
Abstract
Chemotaxis can provide bacteria with competitive advantages for survival in complex environments. The CheZ chemotaxis protein is a phosphatase, affecting the flagellar motor in Escherichia coli by dephosphorylating the response regulator phosphorylated CheY protein (CheY∼P) responsible for clockwise rotation. A cheZ gene has been found in Azorhizobium caulinodans ORS571, in contrast to other rhizobial species studied so far. The CheZ protein in strain ORS571 has a conserved motif similar to that corresponding to the phosphatase active site in E. coli The construction of a cheZ deletion mutant strain and of cheZ mutant strains carrying a mutation in residues of the putative phosphatase active site showed that strain ORS571 participates in chemotaxis and motility, causing a hyperreversal behavior. In addition, the properties of the cheZ deletion mutant revealed that ORS571 CheZ is involved in other physiological processes, since it displayed increased flocculation, biofilm formation, exopolysaccharide (EPS) production, and host root colonization. In particular, it was observed that the expression of several exp genes, involved in EPS synthesis, was upregulated in the cheZ mutant compared to that in the wild type, suggesting that CheZ negatively controls exp gene expression through an unknown mechanism. It is proposed that CheZ influences the Azorhizobium-plant association by negatively regulating early colonization via the regulation of EPS production. This report established that CheZ in A. caulinodans plays roles in chemotaxis and the symbiotic association with the host plant.IMPORTANCE Chemotaxis allows bacteria to swim toward plant roots and is beneficial to the establishment of various plant-microbe associations. The level of CheY phosphorylation (CheY∼P) is central to the chemotaxis signal transduction. The mechanism of the signal termination of CheY∼P remains poorly characterized among Alphaproteobacteria, except for Sinorhizobium meliloti, which does not contain CheZ but which controls CheY∼P dephosphorylation through a phosphate sink mechanism. Azorhizobium caulinodans ORS571, a microsymbiont of Sesbania rostrata, has an orphan cheZ gene besides two cheY genes similar to those in S. meliloti In addition to controlling the chemotaxis response, the CheZ-like protein in strain ORS571 is playing a role by decreasing bacterial adhesion to the host plant, in contrast to the general situation where chemotaxis-associated proteins promote adhesion. In this study, we identified a CheZ-like protein among Alphaproteobacteria functioning in chemotaxis and the A. caulinodans-S. rostrata symbiosis.
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75
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Ho CL, Tan HQ, Chua KJ, Kang A, Lim KH, Ling KL, Yew WS, Lee YS, Thiery JP, Chang MW. Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention. Nat Biomed Eng 2018; 2:27-37. [PMID: 31015663 DOI: 10.1038/s41551-017-0181-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 11/27/2017] [Indexed: 01/07/2023]
Abstract
Chemoprevention-the use of medication to prevent cancer-can be augmented by the consumption of produce enriched with natural metabolites. However, chemopreventive metabolites are typically inactive and have low bioavailability and poor host absorption. Here, we show that engineered commensal microbes can prevent carcinogenesis and promote the regression of colorectal cancer through a cruciferous vegetable diet. The engineered commensal Escherichia coli bound specifically to the heparan sulphate proteoglycan on colorectal cancer cells and secreted the enzyme myrosinase to transform host-ingested glucosinolates-natural components of cruciferous vegetables-to sulphoraphane, an organic small molecule with known anticancer activity. The engineered microbes coupled with glucosinolates resulted in >95% proliferation inhibition of murine, human and colorectal adenocarcinoma cell lines in vitro. We also show that murine models of colorectal carcinoma fed with the engineered microbes and the cruciferous vegetable diet displayed significant tumour regression and reduced tumour occurrence.
