1
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Song J, Zhuang M, Fang Y, Hu X, Wang X. Self-regulated efficient production of L-threonine via an artificial quorum sensing system in engineered Escherichia coli. Microbiol Res 2024; 284:127720. [PMID: 38640767 DOI: 10.1016/j.micres.2024.127720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Imbalance in carbon flux distribution is one of the most important factors affecting the further increase in the yield of high value-added natural products in microbial metabolic engineering. Meanwhile, the most common inducible expression systems are difficult to achieve industrial-scale production due to the addition of high-cost or toxic inducers during the fermentation process. Quorum sensing system, as a typical model for density-dependent induction of gene expression, has been widely applied in synthetic biology. However, there are currently few reports for efficient production of microbial natural products by using quorum sensing system to self-regulate carbon flux distribution. Here, we designed an artificial quorum sensing system to achieve efficient production of L-threonine in engineered Escherichia coli by altering the carbon flux distribution of the central metabolic pathways at specific periods. Under the combination of switch module and production module, the system was applied to divide the microbial fermentation process into two stages including growth and production, and improve the production of L-threonine by self-inducing the expression of pyruvate carboxylase and threonine extracellular transporter protease after a sufficient amount of cell growth. The final strain TWF106/pST1011, pST1042pr could produce 118.2 g/L L-threonine with a yield of 0.57 g/g glucose and a productivity of 2.46 g/(L· h). The establishment of this system has important guidance and application value for the production of other high value-added chemicals in microorganisms by self-regulation.
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Affiliation(s)
- Jie Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Miaomiao Zhuang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yu Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoqing Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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2
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Nguyen DH, Chong A, Hong Y, Min JJ. Bioengineering of bacteria for cancer immunotherapy. Nat Commun 2023; 14:3553. [PMID: 37322031 PMCID: PMC10272223 DOI: 10.1038/s41467-023-39224-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Affiliation(s)
- Dinh-Huy Nguyen
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, Gwangju, 61469, Republic of Korea
- Department of Molecular Medicine (BrainKorea21 Plus), Chonnam National University Graduate School, Gwangju, 61469, Republic of Korea
| | - Ari Chong
- Department of Nuclear Medicine, Chosun University Medical School and Hospital, Gwangju, 61452, Republic of Korea
| | - Yeongjin Hong
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, Gwangju, 61469, Republic of Korea.
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61469, Republic of Korea.
| | - Jung-Joon Min
- Institute for Molecular Imaging and Theranostics, Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, Gwangju, 61469, Republic of Korea.
- Department of Molecular Medicine (BrainKorea21 Plus), Chonnam National University Graduate School, Gwangju, 61469, Republic of Korea.
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3
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Dang Z, Gao M, Wang L, Wu J, Guo Y, Zhu Z, Huang H, Kang G. Synthetic bacterial therapies for intestinal diseases based on quorum- sensing circuits. Biotechnol Adv 2023; 65:108142. [PMID: 36977440 DOI: 10.1016/j.biotechadv.2023.108142] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/28/2023]
Abstract
Bacterial therapy has become a key strategy against intestinal infectious diseases in recent years. Moreover, regulating the gut microbiota through traditional fecal microbiota transplantation and supplementation of probiotics faces controllability, efficacy, and safety challenges. The infiltration and emergence of synthetic biology and microbiome provide an operational and safe treatment platform for live bacterial biotherapies. Synthetic bacterial therapy can artificially manipulate bacteria to produce and deliver therapeutic drug molecules. This method has the advantages of solid controllability, low toxicity, strong therapeutic effects, and easy operation. As an essential tool for dynamic regulation in synthetic biology, quorum sensing (QS) has been widely used for designing complex genetic circuits to control the behavior of bacterial populations and achieve predefined goals. Therefore, QS-based synthetic bacterial therapy might become a new direction for the treatment of diseases. The pre-programmed QS genetic circuit can achieve a controllable production of therapeutic drugs on particular ecological niches by sensing specific signals released from the digestive system in pathological conditions, thereby realizing the integration of diagnosis and treatment. Based on this as well as the modular idea of synthetic biology, QS-based synthetic bacterial therapies are divided into an environmental signal sensing module (senses gut disease physiological signals), a therapeutic molecule producing module (plays a therapeutic role against diseases), and a population behavior regulating module (QS system). This review article summarized the structure and function of these three modules and discussed the rational design of QS gene circuits as a novel intervention strategy for intestinal diseases. Moreover, the application prospects of QS-based synthetic bacterial therapy were summarized. Finally, the challenges faced by these methods were analyzed to make the targeted recommendations for developing a successful therapeutic strategy for intestinal diseases.
