1
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Meng J, Liu S, Wu X. Engineered probiotics as live biotherapeutics for diagnosis and treatment of human diseases. Crit Rev Microbiol 2024; 50:300-314. [PMID: 36946080 DOI: 10.1080/1040841x.2023.2190392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 03/23/2023]
Abstract
The use of probiotics to regulate the intestinal microbiota to prevent and treat a large number of disorders and diseases has been an international research hotspot. Although conventional probiotics have a certain regulatory role in nutrient metabolism, inhibiting pathogens, inducing immune regulation, and maintaining intestinal epithelial barrier function, they are unable to treat certain diseases. In recent years, aided by the continuous development of synthetic biology, engineering probiotics with desired characteristics and functionalities to benefit human health has made significant progress. In this article, we summarise the mechanism of action of conventional probiotics and their limitations and highlight the latest developments in the design and construction of probiotics as living diagnostics and therapeutics for the detection and treatment of a series of diseases, including pathogen infections, cancer, intestinal inflammation, metabolic disorders, vaccine delivery, cognitive health, and fatty liver. Besides we discuss the concerns regarding engineered probiotics and corresponding countermeasures and outline the desired features in the future development of engineered live biotherapeutics.
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Affiliation(s)
- Jiao Meng
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
| | - Shufan Liu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology; College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xin Wu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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2
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Mahdizade Ari M, Dadgar L, Elahi Z, Ghanavati R, Taheri B. Genetically Engineered Microorganisms and Their Impact on Human Health. Int J Clin Pract 2024; 2024:6638269. [PMID: 38495751 PMCID: PMC10944348 DOI: 10.1155/2024/6638269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/20/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
The emergence of antibiotic-resistant strains, the decreased effectiveness of conventional therapies, and the side effects have led researchers to seek a safer, more cost-effective, patient-friendly, and effective method that does not develop antibiotic resistance. With progress in synthetic biology and genetic engineering, genetically engineered microorganisms effective in treatment, prophylaxis, drug delivery, and diagnosis have been developed. The present study reviews the types of genetically engineered bacteria and phages, their impacts on diseases, cancer, and metabolic and inflammatory disorders, the biosynthesis of these modified strains, the route of administration, and their effects on the environment. We conclude that genetically engineered microorganisms can be considered promising candidates for adjunctive treatment of diseases and cancers.
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Affiliation(s)
- Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Leila Dadgar
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | | | - Behrouz Taheri
- Department of Biotechnology, School of Medicine, Ahvaz Jundishapour University of medical Sciences, Ahvaz, Iran
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3
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Kim TH, Ju K, Kim SK, Woo SG, Lee JS, Lee CH, Rha E, Shin J, Kwon KK, Lee H, Kim H, Lee SG, Lee DH. Novel Signal Peptides and Episomal Plasmid System for Enhanced Protein Secretion in Engineered Bacteroides Species. ACS Synth Biol 2024; 13:648-657. [PMID: 38224571 DOI: 10.1021/acssynbio.3c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The genus Bacteroides, a predominant group in the human gut microbiome, presents significant potential for microbiome engineering and the development of live biotherapeutics aimed at treating gut diseases. Despite its promising capabilities, tools for effectively engineering Bacteroides species have been limited. In our study, we have made a breakthrough by identifying novel signal peptides in Bacteroides thetaiotaomicron and Akkermansia muciniphila. These peptides facilitate efficient protein transport across cellular membranes in Bacteroides, a critical step for therapeutic applications. Additionally, we have developed an advanced episomal plasmid system. This system demonstrates superior protein secretion capabilities compared to traditional chromosomal integration plasmids, making it a vital tool for enhancing the delivery of therapeutic proteins in Bacteroides species. Initially, the stability of this episomal plasmid posed a challenge; however, we have overcome this by incorporating an essential gene-based selection system. This novel strategy not only ensures plasmid stability but also aligns with the growing need for antibiotic-free selection methods in clinical settings. Our work, therefore, not only provides a more robust secretion system for Bacteroides but also sets a new standard for the development of live biotherapeutics.
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Affiliation(s)
- Tae Hyun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Kowoon Ju
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Gyun Woo
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si 56212, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jonghyeok Shin
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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4
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Fishbein SRS, Mahmud B, Dantas G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 2023; 21:772-788. [PMID: 37491458 DOI: 10.1038/s41579-023-00933-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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Affiliation(s)
- Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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5
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Han Z, Min Y, Pang K, Wu D. Therapeutic Approach Targeting Gut Microbiome in Gastrointestinal Infectious Diseases. Int J Mol Sci 2023; 24:15654. [PMID: 37958637 PMCID: PMC10650060 DOI: 10.3390/ijms242115654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and probiotics are gaining popularity, especially for diarrhea patients. However, the specific role of the gut microbiome in different gastrointestinal infectious diseases remains uncertain. There is no consensus on whether gut modulation therapy is universally effective for all such infections. In this comprehensive review, we examine recent developments of the gut microbiome's involvement in several gastrointestinal infectious diseases, including infection of Helicobacter pylori, Clostridium difficile, Vibrio cholerae, enteric viruses, Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa Staphylococcus aureus, Candida albicans, and Giardia duodenalis. We have also incorporated information about fungi and engineered bacteria in gastrointestinal infectious diseases, aiming for a more comprehensive overview of the role of the gut microbiome. This review will provide insights into the pathogenic mechanisms of the gut microbiome while exploring the microbiome's potential in the prevention, diagnosis, prediction, and treatment of gastrointestinal infections.
