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Zhang T, Liu D, Zhang Y, Chen L, Zhang W, Sun T. Biomedical engineering utilizing living photosynthetic cyanobacteria and microalgae: Current status and future prospects. Mater Today Bio 2024; 27:101154. [PMID: 39113912 PMCID: PMC11304071 DOI: 10.1016/j.mtbio.2024.101154] [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] [Received: 05/04/2024] [Revised: 06/24/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Cyanobacteria are the only prokaryotes capable of performing oxygenic photosynthesis on Earth. Besides their traditional roles serving as primary producers, cyanobacteria also synthesize abundant secondary metabolites including carotenoids, alkaloids, peptides, which have been reported to possess medicinal potentials. More importantly, the advancement of synthetic biology technology has further expanded their potential biomedical applications especially using living/engineered cyanobacteria, providing promising and attractive strategies for future disease treatments. To improve the understanding and to facilitate future applications, this review aims to discuss the current status and future prospects of cyanobacterial-based biomedical engineering. Firstly, specific properties of cyanobacteria related with biomedical applications like their natural products of bioactive compounds and heavy metal adsorption were concluded. Subsequently, based on these properties of cyanobacteria, we discussed the progress of their applications in various disease models like hypoxia microenvironment alleviation, wound healing, drug delivery, and so on. Finally, the future prospects including further exploration of cyanobacteria secondary metabolites, the integration of bioactive compounds synthesized by cyanobacteria in situ with medical diagnosis and treatment, and the optimization of in vivo application were critically presented. The review will promote the studies related with cyanobacteria-based biomedical engineering and its practical application in clinical trials in the future.
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Affiliation(s)
- Tong Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Dailin Liu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Yingying Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
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2
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Van Den Berghe M, Walworth NG, Dalvie NC, Dupont CL, Springer M, Andrews MG, Romaniello SJ, Hutchins DA, Montserrat F, Silver PA, Nealson KH. Microbial Catalysis for CO 2 Sequestration: A Geobiological Approach. Cold Spring Harb Perspect Biol 2024; 16:a041673. [PMID: 37788887 PMCID: PMC11065169 DOI: 10.1101/cshperspect.a041673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
One of the greatest threats facing the planet is the continued increase in excess greenhouse gasses, with CO2 being the primary driver due to its rapid increase in only a century. Excess CO2 is exacerbating known climate tipping points that will have cascading local and global effects including loss of biodiversity, global warming, and climate migration. However, global reduction of CO2 emissions is not enough. Carbon dioxide removal (CDR) will also be needed to avoid the catastrophic effects of global warming. Although the drawdown and storage of CO2 occur naturally via the coupling of the silicate and carbonate cycles, they operate over geological timescales (thousands of years). Here, we suggest that microbes can be used to accelerate this process, perhaps by orders of magnitude, while simultaneously producing potentially valuable by-products. This could provide both a sustainable pathway for global drawdown of CO2 and an environmentally benign biosynthesis of materials. We discuss several different approaches, all of which involve enhancing the rate of silicate weathering. We use the silicate mineral olivine as a case study because of its favorable weathering properties, global abundance, and growing interest in CDR applications. Extensive research is needed to determine both the upper limit of the rate of silicate dissolution and its potential to economically scale to draw down significant amounts (Mt/Gt) of CO2 Other industrial processes have successfully cultivated microbial consortia to provide valuable services at scale (e.g., wastewater treatment, anaerobic digestion, fermentation), and we argue that similar economies of scale could be achieved from this research.