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4
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Stephens K, Bentley WE. Quorum Sensing from Two Engineers’ Perspectives. Isr J Chem 2023. [DOI: 10.1002/ijch.202200083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kristina Stephens
- Thayer School of Engineering Dartmouth College Hanover NH USA
- Center for Bioenergy Innovation Oak Ridge National Laboratory Oak Ridge TN 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 [e]Robert E. Fischell Institute for Biomedical Devices University of Maryland College Park MD USA
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5
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Chee WKD, Yeoh JW, Dao VL, Poh CL. Thermogenetics: Applications come of age. Biotechnol Adv 2022; 55:107907. [PMID: 35041863 DOI: 10.1016/j.biotechadv.2022.107907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.
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Affiliation(s)
- Wai Kit David Chee
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Viet Linh Dao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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6
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Tas H, Grozinger L, Stoof R, de Lorenzo V, Goñi-Moreno Á. Contextual dependencies expand the re-usability of genetic inverters. Nat Commun 2021; 12:355. [PMID: 33441561 PMCID: PMC7806840 DOI: 10.1038/s41467-020-20656-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
The implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, the context in which the circuit performs is crucial for its outcome. We characterise 20 genetic NOT logic gates in up to 7 bacterial-based contexts each, to generate 135 different functions. The contexts we focus on are combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each gate shows seven different dynamic behaviours, depending on the context. That is, gates can be fine-tuned by changing only contextual parameters, thus improving the compatibility between gates. Finally, we analyse portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expands functionality, and advocate for considering context as a fundamental design parameter.
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Affiliation(s)
- Huseyin Tas
- grid.428469.50000 0004 1794 1018Systems Biology Department, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
| | - Lewis Grozinger
- grid.1006.70000 0001 0462 7212School of Computing, Newcastle University, Newcastle Upon Tyne, NE4 5TG UK
| | - Ruud Stoof
- grid.1006.70000 0001 0462 7212School of Computing, Newcastle University, Newcastle Upon Tyne, NE4 5TG UK
| | - Victor de Lorenzo
- grid.428469.50000 0004 1794 1018Systems Biology Department, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
| | - Ángel Goñi-Moreno
- grid.1006.70000 0001 0462 7212School of Computing, Newcastle University, Newcastle Upon Tyne, NE4 5TG UK ,grid.419190.40000 0001 2300 669XCentro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politénica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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7
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Sohn YJ, Kim HT, Jo SY, Song HM, Baritugo KA, Pyo J, Choi JI, Joo JC, Park SJ. Recent Advances in Systems Metabolic Engineering Strategies for the Production of Biopolymers. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0508-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Hauk P, Stephens K, Virgile C, VanArsdale E, Pottash AE, Schardt JS, Jay SM, Sintim HO, Bentley WE. Homologous Quorum Sensing Regulatory Circuit: A Dual-Input Genetic Controller for Modulating Quorum Sensing-Mediated Protein Expression in E. coli. ACS Synth Biol 2020; 9:2692-2702. [PMID: 32822530 DOI: 10.1021/acssynbio.0c00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We developed a hybrid synthetic circuit that co-opts the genetic regulation of the native bacterial quorum sensing autoinducer-2 and imposes an extra external controller for maintaining tightly controlled gene expression. This dual-input genetic controller was mathematically modeled and, by design, can be operated in three modes: a constitutive mode that enables consistent and high levels of expression; a tightly repressed mode in which there is very little background expression; and an inducible mode in which concentrations of two signals (arabinose and autoinducer-2) determine the net amplification of the gene(s)-of-interest. We demonstrate the utility of the circuit for the controlled expression of human granulocyte macrophage colony stimulating factor in an engineered probiotic E. coli. This dual-input genetic controller is the first homologous AI-2 quorum sensing circuit that has the ability to be operated in three different modes. We believe it has the potential for wide-ranging biotechnological applications due its versatile features.