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Affiliation(s)
- Ziying Han
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, Beijing 100730, China
| | - Yiyang Min
- Peking Union Medical College, Beijing 100730, China
| | - Ke Pang
- Peking Union Medical College, Beijing 100730, China
| | - Dong Wu
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, Beijing 100730, China
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6
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Kim K, Kang M, Cho BK. Systems and synthetic biology-driven engineering of live bacterial therapeutics. Front Bioeng Biotechnol 2023; 11:1267378. [PMID: 37929193 PMCID: PMC10620806 DOI: 10.3389/fbioe.2023.1267378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
The past decade has seen growing interest in bacterial engineering for therapeutically relevant applications. While early efforts focused on repurposing genetically tractable model strains, such as Escherichia coli, engineering gut commensals is gaining traction owing to their innate capacity to survive and stably propagate in the intestine for an extended duration. Although limited genetic tractability has been a major roadblock, recent advances in systems and synthetic biology have unlocked our ability to effectively harness native gut commensals for therapeutic and diagnostic purposes, ranging from the rational design of synthetic microbial consortia to the construction of synthetic cells that execute "sense-and-respond" logic operations that allow real-time detection and therapeutic payload delivery in response to specific signals in the intestine. In this review, we outline the current progress and latest updates on microbial therapeutics, with particular emphasis on gut commensal engineering driven by synthetic biology and systems understanding of their molecular phenotypes. Finally, the challenges and prospects of engineering gut commensals for therapeutic applications are discussed.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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7
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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8
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Chen X, Chi J, Liu Y, Du R, Guo M, Xu W. Synthetic symbiotic bacteria reduces the toxicity of mercury ingested via contaminated food. Food Chem Toxicol 2023:113937. [PMID: 37433354 DOI: 10.1016/j.fct.2023.113937] [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: 05/04/2023] [Revised: 06/22/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Mercury contamination in food poses a significant threat to human health. In this article, we propose a novel approach to solve this problem by enhancing the function of gut microbiota against mercury using a synthetically engineered bacterial strain. An engineered Escherichia coli biosensor MerR with mercury binding function was introduced into the intestines of mice for colonization, whereafter the mice were challenged with oral mercury. Compared with the control mice and mice colonized with unengineered Escherichia coli, the mice with biosensor MerR cells in their gut showed significantly stronger mercury resistance. Furthermore, mercury distribution analysis revealed that biosensor MerR cells promoted the excretion of oral mercury with feces, thereby blocking the entry of mercury into the mice, decreasing the concentration of mercury in the circulatory system and organs, and, thus, attenuating the toxicity of mercury to the liver, kidneys and intestines. Colonization with the biosensor MerR did not result in significant health problems in the mice, nor were genetic circuit mutations or lateral transfers identified during the experiments, thus demonstrating the safety of this approach. This study elucidates the remarkable promise of synthetic biology for modulating gut microbiota function.
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Affiliation(s)
- Xiaolin Chen
- School of Food and Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Jiani Chi
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Yanger Liu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Ruoxi Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Mingzhang Guo
- School of Food and Health, Beijing Technology and Business University, Beijing, 100048, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
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9
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Nieves M, Buschiazzo A, Trajtenberg F. Structural features of sensory two component systems: a synthetic biology perspective. Biochem J 2023; 480:127-140. [PMID: 36688908 DOI: 10.1042/bcj20210798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/24/2023]
Abstract
All living organisms include a set of signaling devices that confer the ability to dynamically perceive and adapt to the fluctuating environment. Two-component systems are part of this sensory machinery that regulates the execution of different genetic and/or biochemical programs in response to specific physical or chemical signals. In the last two decades, there has been tremendous progress in our molecular understanding on how signals are detected, the allosteric mechanisms that control intramolecular information transmission and the specificity determinants that guarantee correct wiring. All this information is starting to be exploited in the development of new synthetic networks. Connecting multiple molecular players, analogous to programming lines of code, can provide the resources to build new sophisticated biocomputing systems. The Synthetic Biology field is starting to revolutionize several scientific fields, such as biomedicine and agriculture, propelling the development of new solutions. Expanding the spectrum of available nanodevices in the toolbox is key to unleash its full potential. This review aims to discuss, from a structural perspective, how to take advantage of the vast array of sensor and effector protein modules involved in two-component systems for the construction of new synthetic circuits.
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Affiliation(s)
- Marcos Nieves
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
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10
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The role of sensory kinase proteins in two-component signal transduction. Biochem Soc Trans 2022; 50:1859-1873. [DOI: 10.1042/bst20220848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
Abstract
Two-component systems (TCSs) are modular signaling circuits that regulate diverse aspects of microbial physiology in response to environmental cues. These molecular circuits comprise a sensor histidine kinase (HK) protein that contains a conserved histidine residue, and an effector response regulator (RR) protein with a conserved aspartate residue. HKs play a major role in bacterial signaling, since they perceive specific stimuli, transmit the message across the cytoplasmic membrane, and catalyze their own phosphorylation, and the trans-phosphorylation and dephosphorylation of their cognate response regulator. The molecular mechanisms by which HKs co-ordinate these functions have been extensively analyzed by genetic, biochemical, and structural approaches. Here, we describe the most common modular architectures found in bacterial HKs, and address the operation mode of the individual functional domains. Finally, we discuss the use of these signaling proteins as drug targets or as sensing devices in whole-cell biosensors with medical and biotechnological applications.