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Affiliation(s)
| | - Nathan G Walworth
- Vesta, San Francisco, California 94114, USA
- University of Southern California, Los Angeles, California 90007, USA
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Neil C Dalvie
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, California 92037, USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | - David A Hutchins
- University of Southern California, Los Angeles, California 90007, USA
| | | | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kenneth H Nealson
- Vesta, San Francisco, California 94114, USA
- University of Southern California, Los Angeles, California 90007, USA
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3
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Nagasawa Y, Nakayama M, Kato Y, Ogawa Y, Aribam SD, Tsugami Y, Iwata T, Mikami O, Sugiyama A, Onishi M, Hayashi T, Eguchi M. A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives. Microbiol Spectr 2024; 12:e0355723. [PMID: 38385737 PMCID: PMC10986568 DOI: 10.1128/spectrum.03557-23] [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: 10/04/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
We propose a novel strategy for quick and easy preparation of suicide live vaccine candidates against bacterial pathogens. This method requires only the transformation of one or more plasmids carrying genes encoding for two types of biological devices, an unnatural amino acid (uAA) incorporation system and toxin-antitoxin systems in which translation of the antitoxins requires the uAA incorporation. Escherichia coli BL21-AI laboratory strains carrying the plasmids were viable in the presence of the uAA, whereas the free toxins killed these strains after the removal of the uAA. The survival time after uAA removal could be controlled by the choice of the uAA incorporation system and toxin-antitoxin systems. Multilayered toxin-antitoxin systems suppressed escape frequency to less than 1 escape per 109 generations in the best case. This conditional suicide system also worked in Salmonella enterica and E. coli clinical isolates. The S. enterica vaccine strains were attenuated with a >105 fold lethal dose. Serum IgG response and protection against the parental pathogenic strain were confirmed. In addition, the live E. coli vaccine strain was significantly more immunogenic and provided greater protection than a formalin-inactivated vaccine. The live E. coli vaccine was not detected after inoculation, presumably because the uAA is not present in the host animals or the natural environment. These results suggest that this strategy provides a novel way to rapidly produce safe and highly immunogenic live bacterial vaccine candidates. IMPORTANCE Live vaccines are the oldest vaccines with a history of more than 200 years. Due to their strong immunogenicity, live vaccines are still an important category of vaccines today. However, the development of live vaccines has been challenging due to the difficulties in achieving a balance between safety and immunogenicity. In recent decades, the frequent emergence of various new and old pathogens at risk of causing pandemics has highlighted the need for rapid vaccine development processes. We have pioneered the use of uAAs to control gene expression and to conditionally kill host bacteria as a biological containment system. This report proposes a quick and easy conversion of bacterial pathogens into live vaccine candidates using this containment system. The balance between safety and immunogenicity can be modulated by the selection of the genetic devices used. Moreover, the uAA-auxotrophy can prevent the vaccine from infecting other individuals or establishing the environment.
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Affiliation(s)
- Yuya Nagasawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Momoko Nakayama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yusuke Kato
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yohsuke Ogawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Swarmistha Devi Aribam
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yusaku Tsugami
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Osamu Mikami
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Aoi Sugiyama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Megumi Onishi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Tomohito Hayashi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Masahiro Eguchi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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4
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Ulanova A, Mansfeldt C. EcoGenoRisk: Developing a computational ecological risk assessment tool for synthetic biology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123647. [PMID: 38402941 DOI: 10.1016/j.envpol.2024.123647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
The expanding field of synthetic biology (synbio) supports new opportunities in the design of targeted bioproducts or modified microorganisms. However, this rapid development of synbio products raises concerns surrounding the potential risks of modified microorganisms contaminating unintended environments. These potential invasion risks require new bioinformatic tools to inform the design phase. EcoGenoRisk is a newly constructed computational risk assessment tool for invasiveness that aims to predict where synbio microorganisms may establish a population by screening for habitats of genetically similar microorganisms. The first module of the tool identifies genetically similar microorganisms and potential ecological relationships such as competition, mutualism, and inhibition. In total, 520 archaeal and 32,828 bacterial complete assembly genomes were analyzed to test the specificity and accuracy of the tool as well as to characterize the enzymatic profiles of different taxonomic lineages. Additionally, ecological relationships were analyzed to determine which would result in the greatest potential overlap between shared functional profiles. Notably, competition displayed the significantly highest overlap of shared functions between compared genomes. Overall, EcoGenoRisk is a flexible software pipeline that assists environmental risk assessors to query large databases of known microorganisms and prioritize follow-up bench scale studies.
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Affiliation(s)
- Anna Ulanova
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO, 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Drive, Boulder, CO, 80303, USA
| | - Cresten Mansfeldt
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO, 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Drive, Boulder, CO, 80303, USA.