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Affiliation(s)
- Pricila Hauk
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Kristina Stephens
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Eric VanArsdale
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Alex Eli Pottash
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - John S. Schardt
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Steven M. Jay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Herman O. Sintim
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
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9
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Stephens K, Bentley WE. Synthetic Biology for Manipulating Quorum Sensing in Microbial Consortia. Trends Microbiol 2020; 28:633-643. [DOI: 10.1016/j.tim.2020.03.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022]
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10
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Wu S, Liu J, Liu C, Yang A, Qiao J. Quorum sensing for population-level control of bacteria and potential therapeutic applications. Cell Mol Life Sci 2020; 77:1319-1343. [PMID: 31612240 PMCID: PMC11104945 DOI: 10.1007/s00018-019-03326-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/13/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023]
Abstract
Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China.
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11
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Charlton SGV, White MA, Jana S, Eland LE, Jayathilake PG, Burgess JG, Chen J, Wipat A, Curtis TP. Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms. J Bacteriol 2019; 201:e00101-19. [PMID: 31182499 PMCID: PMC6707926 DOI: 10.1128/jb.00101-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover.
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Affiliation(s)
- Samuel G V Charlton
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael A White
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Saikat Jana
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - J Grant Burgess
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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12
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Brown SP, Blackwell HE, Hammer BK. The State of the Union Is Strong: a Review of ASM's 6th Conference on Cell-Cell Communication in Bacteria. J Bacteriol 2018; 200:e00291-18. [PMID: 29760210 PMCID: PMC6018360 DOI: 10.1128/jb.00291-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 6th American Society for Microbiology Conference on Cell-Cell Communication in Bacteria convened from 16 to 19 October 2017 in Athens, GA. In this minireview, we highlight some of the research presented at that meeting that addresses central questions emerging in the field, including the following questions. How are cell-cell communication circuits designed to generate responses? Where are bacteria communicating? Finally, why are bacteria engaging in such behaviors?
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Affiliation(s)
- Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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13
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Transcriptional control of motility enables directional movement of Escherichia coli in a signal gradient. Sci Rep 2017; 7:8959. [PMID: 28827562 PMCID: PMC5566481 DOI: 10.1038/s41598-017-08870-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/18/2017] [Indexed: 11/08/2022] Open
Abstract
Manipulation of cellular motility using a target signal can facilitate the development of biosensors or microbe-powered biorobots. Here, we engineered signal-dependent motility in Escherichia coli via the transcriptional control of a key motility gene. Without manipulating chemotaxis, signal-dependent switching of motility, either on or off, led to population-level directional movement of cells up or down a signal gradient. We developed a mathematical model that captures the behaviour of the cells, enables identification of key parameters controlling system behaviour, and facilitates predictive-design of motility-based pattern formation. We demonstrated that motility of the receiver strains could be controlled by a sender strain generating a signal gradient. The modular quorum sensing-dependent architecture for interfacing different senders with receivers enabled a broad range of systems-level behaviours. The directional control of motility, especially combined with the potential to incorporate tuneable sensors and more complex sensing-logic, may lead to tools for novel biosensing and targeted-delivery applications.
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14
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He X, Chen Y, Liang Q, Qi Q. Autoinduced AND Gate Controls Metabolic Pathway Dynamically in Response to Microbial Communities and Cell Physiological State. ACS Synth Biol 2017; 6:463-470. [PMID: 27997131 DOI: 10.1021/acssynbio.6b00177] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Quorum sensing (QS) systems have been widely applied in biotechnology and synthetic biology that require coordinated, community-level behaviors. Meanwhile, the cell physiological state is another key parameter that affects metabolic pathway regulation. Here, we designed an autoinduced AND gate that responds to both microbial communities and the cell physiological state. A series of tunable QS systems in response to different cell densities were obtained through random mutagenesis of LuxR and optimization of the luxRI promoter; the corresponding suitable stationary phase sensing system was selected after monitoring the fluorescence process during cell growth. The application of the final synthetic device was demonstrated using the polyhydroxybutyrate (PHB) production system. The AND gate system increased PHB production by 1-2-fold in Escherichia coli. This synthetic logic gate is a tool for developing a general dynamic regulation system in metabolic engineering in response to complex signals, without using a specific sensor.