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11
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Aggarwal N, Kitano S, Puah GRY, Kittelmann S, Hwang IY, Chang MW. Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies. Chem Rev 2022; 123:31-72. [PMID: 36317983 PMCID: PMC9837825 DOI: 10.1021/acs.chemrev.2c00431] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.
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Affiliation(s)
- Nikhil Aggarwal
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Shohei Kitano
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ginette Ru Ying Puah
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore,Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore,Wilmar
International Limited, Singapore 138568, Singapore
| | - Sandra Kittelmann
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore,Wilmar
International Limited, Singapore 138568, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore,Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore,Singapore
Institute of Technology, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore,Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore,Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore,Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore,E-mail:
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12
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Huang Y, Lin X, Yu S, Chen R, Chen W. Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment. ACS Synth Biol 2022; 11:3134-3153. [PMID: 36094344 DOI: 10.1021/acssynbio.2c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.
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Affiliation(s)
- Yan Huang
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiaojun Lin
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Siyang Yu
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ruiyue Chen
- Team SZU-China at iGEM 2021, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Weizhao Chen
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Shenzhen Key Laboratory for Microbial Gene Engineering, Shenzhen University, Shenzhen 518060, China
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13
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Fang TT, Zou ZP, Zhou Y, Ye BC. Prebiotics-Controlled Disposable Engineered Bacteria for Intestinal Diseases. ACS Synth Biol 2022; 11:3004-3014. [PMID: 36037444 DOI: 10.1021/acssynbio.2c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As a new method of diagnosis and treatment for intestinal diseases, intelligent engineered bacteria based on synthetic biology have been developed vigorously in recent years. However, how to deal with the engineered bacteria in vivo after completing the tasks is an urgent problem to be resolved. In this study, we constructed a thiosulfate (a biomarker of inflammatory bowel disease)-responsive engineered bacteria to generate two signals, sfGFP (monitoring) and gain-of-function (translation activation) mutation (ACG to ATG), in the initiation codon of lysisE (recording) via the CRISPR/Cas9-mediated base editing system. Once these two signals were detected, xylose could be added to induce lysis E expression, resulting in the destruction of the edited bacteria and the release of AvCystain simultaneously. Overall, our innovative engineered bacteria can record instant and historical information of the disease, and especially, the edited bacteria can be artificially attenuated and release drug in situ when needed, ultimately serving as a disposable and recyclable candidate for more types of diseases.
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Affiliation(s)
- Ting-Ting Fang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen-Ping Zou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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14
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Robinson CM, Short NE, Riglar DT. Achieving spatially precise diagnosis and therapy in the mammalian gut using synthetic microbial gene circuits. Front Bioeng Biotechnol 2022; 10:959441. [PMID: 36118573 PMCID: PMC9478464 DOI: 10.3389/fbioe.2022.959441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian gut and its microbiome form a temporally dynamic and spatially heterogeneous environment. The inaccessibility of the gut and the spatially restricted nature of many gut diseases translate into difficulties in diagnosis and therapy for which novel tools are needed. Engineered bacterial whole-cell biosensors and therapeutics have shown early promise at addressing these challenges. Natural and engineered sensing systems can be repurposed in synthetic genetic circuits to detect spatially specific biomarkers during health and disease. Heat, light, and magnetic signals can also activate gene circuit function with externally directed spatial precision. The resulting engineered bacteria can report on conditions in situ within the complex gut environment or produce biotherapeutics that specifically target host or microbiome activity. Here, we review the current approaches to engineering spatial precision for in vivo bacterial diagnostics and therapeutics using synthetic circuits, and the challenges and opportunities this technology presents.
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15
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Engineered microbial systems for advanced drug delivery. Adv Drug Deliv Rev 2022; 187:114364. [PMID: 35654214 DOI: 10.1016/j.addr.2022.114364] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/06/2022] [Accepted: 05/25/2022] [Indexed: 12/11/2022]
Abstract
The human body is a natural habitat for a multitude of microorganisms, with bacteria being the major constituent of the microbiota. These bacteria colonize discrete anatomical locations that provide suitable conditions for their survival. Many bacterial species, both symbiotic and pathogenic, interact with the host via biochemical signaling. Based on these attributes, commensal and attenuated pathogenic bacteria have been engineered to deliver therapeutic molecules to target specific diseases. Recent advances in synthetic biology have enabled us to perform complex genetic modifications in live bacteria and bacteria-derived particles, which simulate micron or submicron lipid-based vectors, for the targeted delivery of therapeutic agents. In this review, we highlight various examples of engineered bacteria or bacteria-derived particles that encapsulate, secrete, or surface-display therapeutic molecules for the treatment or prevention of various diseases. The review highlights recent studies on (i) the production of therapeutics by microbial cell factories, (ii) disease-triggered release of therapeutics by sense and respond systems, (iii) bacteria targeting tumor hypoxia, and (iv) bacteria-derived particles as chassis for drug delivery. In addition, we discuss the potential of such drug delivery systems to be translated into clinical therapies.