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Wang X, Liang Q, Luo Y, Ye J, Yu Y, Chen F. Engineering the next generation of theranostic biomaterials with synthetic biology. Bioact Mater 2024; 32:514-529. [PMID: 38026437 PMCID: PMC10660023 DOI: 10.1016/j.bioactmat.2023.10.018] [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] [Received: 07/19/2023] [Revised: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Biomaterials have evolved from inert materials to responsive entities, playing a crucial role in disease diagnosis, treatment, and modeling. However, their advancement is hindered by limitations in chemical and mechanical approaches. Synthetic biology enabling the genetically reprograming of biological systems offers a new paradigm. It has achieved remarkable progresses in cell reprogramming, engineering designer cells for diverse applications. Synthetic biology also encompasses cell-free systems and rational design of biological molecules. This review focuses on the application of synthetic biology in theranostics, which boost rapid development of advanced biomaterials. We introduce key fundamental concepts of synthetic biology and highlight frontier applications thereof, aiming to explore the intersection of synthetic biology and biomaterials. This integration holds tremendous promise for advancing biomaterial engineering with programable complex functions.
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Affiliation(s)
- Xiang Wang
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qianyi Liang
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yixuan Luo
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianwen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yin Yu
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fei Chen
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Lang H, Wang H, Wang H, Zhong Z, Xie X, Zhang W, Guo J, Meng L, Hu X, Zhang X, Zheng H. Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees. Nat Commun 2023; 14:2778. [PMID: 37210527 DOI: 10.1038/s41467-023-38498-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/05/2023] [Indexed: 05/22/2023] Open
Abstract
Nosema ceranae is an intracellular parasite invading the midgut of honeybees, which causes serious nosemosis implicated in honeybee colony losses worldwide. The core gut microbiota is involved in protecting against parasitism, and the genetically engineering of the native gut symbionts provides a novel and efficient way to fight pathogens. Here, using laboratory-generated bees mono-associated with gut members, we find that Snodgrassella alvi inhibit microsporidia proliferation, potentially via the stimulation of host oxidant-mediated immune response. Accordingly, N. ceranae employs the thioredoxin and glutathione systems to defend against oxidative stress and maintain a balanced redox equilibrium, which is essential for the infection process. We knock down the gene expression using nanoparticle-mediated RNA interference, which targets the γ-glutamyl-cysteine synthetase and thioredoxin reductase genes of microsporidia. It significantly reduces the spore load, confirming the importance of the antioxidant mechanism for the intracellular invasion of the N. ceranae parasite. Finally, we genetically modify the symbiotic S. alvi to deliver dsRNA corresponding to the genes involved in the redox system of the microsporidia. The engineered S. alvi induces RNA interference and represses parasite gene expression, thereby inhibits the parasitism significantly. Specifically, N. ceranae is most suppressed by the recombinant strain corresponding to the glutathione synthetase or by a mixture of bacteria expressing variable dsRNA. Our findings extend our previous understanding of the protection of gut symbionts against N. ceranae and provide a symbiont-mediated RNAi system for inhibiting microsporidia infection in honeybees.
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Affiliation(s)
- Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Hao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Haoqing Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Zhaopeng Zhong
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Xianbing Xie
- Department of Laboratory Animal Science, Nanchang University, 330006, Nanchang, China
| | - Wenhao Zhang
- Faculty of Agriculture and Food, Kunming University of Science and Technology, 650031, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650031, Kunming, China
| | - Liang Meng
- BGI-Qingdao, BGI-Shenzhen, 266555, Qingdao, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Xue Zhang
- College of Plant Protection, China Agricultural University, 100083, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China.
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7
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Pavão G, Sfalcin I, Bonatto D. Biocontainment Techniques and Applications for Yeast Biotechnology. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.
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8
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Gotovtsev P. Microbial Cells as a Microrobots: From Drug Delivery to Advanced Biosensors. Biomimetics (Basel) 2023; 8:biomimetics8010109. [PMID: 36975339 PMCID: PMC10046805 DOI: 10.3390/biomimetics8010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The presented review focused on the microbial cell based system. This approach is based on the application of microorganisms as the main part of a robot that is responsible for the motility, cargo shipping, and in some cases, the production of useful chemicals. Living cells in such microrobots have both advantages and disadvantages. Regarding the advantages, it is necessary to mention the motility of cells, which can be natural chemotaxis or phototaxis, depending on the organism. There are approaches to make cells magnetotactic by adding nanoparticles to their surface. Today, the results of the development of such microrobots have been widely discussed. It has been shown that there is a possibility of combining different types of taxis to enhance the control level of the microrobots based on the microorganisms' cells and the efficiency of the solving task. Another advantage is the possibility of applying the whole potential of synthetic biology to make the behavior of the cells more controllable and complex. Biosynthesis of the cargo, advanced sensing, on/off switches, and other promising approaches are discussed within the context of the application for the microrobots. Thus, a synthetic biology application offers significant perspectives on microbial cell based microrobot development. Disadvantages that follow from the nature of microbial cells such as the number of external factors influence the cells, potential immune reaction, etc. They provide several limitations in the application, but do not decrease the bright perspectives of microrobots based on the cells of the microorganisms.