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Affiliation(s)
- Xinyuan He
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
| | - Yan Chen
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
| | - Quanfeng Liang
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
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15
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Marchand N, Collins CH. Synthetic Quorum Sensing and Cell-Cell Communication in Gram-Positive Bacillus megaterium. ACS Synth Biol 2016. [PMID: 26203497 DOI: 10.1021/acssynbio.5b00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The components of natural quorum-sensing (QS) systems can be used to engineer synthetic communication systems that regulate gene expression in response to chemical signals. We have used the machinery from the peptide-based agr QS system from Staphylococcus aureus to engineer a synthetic QS system in Bacillus megaterium to enable autoinduction of a target gene at high cell densities. Growth and gene expression from these synthetic QS cells were characterized in both complex and minimal media. We also split the signal production and sensing components between two strains of B. megaterium to produce sender and receiver cells and characterized the resulting communication in liquid media and on semisolid agar. The system described in this work represents the first synthetic QS and cell-cell communication system that has been engineered to function in a Gram-positive host, and it has the potential to enable the generation of dynamic gene regulatory networks in B. megaterium and other Gram-positive organisms.
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Affiliation(s)
- Nicholas Marchand
- Department of Chemical and Biological Engineering, ‡Center for Biotechnology
and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Cynthia H. Collins
- Department of Chemical and Biological Engineering, ‡Center for Biotechnology
and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
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16
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Terrell JL, Wu HC, Tsao CY, Barber NB, Servinsky MD, Payne GF, Bentley WE. Nano-guided cell networks as conveyors of molecular communication. Nat Commun 2015; 6:8500. [PMID: 26455828 PMCID: PMC4633717 DOI: 10.1038/ncomms9500] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 08/28/2015] [Indexed: 01/06/2023] Open
Abstract
Advances in nanotechnology have provided unprecedented physical means to sample molecular space. Living cells provide additional capability in that they identify molecules within complex environments and actuate function. We have merged cells with nanotechnology for an integrated molecular processing network. Here we show that an engineered cell consortium autonomously generates feedback to chemical cues. Moreover, abiotic components are readily assembled onto cells, enabling amplified and 'binned' responses. Specifically, engineered cell populations are triggered by a quorum sensing (QS) signal molecule, autoinducer-2, to express surface-displayed fusions consisting of a fluorescent marker and an affinity peptide. The latter provides means for attaching magnetic nanoparticles to fluorescently activated subpopulations for coalescence into colour-indexed output. The resultant nano-guided cell network assesses QS activity and conveys molecular information as a 'bio-litmus' in a manner read by simple optical means.
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Affiliation(s)
- Jessica L Terrell
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Hsuan-Chen Wu
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Chen-Yu Tsao
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - Nathan B Barber
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA
| | - Matthew D Servinsky
- U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20783, USA
| | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, 2330 Jeong H. Kim Engineering Building, College Park, Maryland 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA
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Artificial cell-cell communication as an emerging tool in synthetic biology applications. J Biol Eng 2015; 9:13. [PMID: 26265937 PMCID: PMC4531478 DOI: 10.1186/s13036-015-0011-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/25/2015] [Indexed: 01/14/2023] Open
Abstract
Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication modes offer the possibility to control the behavior of an entire community by modifying the performance of individual cells in specific ways. Synthetic biology, i.e., the implementation of artificial functions within biological systems, is a promising approach towards the engineering of sophisticated, autonomous devices based on specifically functionalized cells. With the growing complexity of the functions performed by such systems, both the risk of circuit crosstalk and the metabolic burden resulting from the expression of numerous foreign genes are increasing. Therefore, systems based on a single type of cells are no longer feasible. Synthetic biology approaches with multiple subpopulations of specifically functionalized cells, wired by artificial cell-cell communication systems, provide an attractive and powerful alternative. Here we review recent applications of synthetic cell-cell communication systems with a specific focus on recent advances with fungal hosts.
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Soma Y, Hanai T. Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production. Metab Eng 2015; 30:7-15. [DOI: 10.1016/j.ymben.2015.04.005] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 11/30/2022]
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19
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Synthetic biology expands chemical control of microorganisms. Curr Opin Chem Biol 2015; 28:20-8. [PMID: 26056951 DOI: 10.1016/j.cbpa.2015.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/30/2015] [Accepted: 05/15/2015] [Indexed: 01/21/2023]
Abstract
The tools of synthetic biology allow researchers to change the ways engineered organisms respond to chemical stimuli. Decades of basic biology research and new efforts in computational protein and RNA design have led to the development of small molecule sensors that can be used to alter organism function. These new functions leap beyond the natural propensities of the engineered organisms. They can range from simple fluorescence or growth reporting to pathogen killing, and can involve metabolic coordination among multiple cells or organisms. Herein, we discuss how synthetic biology alters microorganisms' responses to chemical stimuli resulting in the development of microbes as toxicity sensors, disease treatments, and chemical factories.