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16
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Cruz KCP, Enekegho LO, Stuart DT. Bioengineered Probiotics: Synthetic Biology Can Provide Live Cell Therapeutics for the Treatment of Foodborne Diseases. Front Bioeng Biotechnol 2022; 10:890479. [PMID: 35656199 PMCID: PMC9152101 DOI: 10.3389/fbioe.2022.890479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/29/2022] [Indexed: 11/15/2022] Open
Abstract
The rising prevalence of antibiotic resistant microbial pathogens presents an ominous health and economic challenge to modern society. The discovery and large-scale development of antibiotic drugs in previous decades was transformational, providing cheap, effective treatment for what would previously have been a lethal infection. As microbial strains resistant to many or even all antibiotic drug treatments have evolved, there is an urgent need for new drugs or antimicrobial treatments to control these pathogens. The ability to sequence and mine the genomes of an increasing number of microbial strains from previously unexplored environments has the potential to identify new natural product antibiotic biosynthesis pathways. This coupled with the power of synthetic biology to generate new production chassis, biosensors and “weaponized” live cell therapeutics may provide new means to combat the rapidly evolving threat of drug resistant microbial pathogens. This review focuses on the application of synthetic biology to construct probiotic strains that have been endowed with functionalities allowing them to identify, compete with and in some cases kill microbial pathogens as well as stimulate host immunity. Weaponized probiotics may have the greatest potential for use against pathogens that infect the gastrointestinal tract: Vibrio cholerae, Staphylococcus aureus, Clostridium perfringens and Clostridioides difficile. The potential benefits of engineered probiotics are highlighted along with the challenges that must still be met before these intriguing and exciting new therapeutic tools can be widely deployed.
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17
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Han L, Liu X, Cheng Z, Cui W, Guo J, Yin J, Zhou Z. Construction and Application of a High-Throughput In Vivo Screening Platform for the Evolution of Nitrile Metabolism-Related Enzymes Based on a Desensitized Repressive Biosensor. ACS Synth Biol 2022; 11:1577-1587. [PMID: 35266713 DOI: 10.1021/acssynbio.1c00642] [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] [Indexed: 11/30/2022]
Abstract
Transcription factor (TF)-based biosensors are expected to serve as powerful tools for the high-throughput screening of biocatalytic systems; however, most of them respond to ligands in a narrow concentration range, which limits their application. In this study, we constructed a heterogenous niacin biosensor using the repressive TF BsNadR and its target promoters from Bacillus subtilis. The fine-tunable output of the niacin biosensor was expanded to a wide range of niacin concentrations (0-50 mM) through desensitization engineering, which was suitable for the accurate identification of differences in enzyme activity. Structural mechanism analysis indicated that weakening the affinity of BsNadR with the ligand niacin and with DNA alters its regulatory properties. Based on the desensitized niacin biosensor, a high-throughput in vivo screening platform was developed for evolving nitrile metabolism-related enzymes. The evolved nitrilase, amidase, and nitrile hydratase with 6.6-, 2.1-, and 21.3-fold improvements in activity were achieved, respectively. In addition, these mutants also exhibited elevated activity toward other cognate substrates, indicating the broad applicability of the screening platform. This study not only provided a universal high-throughput screening platform for different nitrile metabolism-related enzymes but also demonstrated the advantages of repressive biosensors and the vital role of desensitization engineering of the TF in the development of high-throughput screening platforms for enzymes.
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Affiliation(s)
- Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinyue Liu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhongyi Cheng
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenjing Cui
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Junling Guo
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Yin
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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18
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Walker RSK, Pretorius IS. Synthetic biology for the engineering of complex wine yeast communities. NATURE FOOD 2022; 3:249-254. [PMID: 37118192 DOI: 10.1038/s43016-022-00487-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/11/2022] [Indexed: 04/30/2023]
Abstract
Wine fermentation is a representation of complex higher-order microbial interactions. Despite the beneficial properties that these communities bring to wine, their complexity poses challenges in predicting the nature and outcome of fermentation. Technological developments in synthetic biology enable the potential to engineer synthetic microbial communities for new purposes. Here we present the challenges and applications of engineered yeast communities in the context of a wine fermentation vessel, how this represents a model system to enable novel solutions for winemaking and introduce the concept of a 'synthetic' terroir. Furthermore, we introduce our vision for the application of control engineering.
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Affiliation(s)
- Roy S K Walker
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia.
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia.
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19
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Khan A, Ostaku J, Aras E, Safak Seker UO. Combating Infectious Diseases with Synthetic Biology. ACS Synth Biol 2022; 11:528-537. [PMID: 35077138 PMCID: PMC8895449 DOI: 10.1021/acssynbio.1c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Over
the past decades, there have been numerous outbreaks, including
parasitic, fungal, bacterial, and viral infections, worldwide. The
rate at which infectious diseases are emerging is disproportionate
to the rate of development for new strategies that could combat them.
Therefore, there is an increasing demand to develop novel, specific,
sensitive, and effective methods for infectious disease diagnosis
and treatment. Designed synthetic systems and devices are becoming
powerful tools to treat human diseases. The advancement in synthetic
biology offers efficient, accurate, and cost-effective platforms for
detecting and preventing infectious diseases. Herein we focus on the
latest state of living theranostics and its implications.