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Affiliation(s)
- Chun Loong Ho
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hui Qing Tan
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore, Singapore
| | - Koon Jiew Chua
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Aram Kang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Khoon Lin Ling
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore, Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jean Paul Thiery
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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76
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Pham HL, Ho CL, Wong A, Lee YS, Chang MW. Applying the design-build-test paradigm in microbiome engineering. Curr Opin Biotechnol 2017; 48:85-93. [DOI: 10.1016/j.copbio.2017.03.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/11/2022]
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77
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McKay R, Hauk P, Wu HC, Pottash AE, Shang W, Terrell J, Payne GF, Bentley WE. Controlling localization of Escherichia coli populations using a two-part synthetic motility circuit: An accelerator and brake. Biotechnol Bioeng 2017; 114:2883-2895. [PMID: 28755474 DOI: 10.1002/bit.26391] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/21/2017] [Accepted: 07/23/2017] [Indexed: 12/30/2022]
Abstract
Probiotics, whether taken as capsules or consumed in foods, have been regarded as safe for human use by regulatory agencies. Being living cells, they serve as "tunable" factories for the synthesis of a vast array of beneficial molecules. The idea of reprogramming probiotics to act as controllable factories, producing potential therapeutic molecules under user-specified conditions, represents a new and powerful concept in drug synthesis and delivery. Probiotics that serve as drug delivery vehicles pose several challenges, one being targeting (as seen with nanoparticle approaches). Here, we employ synthetic biology to control swimming directionality in a process referred to as "pseudotaxis." Escherichia coli, absent the motility regulator cheZ, swim sporadically, missing the traditional "run" in the run:tumble swimming paradigm. Upon introduction of cheZ in trans and its signal-generated upregulation, engineered bacteria can be "programmed" to swim toward the source of the chemical cue. Here, engineered cells that encounter sufficient levels of the small signal molecule pyocyanin, produce an engineered CheZ and swim with programmed directionality. By incorporating a degradation tag at the C-terminus of CheZ, the cells stop running when they exit spaces containing pyocyanin. That is, the engineered CheZ modified with a C-terminal extension derived from the putative DNA-binding transcriptional regulator YbaQ (RREERAAKKVA) is consumed by the ClpXP protease machine at a rate sufficient to "brake" the cells when pyocyanin levels are too low. Through this process, we demonstrate that over time, these engineered E. coli accumulate in pyocyanin-rich locales. We suggest that such approaches may find utility in engineering probiotics so that their beneficial functions can be focused in areas of principal benefit.
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Affiliation(s)
- Ryan McKay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - Alex Eli Pottash
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Wu Shang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | | | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
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78
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Higashikuni Y, Chen WC, Lu TK. Advancing therapeutic applications of synthetic gene circuits. Curr Opin Biotechnol 2017; 47:133-141. [PMID: 28750201 DOI: 10.1016/j.copbio.2017.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023]
Abstract
Synthetic biology aims to introduce new sense-and-respond capabilities into living cells, which would enable novel therapeutic strategies. The development of regulatory elements, molecular computing devices, and effector screening technologies has enabled researchers to design synthetic gene circuits in many organisms, including mammalian cells. Engineered gene networks, such as closed-loop circuits or Boolean logic gate circuits, can be used to program cells to perform specific functions with spatiotemporal control and restoration of homeostasis in response to the extracellular environment and intracellular signaling. In addition, genetically modified microbes can be designed as local delivery of therapeutic molecules. In this review, we will discuss recent advances in therapeutic applications of synthetic gene circuits, as well as challenges and future opportunities for biomedicine.
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Affiliation(s)
- Yasutomi Higashikuni
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA
| | - William Cw Chen
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA.
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79
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Álvarez B, Fernández LÁ. Sustainable therapies by engineered bacteria. Microb Biotechnol 2017; 10:1057-1061. [PMID: 28696008 PMCID: PMC5609241 DOI: 10.1111/1751-7915.12778] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
The controlled in situ delivery of biologics (e.g. enzymes, cytokines, antibodies) by engineered bacteria of our microbiome will allow the sustainable production of these complex and expensive drugs locally in the human body, overcoming many of the technical and economical barriers currently associated with the global use of these potent medicines. We provide examples showing how engineered bacteria can be effective treatments against multiple pathologies, including autoimmune and inflammatory diseases, metabolic disorders, diabetes, obesity, infectious diseases and cancer, hence contributing to achieve the Global Sustainable Goal 3: ensure healthy lives and promote well‐being for all at all ages.