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Zucca S, Pasotti L, Politi N, Casanova M, Mazzini G, Cusella De Angelis MG, Magni P. Multi-Faceted Characterization of a Novel LuxR-Repressible Promoter Library for Escherichia coli. PLoS One 2015; 10:e0126264. [PMID: 26010244 PMCID: PMC4444344 DOI: 10.1371/journal.pone.0126264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
The genetic elements regulating the natural quorum sensing (QS) networks of several microorganisms are widely used in synthetic biology to control the behaviour of single cells and engineered bacterial populations via ad-hoc constructed synthetic circuits. A number of novel engineering-inspired biological functions have been implemented and model systems have also been constructed to improve the knowledge on natural QS systems. Synthetic QS-based parts, such as promoters, have been reported in literature, to provide biological components with functions that are not present in nature, like modified induction logic or activation/repression by additional molecules. In this work, a library of promoters that can be repressed by the LuxR protein in presence of the QS autoinducer N-3-oxohexanoyl-L-homoserine lactone (AHL) was reported for Escherichia coli, to expand the toolkit of genetic parts that can be used to engineer novel synthetic QS-based systems. The library was constructed via polymerase chain reaction with highly constrained degenerate oligonucleotides, designed according to the consensus -35 and -10 sequences of a previously reported constitutive promoter library of graded strength, to maximize the probability of obtaining functional clones. All the promoters have a lux box between the -35 and -10 regions, to implement a LuxR-repressible behaviour. Twelve unique library members of graded strength (about 100-fold activity range) were selected to form the final library and they were characterized in several genetic contexts, such as in different plasmids, via different reporter genes, in presence of a LuxR expression cassette in different positions and in response to different AHL concentrations. The new obtained regulatory parts and corresponding data can be exploited by synthetic biologists to implement an artificial AHL-dependent repression of transcription in genetic circuits. The target transcriptional activity can be selected among the available library members to meet the design specifications of the biological system.
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Affiliation(s)
- Susanna Zucca
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | - Lorenzo Pasotti
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | - Nicolò Politi
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | - Michela Casanova
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
| | | | | | - Paolo Magni
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università degli Studi di Pavia, Pavia, Italy
- Centro di Ingegneria Tissutale, Università degli Studi di Pavia, Pavia, Italy
- * E-mail:
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Liu H, Lu T. Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered Escherichia coli. Metab Eng 2015; 29:135-141. [DOI: 10.1016/j.ymben.2015.03.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
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22
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A yeast pheromone-based inter-species communication system. Appl Microbiol Biotechnol 2014; 99:1299-308. [PMID: 25331280 DOI: 10.1007/s00253-014-6133-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
We report on a pheromone-based inter-species communication system, allowing for a controlled cell-cell communication between the two species Saccharomyces cerevisiae and Schizosaccharomyces pombe as a proof of principle. It exploits the mating response pathways of the two yeast species employing the pheromones, α- or P-factor, as signaling molecules. The authentic and chimeric pheromone-encoding genes were engineered to code for the P-factor in S. cerevisiae and the α-factor in S. pombe. Upon transformation of the respective constructs, cells were enabled to express the mating pheromone of the opposite species. The supernatant of cultures of S. pombe cells expressing α-factor were able to induce a G1 arrest in the cell cycle, a change in morphology to the typical shmoo effect and expression driven by the pheromone-responsive FIG1 promoter in S. cerevisiae. The supernatant of cultures of S. cerevisiae cells expressing P-factor similarly induced cell cycle arrest in G1, an alteration in morphology typical for mating as well as the activation of the pheromone-responsive promoters of the rep1 and sxa2 genes in a pheromone-hypersensitive reporter strain of S. pombe. Apparently, both heterologous pheromones were correctly processed and secreted in an active form by the cells of the other species. Our data clearly show that the species-specific pheromone systems of yeast species can be exploited for a controlled inter-species communication.
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Woo HM, Park JB. Recent progress in development of synthetic biology platforms and metabolic engineering of Corynebacterium glutamicum. J Biotechnol 2014; 180:43-51. [DOI: 10.1016/j.jbiotec.2014.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/08/2014] [Accepted: 03/03/2014] [Indexed: 01/21/2023]
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