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Affiliation(s)
- Anooshay Khan
- UNAM − National Nanotechnology Research Center, Institute of Materials Science and Nanotechnology Bilkent University, 06800 Ankara, Turkey
| | - Julian Ostaku
- UNAM − National Nanotechnology Research Center, Institute of Materials Science and Nanotechnology Bilkent University, 06800 Ankara, Turkey
| | - Ebru Aras
- UNAM − National Nanotechnology Research Center, Institute of Materials Science and Nanotechnology Bilkent University, 06800 Ankara, Turkey
| | - Urartu Ozgur Safak Seker
- UNAM − National Nanotechnology Research Center, Institute of Materials Science and Nanotechnology Bilkent University, 06800 Ankara, Turkey
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20
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Brennan AM. Development of Synthetic Biotics as Treatments for Human Diseases. Synth Biol (Oxf) 2022; 7:ysac001. [PMID: 35350191 PMCID: PMC8944296 DOI: 10.1093/synbio/ysac001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/19/2021] [Accepted: 01/29/2022] [Indexed: 12/02/2022] Open
Abstract
Advances in synthetic biology have allowed the generation of strains of bacteria that are genetically altered to have specific therapeutic benefits. These synthetic biotics, also widely referred to as engineered living therapeutics, have tremendous potential as a new therapeutic modality, and several have advanced into the clinic and human testing. This review outlines some of the unique attributes of synthetic biotics as well as some of the challenges in their development as prescription products. Regulatory considerations are discussed, and a case study of a program that has advanced into Phase 2 testing is provided: SYNB1618 for the treatment of PKU.
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21
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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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22
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Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
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Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
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23
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Garrido V, Piñero-Lambea C, Rodriguez-Arce I, Paetzold B, Ferrar T, Weber M, Garcia-Ramallo E, Gallo C, Collantes M, Peñuelas I, Serrano L, Grilló MJ, Lluch-Senar M. Engineering a genome-reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo. Mol Syst Biol 2021; 17:e10145. [PMID: 34612607 PMCID: PMC8493563 DOI: 10.15252/msb.202010145] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 01/25/2023] Open
Abstract
Bacteria present a promising delivery system for treating human diseases. Here, we engineered the genome‐reduced human lung pathogen Mycoplasma pneumoniae as a live biotherapeutic to treat biofilm‐associated bacterial infections. This strain has a unique genetic code, which hinders gene transfer to most other bacterial genera, and it lacks a cell wall, which allows it to express proteins that target peptidoglycans of pathogenic bacteria. We first determined that removal of the pathogenic factors fully attenuated the chassis strain in vivo. We then designed synthetic promoters and identified an endogenous peptide signal sequence that, when fused to heterologous proteins, promotes efficient secretion. Based on this, we equipped the chassis strain with a genetic platform designed to secrete antibiofilm and bactericidal enzymes, resulting in a strain capable of dissolving Staphylococcus aureus biofilms preformed on catheters in vitro, ex vivo, and in vivo. To our knowledge, this is the first engineered genome‐reduced bacterium that can fight against clinically relevant biofilm‐associated bacterial infections.
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Affiliation(s)
- Victoria Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institute of Agrobiotechnology (IdAB; CSIC-Navarra Government), Mutilva, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Pulmobiotics Ltd, Barcelona, Spain
| | - Irene Rodriguez-Arce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institute of Agrobiotechnology (IdAB; CSIC-Navarra Government), Mutilva, Spain
| | - Bernhard Paetzold
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,S-Biomedic N.V., Beerse, Belgium
| | - Tony Ferrar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Weber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eva Garcia-Ramallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Pulmobiotics Ltd, Barcelona, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - María Collantes
- RADIOMIN Research Group, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Iván Peñuelas
- RADIOMIN Research Group, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - María-Jesús Grilló
- Institute of Agrobiotechnology (IdAB; CSIC-Navarra Government), Mutilva, Spain
| | - María Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Pulmobiotics Ltd, Barcelona, Spain.,Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
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24
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Design and in situ biosynthesis of precision therapies against gastrointestinal pathogens. CURRENT OPINION IN PHYSIOLOGY 2021. [DOI: 10.1016/j.cophys.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Wu Y, Wang CW, Wang D, Wei N. A Whole-Cell Biosensor for Point-of-Care Detection of Waterborne Bacterial Pathogens. ACS Synth Biol 2021; 10:333-344. [PMID: 33496568 DOI: 10.1021/acssynbio.0c00491] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water contamination by pathogenic bacteria is a major public health concern globally. Monitoring bacterial contamination in water is critically important to protect human health, but this remains a critical challenge. Engineered whole-cell biosensors created through synthetic biology hold great promise for rapid and cost-effective detection of waterborne pathogens. In this study, we created a novel whole-cell biosensor to detect water contamination by Pseudomonas aeruginosa and Burkholderia pseudomallei, which are two critical bacterial pathogens and are recognized as common causative agents for waterborne diseases. The biosensor detects the target bacterial pathogens by responding to the relevant quorum sensing signal molecules. Particularly, this study constructed and characterized the biosensor on the basis of the QscR quorum sensing signal system for the first time. We first designed and constructed a QscR on the basis of the sensing module in the E. coli host cell and integrated the QscR sensing module with a reporting module that expressed an enhanced green fluorescent protein (EGFP). The results demonstrated that the biosensor had high sensitivity in response to the quorum sensing signals of the target bacterial pathogens. We further engineered a biosensor that expressed a red pigment lycopene in the reporting module to produce a visible signal readout for the pathogen detection. Additionally, we investigated the feasibility of a paper-based assay by immobilizing the lycopene-based whole-cell biosensor on paper with the aim to build a prototype for developing portable detection devices. The biosensor would provide a simple and inexpensive alternative for timely and point-of-care detection of water contamination and protect human health.