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Affiliation(s)
- Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus UAM Cantoblanco, 28049, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus UAM Cantoblanco, 28049, Madrid, Spain
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80
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Natarajan A, Haitjema CH, Lee R, Boock JT, DeLisa MP. An Engineered Survival-Selection Assay for Extracellular Protein Expression Uncovers Hypersecretory Phenotypes in Escherichia coli. ACS Synth Biol 2017; 6:875-883. [PMID: 28182400 DOI: 10.1021/acssynbio.6b00366] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The extracellular expression of recombinant proteins using laboratory strains of Escherichia coli is now routinely achieved using naturally secreted substrates, such as YebF or the osmotically inducible protein Y (OsmY), as carrier molecules. However, secretion efficiency through these pathways needs to be improved for most synthetic biology and metabolic engineering applications. To address this challenge, we developed a generalizable survival-based selection strategy that effectively couples extracellular protein secretion to antibiotic resistance and enables facile isolation of rare mutants from very large populations (i.e., 1010-12 clones) based simply on cell growth. Using this strategy in the context of the YebF pathway, a comprehensive library of E. coli single-gene knockout mutants was screened and several gain-of-function mutations were isolated that increased the efficiency of extracellular expression without compromising the integrity of the outer membrane. We anticipate that this user-friendly strategy could be leveraged to better understand the YebF pathway and other secretory mechanisms-enabling the exploration of protein secretion in pathogenesis as well as the creation of designer E. coli strains with greatly expanded secretomes-all without the need for expensive exogenous reagents, assay instruments, or robotic automation.
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Affiliation(s)
- Aravind Natarajan
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Charles H. Haitjema
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Robert Lee
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jason T. Boock
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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81
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Wang H, Ling MH, Chua TK, Poh CL. Two cellular resource‐based models linking growth and parts characteristics aids the study and optimisation of synthetic gene circuits. ENGINEERING BIOLOGY 2017. [DOI: 10.1049/enb.2017.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Huijuan Wang
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Maurice H.T. Ling
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Tze Kwang Chua
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
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82
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Chua KJ, Kwok WC, Aggarwal N, Sun T, Chang MW. Designer probiotics for the prevention and treatment of human diseases. Curr Opin Chem Biol 2017; 40:8-16. [PMID: 28478369 DOI: 10.1016/j.cbpa.2017.04.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/04/2017] [Accepted: 04/13/2017] [Indexed: 12/24/2022]
Abstract
Various studies have shown the beneficial effects of probiotics in humans. The use of synthetic biology to engineer programmable probiotics that specifically targets cancer, infectious agents, or other metabolic diseases has gained much interest since the last decade. Developments made in synthetic probiotics as therapeutics within the last three years will be discussed in this review.
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Affiliation(s)
- Koon Jiew Chua
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Wee Chiew Kwok
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Nikhil Aggarwal
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Tao Sun
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore.
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83
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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84
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- 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.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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85
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Li J, Liu Y, Kim E, March JC, Bentley WE, Payne GF. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology. Free Radic Biol Med 2017; 105:110-131. [PMID: 28040473 DOI: 10.1016/j.freeradbiomed.2016.12.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/06/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022]
Abstract
The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H2O2) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this electrochemical tool for in vitro redox-probing.
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Affiliation(s)
- Jinyang Li
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Yi Liu
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Eunkyoung Kim
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - John C March
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA.