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Affiliation(s)
- Pavel Gotovtsev
- National Research Center "Kurchatov Institute", Biotechnology and Bioenergy Department, Akademika Kurchatova pl. 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy per., 141701 Moscow, Russia
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9
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Asin-Garcia E, Robaey Z, Kampers LFC, Martins Dos Santos VAP. Exploring the Impact of Tensions in Stakeholder Norms on Designing for Value Change: The Case of Biosafety in Industrial Biotechnology. SCIENCE AND ENGINEERING ETHICS 2023; 29:9. [PMID: 36882674 PMCID: PMC9992083 DOI: 10.1007/s11948-023-00432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Synthetic biologists design and engineer organisms for a better and more sustainable future. While the manifold prospects are encouraging, concerns about the uncertain risks of genome editing affect public opinion as well as local regulations. As a consequence, biosafety and associated concepts, such as the Safe-by-design framework and genetic safeguard technologies, have gained notoriety and occupy a central position in the conversation about genetically modified organisms. Yet, as regulatory interest and academic research in genetic safeguard technologies advance, the implementation in industrial biotechnology, a sector that is already employing engineered microorganisms, lags behind. The main goal of this work is to explore the utilization of genetic safeguard technologies for designing biosafety in industrial biotechnology. Based on our results, we posit that biosafety is a case of a changing value, by means of further specification of how to realize biosafety. Our investigation is inspired by the Value Sensitive Design framework, to investigate scientific and technological choices in their appropriate social context. Our findings discuss stakeholder norms for biosafety, reasonings about genetic safeguards, and how these impact the practice of designing for biosafety. We show that tensions between stakeholders occur at the level of norms, and that prior stakeholder alignment is crucial for value specification to happen in practice. Finally, we elaborate in different reasonings about genetic safeguards for biosafety and conclude that, in absence of a common multi-stakeholder effort, the differences in informal biosafety norms and the disparity in biosafety thinking could end up leading to design requirements for compliance instead of for safety.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands.
- Bioprocess Engineering Group, Wageningen University & Research, 6700, AA, Wageningen, The Netherlands.
| | - Zoë Robaey
- Department of Social Sciences, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
| | - Linde F C Kampers
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
- Bioprocess Engineering Group, Wageningen University & Research, 6700, AA, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
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10
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Kato Y. A strategy for addicting transgene-free bacteria to synthetic modified metabolites. Front Microbiol 2023; 14:1086094. [PMID: 36846762 PMCID: PMC9950777 DOI: 10.3389/fmicb.2023.1086094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Biological containment is a safeguard technology to prevent uncontrolled proliferation of "useful but dangerous" microbes. Addiction to synthetic chemicals is ideal for biological containment, but this currently requires introduction of transgenes containing synthetic genetic elements for which environmental diffusion has to be prevented. Here, I designed a strategy for addicting transgene-free bacteria to synthetic modified metabolites, in which the target organism that can neither produce an essential metabolite nor use the extracellularly supplied metabolite, is rescued by a synthetic derivative that is taken up from a medium and converted into the metabolite in the cell. Because design of the synthetic modified metabolite is the key technology, our strategy differs distinctly from conventional biological containment, which mainly depends on genetic manipulation of the target microorganisms. Our strategy is particularly promising for containment of non-genetically modified organisms such as pathogens and live vaccines.