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26
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Mabwi HA, Kim E, Song DG, Yoon HS, Pan CH, Komba E, Ko G, Cha KH. Synthetic gut microbiome: Advances and challenges. Comput Struct Biotechnol J 2020; 19:363-371. [PMID: 33489006 PMCID: PMC7787941 DOI: 10.1016/j.csbj.2020.12.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
An exponential rise in studies regarding the association among human gut microbial communities, human health, and diseases is currently attracting the attention of researchers to focus on human gut microbiome research. However, even with the ever-growing number of studies on the human gut microbiome, translation into improved health is progressing slowly. This hampering is due to the complexities of the human gut microbiome, which is composed of >1,000 species of microorganisms, such as bacteria, archaea, viruses, and fungi. To overcome this complexity, it is necessary to reduce the gut microbiome, which can help simplify experimental variables to an extent, such that they can be deliberately manipulated and controlled. Reconstruction of synthetic or established gut microbial communities would make it easier to understand the structure, stability, and functional activities of the complex microbial community of the human gut. Here, we provide an overview of the developments and challenges of the synthetic human gut microbiome, and propose the incorporation of multi-omics and mathematical methods in a better synthetic gut ecosystem design, for easy translation of microbiome information to therapies.
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Affiliation(s)
- Humphrey A. Mabwi
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
- SACIDS Foundation for One Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 25523, Tanzania
| | - Eunjung Kim
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Dae-Geun Song
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Hyo Shin Yoon
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Cheol-Ho Pan
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Erick.V.G. Komba
- SACIDS Foundation for One Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 25523, Tanzania
| | - GwangPyo Ko
- Department of Environmental Health Sciences, School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Center for Human and Environmental Microbiome, Seoul National University, Seoul 08826, Republic of Korea
- KoBioLabs, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kwang Hyun Cha
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
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27
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Davies JE, Behroozian S. An ancient solution to a modern problem. Mol Microbiol 2020; 113:546-549. [PMID: 32185831 DOI: 10.1111/mmi.14481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 11/30/2022]
Abstract
The dearth of new antibiotics and escalating emergence of multidrug resistant bacteria have created a global healthcare crisis and highlight the drastic need for novel antimicrobial agents. Complementary and alternative strategies including the investigation of ancient medicinals could address this problem. Natural clay minerals with a long history of medicinal and biomedical applications have become an interest due to their broad-spectrum antimicrobial activity. Such untapped natural sources may provide new therapeutic agents in the battle against infectious diseases in the post-antibiotic era.
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Affiliation(s)
- Julian E Davies
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Shekooh Behroozian
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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28
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Kang M, Choe D, Kim K, Cho BK, Cho S. Synthetic Biology Approaches in The Development of Engineered Therapeutic Microbes. Int J Mol Sci 2020; 21:ijms21228744. [PMID: 33228099 PMCID: PMC7699352 DOI: 10.3390/ijms21228744] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022] Open
Abstract
Since the intimate relationship between microbes and human health has been uncovered, microbes have been in the spotlight as therapeutic targets for several diseases. Microbes contribute to a wide range of diseases, such as gastrointestinal disorders, diabetes and cancer. However, as host-microbiome interactions have not been fully elucidated, treatments such as probiotic administration and fecal transplantations that are used to modulate the microbial community often cause nonspecific results with serious safety concerns. As an alternative, synthetic biology can be used to rewire microbial networks such that the microbes can function as therapeutic agents. Genetic sensors can be transformed to detect biomarkers associated with disease occurrence and progression. Moreover, microbes can be reprogrammed to produce various therapeutic molecules from the host and bacterial proteins, such as cytokines, enzymes and signaling molecules, in response to a disturbed physiological state of the host. These therapeutic treatment systems are composed of several genetic parts, either identified in bacterial endogenous regulation systems or developed through synthetic design. Such genetic components are connected to form complex genetic logic circuits for sophisticated therapy. In this review, we discussed the synthetic biology strategies that can be used to construct engineered therapeutic microbes for improved microbiome-based treatment.
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Affiliation(s)
- Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (M.K.); (D.C.); (K.K.)
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (M.K.); (D.C.); (K.K.)
| | - Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (M.K.); (D.C.); (K.K.)
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (M.K.); (D.C.); (K.K.)
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Intelligent Synthetic Biology Center, Daejeon 34141, Korea
- Correspondence: (B.-K.C.); (S.C.)
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (M.K.); (D.C.); (K.K.)
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Correspondence: (B.-K.C.); (S.C.)