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86
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Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles. mBio 2017; 8:mBio.02312-16. [PMID: 28223461 PMCID: PMC5358918 DOI: 10.1128/mbio.02312-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1. We identified a conserved sequence motif targeted by an adenine methyltransferase of a type I R-M system and quantified the presence of N6-methyladenine using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Changes in the PAO1 methylation status were dependent on growth conditions and affected P. aeruginosa pathogenicity in a Galleria mellonella infection model. Furthermore, we found that methylated motifs in promoter regions led to shifts in sense and antisense gene expression, emphasizing the role of enzymatic DNA methylation as an epigenetic control of phenotypic traits in P. aeruginosa. Since the DNA methylation enzymes are not encoded in the core genome, our findings illustrate how the acquisition of accessory genes can shape the global P. aeruginosa transcriptome and thus may facilitate adaptation to new and challenging habitats. With the introduction of advanced technologies, epigenetic regulation by DNA methyltransferases in bacteria has become a subject of intense studies. Here we identified an adenosine DNA methyltransferase in the opportunistic pathogen Pseudomonas aeruginosa PAO1, which is responsible for DNA methylation of a conserved sequence motif. The methylation level of all target sequences throughout the PAO1 genome was approximated to be in the range of 65 to 85% and was dependent on growth conditions. Inactivation of the methyltransferase revealed an attenuated-virulence phenotype in the Galleria mellonella infection model. Furthermore, differential expression of more than 90 genes was detected, including the small regulatory RNA prrF1, which contributes to a global iron-sparing response via the repression of a set of gene targets. Our finding of a methylation-dependent repression of the antisense transcript of the prrF1 small regulatory RNA significantly expands our understanding of the regulatory mechanisms underlying active DNA methylation in bacteria.
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87
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Foo JL, Ling H, Lee YS, Chang MW. Microbiome engineering: Current applications and its future. Biotechnol J 2017; 12. [PMID: 28133942 DOI: 10.1002/biot.201600099] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 01/07/2023]
Abstract
Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
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88
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Sola-Oladokun B, Culligan EP, Sleator RD. Engineered Probiotics: Applications and Biological Containment. Annu Rev Food Sci Technol 2017; 8:353-370. [PMID: 28125354 DOI: 10.1146/annurev-food-030216-030256] [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] [Indexed: 11/09/2022]
Abstract
Bioengineered probiotics represent the next generation of whole cell-mediated biotherapeutics. Advances in synthetic biology, genome engineering, and DNA sequencing and synthesis have enabled scientists to design and develop probiotics with increased stress tolerance and the ability to target specific pathogens and their associated toxins, as well as to mediate targeted delivery of vaccines, drugs, and immunomodulators directly to host cells. Herein, we review the most significant advances in the development of this field. We discuss the critical issue of biological containment and consider the role of synthetic biology in the design and construction of the probiotics of the future.
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Affiliation(s)
- Babasola Sola-Oladokun
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , ,
| | - Eamonn P Culligan
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , ,
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , , .,APC Microbiome Institute, University College Cork, Cork, Ireland
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89
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Pottash AE, McKay R, Virgile CR, Ueda H, Bentley WE. TumbleScore: Run and tumble analysis for low frame-rate motility videos. Biotechniques 2017; 62:31-36. [PMID: 28118813 DOI: 10.2144/000114493] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/05/2016] [Indexed: 11/23/2022] Open
Abstract
Scientists often exploit the motility of peritrichously flagellated bacteria for various applications. A common alteration is modifying the frequency of mid-movement changes in direction, known as tumbles. Such differences in bacterial swimming patterns can prove difficult to quantify, especially for those without access to high-speed optical equipment. Traditionally, scientists have resorted to less accurate techniques, such as soft agar plate assays, or have been forced to invest in costly equipment. Here, we present TumbleScore, software designed to track and quantify bacterial movies with slow, as well as fast, frame-rates. Developed and fully contained within MATLAB, TumbleScore processes motility videos and returns pertinent tumbling metrics, including: (i) linear speed, (ii) rotational speed, (iii) percentage of angle changes below a given threshold, and (iv) ratio of total path length to Euclidian distance, or arc-chord ratio (ACR). In addition, TumbleScore produces a "rose graph" visualization of bacterial paths. The software was validated using both fabricated and experimental motility videos.