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11
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Hirota R, Katsuura ZI, Momokawa N, Murakami H, Watanabe S, Ishida T, Ikeda T, Funabashi H, Kuroda A. Gatekeeper Residue Replacement in a Phosphite Transporter Enhances Mutational Robustness of the Biocontainment Strategy. ACS Synth Biol 2022; 11:3397-3404. [PMID: 36202772 DOI: 10.1021/acssynbio.2c00296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Biocontainment is a key methodology to reduce environmental risk through the deliberate release of genetically modified microorganisms. Previously, we developed a phosphite (HPO32-)-dependent biocontainment strategy, by expressing a phosphite-specific transporter HtxBCDE and phosphite dehydrogenase in bacteria devoid of their indigenous phosphate (HPO42-) transporters. This strategy did not allow Escherichia coli to generate escape mutants (EMs) in growth media containing phosphate as a phosphorus source using an assay with a detection limit of 1.9 × 10-13. In this study, we found that the coexistence of a high dose of phosphate (>0.5 mM) with phosphite in the growth medium allows the phosphite-dependent E. coli strain to generate EMs at a frequency of approximately 5.4 × 10-10. In all EMs, the mutation was a single amino acid substitution of phenylalanine to cysteine or serine at position 210 of HtxC, the transmembrane domain protein of the phosphorus compound transporter HtxBCDE. Replacement of the HtxC F210 residue with the other 17 amino acids revealed that HtxC F210 is crucial in determining substrate specificity of HtxBCDE. Based on the finding of the role of HtxC F210 as a "gatekeeper" residue for this transporter, we demonstrate that the replacement of HtxC F210 with amino acids resulting from codons that require two simultaneous point mutations to generate phosphate permissive HtxC mutants can reduce the rate of EM generation to an undetectable level. These findings also provide novel insights into the functional classification of HtxBCDE as a noncanonical ATP-binding cassette transporter in which the transmembrane domain protein participates in substrate recognition.
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Affiliation(s)
- Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Zen-Ichiro Katsuura
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Naoki Momokawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hiroki Murakami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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12
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [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: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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13
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Asin-Garcia E, Batianis C, Li Y, Fawcett JD, de Jong I, Dos Santos VAPM. Phosphite synthetic auxotrophy as an effective biocontainment strategy for the industrial chassis Pseudomonas putida. Microb Cell Fact 2022; 21:156. [PMID: 35934698 PMCID: PMC9358898 DOI: 10.1186/s12934-022-01883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/26/2022] [Indexed: 11/12/2022] Open
Abstract
The inclusion of biosafety strategies into strain engineering pipelines is crucial for safe-by-design biobased processes. This in turn might enable a more rapid regulatory acceptance of bioengineered organisms in both industrial and environmental applications. For this reason, we equipped the industrially relevant microbial chassis Pseudomonas putida KT2440 with an effective biocontainment strategy based on a synthetic dependency on phosphite, which is generally not readily available in the environment. The produced PSAG-9 strain was first engineered to assimilate phosphite through the genome-integration of a phosphite dehydrogenase and a phosphite-specific transport complex. Subsequently, to deter the strain from growing on naturally assimilated phosphate, all native genes related to its transport were identified and deleted generating a strain unable to grow on media containing any phosphorous source other than phosphite. PSAG-9 exhibited fitness levels with phosphite similar to those of the wild type with phosphate, and low levels of escape frequency. Beyond biosafety, this strategy endowed P. putida with the capacity to be cultured under non-sterile conditions using phosphite as the sole phosphorous source with a reduced risk of contamination by other microbes, while displaying enhanced NADH regenerative capacity. These industrially beneficial features complement the metabolic advantages for which this species is known for, thereby strengthening it as a synthetic biology chassis with potential uses in industry, with suitability towards environmental release.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Yunsong Li
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - James D Fawcett
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands.,Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, SW72BX, UK
| | - Ivar de Jong
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands. .,LifeGlimmer GmbH, 12163, Berlin, Germany. .,Bioprocess Engineering Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands.