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29
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Engineering probiotics for therapeutic applications: recent examples and translational outlook. Curr Opin Biotechnol 2020; 65:171-179. [DOI: 10.1016/j.copbio.2020.02.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 02/07/2023]
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30
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Tan Y, Shen J, Si T, Ho CL, Li Y, Dai L. Engineered Live Biotherapeutics: Progress and Challenges. Biotechnol J 2020; 15:e2000155. [DOI: 10.1002/biot.202000155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/29/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Yang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT) Chinese Academy of Sciences Shenzhen 518055 China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT) Chinese Academy of Sciences Shenzhen 518055 China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT) Chinese Academy of Sciences Shenzhen 518055 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chun Loong Ho
- Department of Biomedical Engineering, SUSTech Academy for Advanced Interdisciplinary Studies Southern University of Science and Technology (SUSTech) Shenzhen 518055 China
| | - Yinqing Li
- School of Pharmaceutical Sciences Tsinghua University IDG‐McGovern Institute for Brain Research Beijing 100084 China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT) Chinese Academy of Sciences Shenzhen 518055 China
- University of Chinese Academy of Sciences Beijing 100049 China
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31
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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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Engineering commensal bacteria to rewire host–microbiome interactions. Curr Opin Biotechnol 2020; 62:116-122. [DOI: 10.1016/j.copbio.2019.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023]
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Inducible cell-to-cell signaling for tunable dynamics in microbial communities. Nat Commun 2020; 11:1193. [PMID: 32132536 PMCID: PMC7055273 DOI: 10.1038/s41467-020-15056-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/06/2020] [Indexed: 11/09/2022] Open
Abstract
The last decade has seen bacteria at the forefront of biotechnological innovation, with applications including biomolecular computing, living therapeutics, microbiome engineering and microbial factories. These emerging applications are all united by the need to precisely control complex microbial dynamics in spatially extended environments, requiring tools that can bridge the gap between intracellular and population-level coordination. To address this need, we engineer an inducible quorum sensing system which enables precise tunability of bacterial dynamics both at the population and community level. As a proof-of-principle, we demonstrate the advantages of this system when genetically equipped for cargo delivery. In addition, we exploit the absence of cross-talk with respect to the majority of well-characterized quorum sensing systems to demonstrate inducibility of multi-strain communities. More broadly, this work highlights the unexplored potential of remotely inducible quorum sensing systems which, coupled to any gene of interest, may facilitate the translation of circuit designs into applications.
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Rottinghaus AG, Amrofell MB, Moon TS. Biosensing in Smart Engineered Probiotics. Biotechnol J 2020; 15:e1900319. [PMID: 31860168 DOI: 10.1002/biot.201900319] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/05/2019] [Indexed: 01/01/2023]
Abstract
Engineered microbes are exciting alternatives to current diagnostics and therapeutics. Researchers have developed a wide range of genetic tools and parts to engineer probiotic and commensal microbes. Among these tools and parts, biosensors allow the microbes to sense and record or to sense and respond to chemical and environmental signals in the body, enabling them to report on health conditions of the animal host and/or deliver therapeutics in a controlled manner. This review focuses on how biosensing is applied to engineer "smart" microbes for in vivo diagnostic, therapeutic, and biocontainment goals. Hurdles that need to be overcome when transitioning from high-throughput in vitro systems to low-throughput in vivo animal models, new technologies that can be implemented to alleviate this experimental gap, and areas where future advancements can be made to maximize the utility of biosensing for medical applications are also discussed. As technologies for engineering microbes continue to be developed, these engineered organisms will be used to address many medical challenges.
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Affiliation(s)
- Austin G Rottinghaus
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Matthew B Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
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Abstract
Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.
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Affiliation(s)
- Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), SFR ICAT 4208, UNIV Angers, UNIV Brest, Angers, France
| | - Ann M Stock
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
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Inda ME, Broset E, Lu TK, de la Fuente-Nunez C. Emerging Frontiers in Microbiome Engineering. Trends Immunol 2019; 40:952-973. [PMID: 31601521 DOI: 10.1016/j.it.2019.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 08/15/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023]
Abstract
The gut microbiome has a significant impact on health and disease and can actively contribute to obesity, diabetes, inflammatory bowel disease, cardiovascular disease, and neurological disorders. We do not yet have the necessary tools to fine-tune the microbial communities that constitute the microbiome, though such tools could unlock extensive benefits to human health. Here, we provide an overview of the current state of technological tools that may be used for microbiome engineering. These tools can enable investigators to define the parameters of a healthy microbiome and to determine how gut bacteria may contribute to the etiology of a variety of diseases. These tools may also allow us to explore the exciting prospect of developing targeted therapies and personalized treatments for microbiome-linked diseases.