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Affiliation(s)
- Alex Eli Pottash
- Fischell Department of Bioengineering.,Institute for Bioscience and Biotechnology Research
| | - Ryan McKay
- Fischell Department of Bioengineering.,Institute for Bioscience and Biotechnology Research
| | - Chelsea R Virgile
- Fischell Department of Bioengineering.,Institute for Bioscience and Biotechnology Research
| | - Hana Ueda
- Institute for Bioscience and Biotechnology Research.,Department of Mathematics, University of Maryland, College Park, MD
| | - William E Bentley
- Fischell Department of Bioengineering.,Institute for Bioscience and Biotechnology Research
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90
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Moon S, Fritz IL, Singer ZS, Danino T. Spatial Control of Bacteria Using Screen Printing. 3D PRINTING AND ADDITIVE MANUFACTURING 2016; 3:194-203. [PMID: 29577061 PMCID: PMC5363221 DOI: 10.1089/3dp.2016.0040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Synthetic biology has led to advances in both our understanding and engineering of genetic circuits that affect spatial and temporal behaviors in living cells. A growing array of native and synthetic circuits such as oscillators, pattern generators, and cell-cell communication systems has been studied, which exhibit spatiotemporal properties. To better understand the design principles of these genetic circuits, there is a need for versatile and precise methods for patterning cell populations in various configurations. In this study, we develop a screen printing methodology to pattern bacteria on agar, glass, and paper surfaces. Initially, we tested three biocompatible resuspension media with appropriate rheological properties for screen printing. Using microscopy, we characterized the resolution and bleed of bacteria screen prints on agar and glass surfaces, obtaining resolutions as low as 188 μm. Next, we engineered bacterial strains producing visible chromoproteins analogous to the cyan, magenta, and yellow subtractive color system for the creation of multicolored bacteria images. Using this system, we printed distinct populations in overlapping or interlocking designs on both paper and agar substrates. These proof-of-principle experiments demonstrated how the screen printing method could be used to study microbial community interactions and pattern formation of biofilms at submillimeter length scales. Overall, our approach allows for rapid and precise prototyping of patterned bacteria species that will be useful in the understanding and engineering of spatiotemporal behaviors in microbial communities.
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Affiliation(s)
- Soonhee Moon
- Department of Biomedical Engineering, Columbia University, New York, New York
| | - Ian L. Fritz
- Department of Biomedical Engineering, Columbia University, New York, New York
| | - Zakary S. Singer
- Department of Biomedical Engineering, Columbia University, New York, New York
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, New York
- Data Science Institute, Columbia University, New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
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91
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Sun J, Alper H. Synthetic Biology: An Emerging Approach for Strain Engineering. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Jie Sun
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
| | - Hal Alper
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
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92
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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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93
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Hauk P, Stephens K, Mckay R, Virgile CR, Ueda H, Ostermeier M, Ryu KS, Sintim HO, Bentley WE. Insightful directed evolution of Escherichia coli quorum sensing promoter region of the lsrACDBFG operon: a tool for synthetic biology systems and protein expression. Nucleic Acids Res 2016; 44:10515-10525. [PMID: 27915294 PMCID: PMC5137460 DOI: 10.1093/nar/gkw981] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 01/17/2023] Open
Abstract
Quorum sensing (QS) regulates many natural phenotypes (e.q. virulence, biofilm formation, antibiotic resistance), and its components, when incorporated into synthetic genetic circuits, enable user-directed phenotypes. We created a library of Escherichia coli lsr operon promoters using error-prone PCR (ePCR) and selected for promoters that provided E. coli with higher tetracycline resistance over the native promoter when placed upstream of the tet(C) gene. Among the fourteen clones identified, we found several mutations in the binding sites of QS repressor, LsrR. Using site-directed mutagenesis we restored all p-lsrR-box sites to the native sequence in order to maintain LsrR repression of the promoter, preserving the other mutations for analysis. Two promoter variants, EP01rec and EP14rec, were discovered exhibiting enhanced protein expression. In turn, these variants retained their ability to exhibit the LsrR-mediated QS switching activity. Their sequences suggest regulatory linkage between CytR (CRP repressor) and LsrR. These promoters improve upon the native system and exhibit advantages over synthetic QS promoters previously reported. Incorporation of these promoters will facilitate future applications of QS-regulation in synthetic biology and metabolic engineering.