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14
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Pei L, Garfinkel M, Schmidt M. Bottlenecks and opportunities for synthetic biology biosafety standards. Nat Commun 2022; 13:2175. [PMID: 35449163 PMCID: PMC9023567 DOI: 10.1038/s41467-022-29889-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Lei Pei
- Biofaction KG, Vienna, Austria
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15
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Pantoja Angles A, Valle-Pérez AU, Hauser C, Mahfouz MM. Microbial Biocontainment Systems for Clinical, Agricultural, and Industrial Applications. Front Bioeng Biotechnol 2022; 10:830200. [PMID: 35186907 PMCID: PMC8847691 DOI: 10.3389/fbioe.2022.830200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Many applications of synthetic biology require biological systems in engineered microbes to be delivered into diverse environments, such as for in situ bioremediation, biosensing, and applications in medicine and agriculture. To avoid harming the target system (whether that is a farm field or the human gut), such applications require microbial biocontainment systems (MBSs) that inhibit the proliferation of engineered microbes. In the past decade, diverse molecular strategies have been implemented to develop MBSs that tightly control the proliferation of engineered microbes; this has enabled medical, industrial, and agricultural applications in which biological processes can be executed in situ. The customization of MBSs also facilitate the integration of sensing modules for which different compounds can be produced and delivered upon changes in environmental conditions. These achievements have accelerated the generation of novel microbial systems capable of responding to external stimuli with limited interference from the environment. In this review, we provide an overview of the current approaches used for MBSs, with a specific focus on applications that have an immediate impact on multiple fields.
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Affiliation(s)
- Aaron Pantoja Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alexander U. Valle-Pérez
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
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16
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Tamzil MS, Alfiko Y, Mubarok AF, Purwantomo S, Suwanto A, Budiarti S. Development of Auxotrophic Agrobacterium tumefaciens AGL1 by Tn5 Transposon for Rice (Oryza sativa L.) Transformation. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0244-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Beiranvand N, Freindorf M, Kraka E. Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study. Molecules 2021; 26:2268. [PMID: 33919989 PMCID: PMC8071019 DOI: 10.3390/molecules26082268] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.
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Affiliation(s)
| | | | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA; (N.B.); (M.F.)
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18
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Kubyshkin V, Davis R, Budisa N. Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement. Beilstein J Org Chem 2021; 17:439-460. [PMID: 33727970 PMCID: PMC7934785 DOI: 10.3762/bjoc.17.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Due to the heterocyclic structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades. We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide proline-to-fluoroproline substitutions could be possible. We suggest a hypothetical scenario for the use of laboratory evolutionary methods with fluoroprolines as a suitable vehicle to introduce fluorine into living cells. This approach may enable creation of synthetic cells endowed with artificial biodiversity, containing fluorine as a bioelement.
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Affiliation(s)
- Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Rebecca Davis
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
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19
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De Saeger J, Park J, Chung HS, Hernalsteens JP, Van Lijsebettens M, Inzé D, Van Montagu M, Depuydt S. Agrobacterium strains and strain improvement: Present and outlook. Biotechnol Adv 2020; 53:107677. [PMID: 33290822 DOI: 10.1016/j.biotechadv.2020.107677] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/03/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022]
Abstract
Almost 40 years ago the first transgenic plant was generated through Agrobacterium tumefaciens-mediated transformation, which, until now, remains the method of choice for gene delivery into plants. Ever since, optimized Agrobacterium strains have been developed with additional (genetic) modifications that were mostly aimed at enhancing the transformation efficiency, although an optimized strain also exists that reduces unwanted plasmid recombination. As a result, a collection of very useful strains has been created to transform a wide variety of plant species, but has also led to a confusing Agrobacterium strain nomenclature. The latter is often misleading for choosing the best-suited strain for one's transformation purposes. To overcome this issue, we provide a complete overview of the strain classification. We also indicate different strain modifications and their purposes, as well as the obtained results with regard to the transformation process sensu largo. Furthermore, we propose additional improvements of the Agrobacterium-mediated transformation process and consider several worthwhile modifications, for instance, by circumventing a defense response in planta. In this regard, we will discuss pattern-triggered immunity, pathogen-associated molecular pattern detection, hormone homeostasis and signaling, and reactive oxygen species in relationship to Agrobacterium transformation. We will also explore alterations that increase agrobacterial transformation efficiency, reduce plasmid recombination, and improve biocontainment. Finally, we recommend the use of a modular system to best utilize the available knowledge for successful plant transformation.