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Affiliation(s)
- María Eugenia Inda
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Esther Broset
- Machine Biology Group, Departments of Psychiatry and Microbiology, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, 50009, Spain
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
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Yeoh JW, Ng KBI, Teh AY, Zhang J, Chee WKD, Poh CL. An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs. ACS Synth Biol 2019; 8:1484-1497. [PMID: 31035759 DOI: 10.1021/acssynbio.8b00523] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Constructing a complex functional gene circuit composed of different modular biological parts to achieve the desired performance remains challenging without a proper understanding of how the individual module behaves. To address this, mathematical models serve as an important tool toward better interpretation by quantifying the performance of the overall gene circuit, providing insights, and guiding the experimental designs. As different gene circuits might require exclusively different mathematical representations in the form of ordinary differential equations to capture their transient dynamic behaviors, a recurring challenge in model development is the selection of the appropriate model. Here, we developed an automated biomodel selection system (BMSS) which includes a library of pre-established models with intuitive or unintuitive features derived from a vast array of expression profiles. Selection of models is built upon the Akaike information criteria (AIC). We tested the automated platform using characterization data of routinely used inducible systems, constitutive expression systems, and several different logic gate systems (NOT, AND, and OR gates). The BMSS achieved a good agreement for all the different characterization data sets and managed to select the most appropriate model accordingly. To enable exchange and reproducibility of gene circuit design models, the BMSS platform also generates Synthetic Biology Open Language (SBOL)-compliant gene circuit diagrams and Systems Biology Markup Language (SBML) output files. All aspects of the algorithm were programmed in a modular manner to ease the efforts on model extensions or customizations by users. Taken together, the BMSS which is implemented in Python supports users in deriving the best mathematical model candidate in a fast, efficient, and automated way using part/circuit characterization data.
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Affiliation(s)
- Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 119077
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 119077
| | - Kai Boon Ivan Ng
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 119077
| | - Ai Ying Teh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 119077
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 119077
| | - JingYun Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 119077
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 119077
| | - Wai Kit David Chee
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 119077
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 119077
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 119077
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 119077
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38
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Tekel SJ, Smith CL, Lopez B, Mani A, Connot C, Livingstone X, Haynes KA. Engineered Orthogonal Quorum Sensing Systems for Synthetic Gene Regulation in Escherichia coli. Front Bioeng Biotechnol 2019; 7:80. [PMID: 31058147 PMCID: PMC6478669 DOI: 10.3389/fbioe.2019.00080] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/29/2019] [Indexed: 11/13/2022] Open
Abstract
Gene regulators that are controlled by membrane-permeable compounds called homoserine lactones (HSLs) have become popular tools for building synthetic gene networks that coordinate behaviors across populations of engineered bacteria. Synthetic HSL-signaling systems are derived from natural DNA and protein elements from microbial quorum signaling pathways. Crosstalk, where a single HSL can activate multiple regulators, can lead to faults in networks composed of parallel signaling pathways. Here, we report an investigation of quorum sensing components to identify synthetic pathways that exhibit little to no crosstalk in liquid and solid cultures. In previous work, we characterized the response of a single regulator (LuxR) to 10 distinct HSL-synthase enzymes. Our current study determined the responses of five different regulators (LuxR, LasR, TraR, BjaR, and AubR) to the same set of synthases. We identified two sets of orthogonal synthase-regulator pairs (BjaI/BjaR + EsaI/TraR and LasI/LasR + EsaI/TraR) that show little to no crosstalk when they are expressed in Escherichia coli BL21. These results expand the toolbox of characterized components for engineering microbial communities.
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Affiliation(s)
- Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, United States
| | - Christina L Smith
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, United States
| | - Brianna Lopez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Amber Mani
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Christopher Connot
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Xylaan Livingstone
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, United States
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39
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Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations. Nat Biotechnol 2019; 37:755-760. [DOI: 10.1038/s41587-019-0105-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/13/2019] [Indexed: 01/21/2023]
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40
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Cao X, Hamilton JJ, Venturelli OS. Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. Biochemistry 2018; 58:94-107. [PMID: 30457843 DOI: 10.1021/acs.biochem.8b01006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [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)
- Xinyun Cao
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Joshua J Hamilton
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Ophelia S Venturelli
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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41
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Jayaraman P, Yeoh JW, Zhang J, Poh CL. Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System. ACS Synth Biol 2018; 7:2627-2639. [PMID: 30359530 DOI: 10.1021/acssynbio.8b00280] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice, modulating gene expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability and spatiotemporal resolution. Here, we built two dual-input hybrid promoters, each retaining the function of the ligand-inducible promoter while being enhanced with a blue-light-switchable tuning knob. Using the new promoters, we show that both ligand and light inputs can be synchronously modulated to achieve desired amplitude or independently regulated to generate desired frequency at a specific amplitude. We exploit the versatile programmability and orthogonality of the two promoters to build the first reprogrammable logic gene circuit capable of reconfiguring into logic OR and N-IMPLY logic on the fly in both space and time without the need to modify the circuit. Overall, we demonstrate concentration- and time-based combinatorial regulation in live bacterial cells with potential applications in biotechnology and synthetic biology.
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Affiliation(s)
- Premkumar Jayaraman
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 117456
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 117456
| | - Jingyun Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 117456
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore 117456
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42
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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: 79] [Impact Index Per Article: 13.2] [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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43
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The Potential for Convergence between Synthetic Biology and Bioelectronics. Cell Syst 2018; 7:231-244. [DOI: 10.1016/j.cels.2018.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/30/2018] [Accepted: 08/13/2018] [Indexed: 01/20/2023]
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44
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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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45
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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: 70] [Impact Index Per Article: 11.7] [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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46
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Gerstmans H, Criel B, Briers Y. Synthetic biology of modular endolysins. Biotechnol Adv 2018; 36:624-640. [DOI: 10.1016/j.biotechadv.2017.12.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 01/15/2023]
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