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Affiliation(s)
- Pricila Hauk
- Institute for Bioscience and Biotechnology Research, College Park, MD, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Kristina Stephens
- Institute for Bioscience and Biotechnology Research, College Park, MD, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Ryan Mckay
- Institute for Bioscience and Biotechnology Research, College Park, MD, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Chelsea Ryan Virgile
- Institute for Bioscience and Biotechnology Research, College Park, MD, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Hana Ueda
- Department of Mathematics, University of Maryland, College Park, MD 20742, USA
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Kyoung-Seok Ryu
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudangi-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 363-883, South Korea
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research, College Park, MD, USA .,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
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94
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Advances in the Microbiome: Applications to Clostridium difficile Infection. J Clin Med 2016; 5:jcm5090083. [PMID: 27657145 PMCID: PMC5039486 DOI: 10.3390/jcm5090083] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/14/2022] Open
Abstract
Clostridium difficile is a major cause of morbidity and mortality worldwide, causing over 400,000 infections and approximately 29,000 deaths in the United States alone each year. C. difficile is the most common cause of nosocomial diarrhoea in the developed world, and, in recent years, the emergence of hyper-virulent (mainly ribotypes 027 and 078, sometimes characterised by increased toxin production), epidemic strains and an increase in the number of community-acquired infections has caused further concern. Antibiotic therapy with metronidazole, vancomycin or fidaxomicin is the primary treatment for C. difficile infection (CDI). However, CDI is unique, in that, antibiotic use is also a major risk factor for acquiring CDI or recurrent CDI due to disruption of the normal gut microbiota. Therefore, there is an urgent need for alternative, non-antibiotic therapeutics to treat or prevent CDI. Here, we review a number of such potential treatments which have emerged from advances in the field of microbiome research.
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95
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Hwang IY, Koh E, Kim HR, Yew WS, Chang MW. Reprogrammable microbial cell-based therapeutics against antibiotic-resistant bacteria. Drug Resist Updat 2016; 27:59-71. [DOI: 10.1016/j.drup.2016.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 01/01/2023]
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96
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Jia X, Liu C, Song H, Ding M, Du J, Ma Q, Yuan Y. Design, analysis and application of synthetic microbial consortia. Synth Syst Biotechnol 2016; 1:109-117. [PMID: 29062933 PMCID: PMC5640696 DOI: 10.1016/j.synbio.2016.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 01/28/2016] [Accepted: 02/12/2016] [Indexed: 12/17/2022] Open
Abstract
The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.
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Affiliation(s)
- Xiaoqiang Jia
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Chang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Jin Du
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Qian Ma
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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97
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Tien SM, Hsu CY, Chen BS. Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method. PLoS One 2016; 11:e0152146. [PMID: 27096615 PMCID: PMC4838244 DOI: 10.1371/journal.pone.0152146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/09/2016] [Indexed: 11/18/2022] Open
Abstract
Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella’s rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the “brake component” in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each “brake component” were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the “brake component”. Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate “brake component” in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.
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Affiliation(s)
- Shin-Ming Tien
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Yuan Hsu
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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98
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Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med 2016; 8:39. [PMID: 27074706 PMCID: PMC4831151 DOI: 10.1186/s13073-016-0294-z] [Citation(s) in RCA: 528] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.
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Affiliation(s)
- Amy Langdon
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA
- Clinical Research Training Center, Washington University School of Medicine, Campus Box 8051, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA
| | - Nathan Crook
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA
- Department of Pathology & Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Ave, St. Louis, MO, 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Ave, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in Saint Louis, Campus Box 1097, 1 Brookings Drive, Saint Louis, MO, 63130, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.
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99
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Woloszynek S, Pastor S, Mell JC, Nandi N, Sokhansanj B, Rosen GL. Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:67-124. [PMID: 27017007 DOI: 10.1016/bs.ircmb.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.
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Affiliation(s)
- S Woloszynek
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America
| | - S Pastor
- Department of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - J C Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - N Nandi
- Division of Gastroenterology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - B Sokhansanj
- McKool Smith Hennigan, P. C., Redwood Shores, CA, United States of America
| | - G L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America.
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100
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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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