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Affiliation(s)
- Jonas De Saeger
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jihae Park
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Marine Sciences, Incheon National University, Incheon 406-840, South Korea
| | - Hoo Sun Chung
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Stephen Depuydt
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
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20
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Abstract
Preventing the escape of hazardous genes from genetically modified organisms (GMOs) into the environment is one of the most important issues in biotechnology research. Various strategies were developed to create "genetic firewalls" that prevent the leakage of GMOs; however, they were not specially designed to prevent the escape of genes. To address this issue, we developed amino acid (AA)-swapped genetic codes orthogonal to the standard genetic code, namely SL (Ser and Leu were swapped) and SLA genetic codes (Ser, Leu, and Ala were swapped). From mRNAs encoded by the AA-swapped genetic codes, functional proteins were only synthesized in translation systems featuring the corresponding genetic codes. These results clearly demonstrated the orthogonality of the AA-swapped genetic codes against the standard genetic code and their potential to function as "genetic firewalls for genes". Furthermore, we propose "a codon-bypass strategy" to develop a GMO with an AA-swapped genetic code.
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Masahiro Tozaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, 464-8603, Japan
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21
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Ke J, Wang B, Yoshikuni Y. Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture. Trends Biotechnol 2020; 39:244-261. [PMID: 32800605 DOI: 10.1016/j.tibtech.2020.07.008] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/28/2022]
Abstract
To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helping to solve these challenges. However, the results of their use in agriculture have been variable, probably because of poor colonization. Phytomicrobiome engineering is an emerging field of synthetic biology that may offer ways to alleviate this limitation. This review highlights recent advances in both bottom-up and top-down approaches to engineering non-model bacteria and microbiomes to promote beneficial plant-microbe interactions, as well as advances in strategies to evaluate these interactions. Biosafety, biosecurity, and biocontainment strategies to address the environmental concerns associated with field use of synthetic microbes are also discussed.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bing Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido 060-8589, Japan.
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22
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Asin-Garcia E, Kallergi A, Landeweerd L, Martins Dos Santos VAP. Genetic Safeguards for Safety-by-design: So Close Yet So Far. Trends Biotechnol 2020; 38:1308-1312. [PMID: 32402415 DOI: 10.1016/j.tibtech.2020.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/01/2020] [Accepted: 04/13/2020] [Indexed: 01/10/2023]
Abstract
Safety-by-design (SbD) is paramount for risk management in synthetic biology, with genetic safeguards being a key technology for its implementation. While attractive in theory, the integration of genetic safeguards into SbD strategies is rarely exercised in practice, despite technological advances. Here we question why and what might be done about it.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708, WE, The Netherlands
| | - Amalia Kallergi
- Institute for Science in Society, Radboud University, Nijmegen, 6500, GL, The Netherlands
| | - Laurens Landeweerd
- Institute for Science in Society, Radboud University, Nijmegen, 6500, GL, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708, WE, The Netherlands; LifeGlimmer GmbH, Berlin, Germany.
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23
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Whitfill T, Oh J. Recoding the metagenome: microbiome engineering in situ. Curr Opin Microbiol 2019; 50:28-34. [PMID: 31622928 DOI: 10.1016/j.mib.2019.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/19/2019] [Accepted: 09/06/2019] [Indexed: 12/24/2022]
Abstract
Synthetic biology has enabled a new generation of tools for engineering the microbiome, including targeted antibiotics, protein delivery, living biosensors and diagnostics, and metabolic factories. Here, we discuss opportunities and limitations in microbiome engineering, focusing on a new generation of tools for in situ genetic modification of a microbiome that hold particular promise in circumventing these limitations.
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Affiliation(s)
- Travis Whitfill
- Azitra, Inc., 400 Farmington Ave, Farmington, CT 06032, United States
| | - Julia Oh
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT 06032, United States.
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24
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Kato Y. Translational Control using an Expanded Genetic Code. Int J Mol Sci 2019; 20:ijms20040887. [PMID: 30781713 PMCID: PMC6412442 DOI: 10.3390/ijms20040887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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25
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Huang WE, Nikel PI. The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back. Microb Biotechnol 2019; 12:5-7. [PMID: 30461208 PMCID: PMC6302714 DOI: 10.1111/1751-7915.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
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26
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Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation. Genes (Basel) 2018; 10:genes10010017. [PMID: 30597824 PMCID: PMC6356944 DOI: 10.3390/genes10010017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 02/08/2023] Open
Abstract
The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. Here, we present the strategies that have been utilized to fundamentally alter the genetic code in its decoding rules or its molecular representation and anticipate future avenues in the pursuit of robust biocontainment.
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