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Ecological firewalls for synthetic biology. iScience 2022; 25:104658. [PMID: 35832885 PMCID: PMC9272386 DOI: 10.1016/j.isci.2022.104658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while—when required—preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined. Population control of synthetic strains can be achieved by engineering ecological links We introduce ecological firewalls, inspired in four types of ecological interactions Our firewalls are shown to maintain diversity while performing designed functions Ecological firewalls will help to tackle future bioremediation strategies
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Schmidt M, Kubyshkin V. How To Quantify a Genetic Firewall? A Polarity-Based Metric for Genetic Code Engineering. Chembiochem 2021; 22:1268-1284. [PMID: 33231343 PMCID: PMC8049029 DOI: 10.1002/cbic.202000758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Indexed: 12/14/2022]
Abstract
Genetic code engineering aims to produce organisms that translate genetic information in a different way from that prescribed by the standard genetic code. This endeavor could eventually lead to genetic isolation, where an organism that operates under a different genetic code will not be able to transfer functional genes with other living species, thereby standing behind a genetic firewall. It is not clear however, how distinct the code should be, or how to measure the distance. We have developed a metric (Δcode ) where we assigned polarity indices (clog D7 ) to amino acids to calculate the distances between pairs of genetic codes. We then calculated the distance between a set of 204 genetic codes, including the 24 known distinct natural codes, 11 extreme-distance codes created computationally, nine theoretical special purpose codes from literature and 160 codes in which canonical amino acids were replaced by noncanonical chemical analogues. The metric can be used for building strategies towards creating semantically alienated organisms, and testing the strength of genetic firewalls. This metric provides the basis for a map of the genetic codes that could guide future efforts towards novel biochemical worlds, biosafety and deep barcoding applications.
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Affiliation(s)
| | - Vladimir Kubyshkin
- Department of ChemistryUniversity of ManitobaDysart Road 144WinnipegR3T 2N2Canada
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Kim D, Lee JW. Genetic Biocontainment Systems for the Safe Use of Engineered Microorganisms. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0070-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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de Lorenzo V, Krasnogor N, Schmidt M. For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is! N Biotechnol 2020; 60:44-51. [PMID: 32889152 DOI: 10.1016/j.nbt.2020.08.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
At the onset of the 4th Industrial Revolution, the role of synthetic biology (SynBio) as a fuel for the bioeconomy requires clarification of the terms typically adopted by this growing scientific-technical field. The concept of the chassis as a defined, reusable biological frame where non-native components can be plugged in and out to create new functionalities lies at the boundary between frontline bioengineering and more traditional recombinant DNA technology. As synthetic biology leaves academic laboratories and starts penetrating industrial and environmental realms regulatory agencies demand clear definitions and descriptions of SynBio constituents, processes and products. In this article, the state of the ongoing discussion on what is a chassis is reviewed, a non-equivocal nomenclature for the jargon used is proposed and objective criteria are recommended for distinguishing SynBio agents from traditional GMOs. The use of genomic barcodes as unique identifiers is strongly advocated. Finally the soil bacterium Pseudomonas putida is shown as an example of the roadmap that one environmental isolate may go through to become a bona fide SynBio chassis.
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Affiliation(s)
- Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Madrid 28049, Spain.
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems (ICOS) research group, Newcastle University, Newcastle Upon Tyne NE4 5TG UK
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Algar E, Al‐Ramahi Y, Lorenzo V, Martínez‐García E. Environmental Performance of
Pseudomonas putida
with a Uracylated Genome. Chembiochem 2020; 21:3255-3265. [DOI: 10.1002/cbic.202000330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/27/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Elena Algar
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
| | - Yamal Al‐Ramahi
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
| | - Víctor Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
| | - Esteban Martínez‐García
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
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Stirling F, Silver PA. Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer? Mol Cell 2020; 78:614-623. [PMID: 32442504 PMCID: PMC7307494 DOI: 10.1016/j.molcel.2020.03.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022]
Abstract
Synthetic biology has promised and delivered on an impressive array of applications based on genetically modified microorganisms. While novel biotechnology undoubtedly offers benefits, like all new technology, precautions should be considered during implementation to reduce the risk of both known and unknown adverse effects. To achieve containment of transgenic microorganisms, confidence to a near-scientific certainty that they cannot transfer their transgenic genes to other organisms, and that they cannot survive to propagate in unintended environments, is a priority. Here, we present an in-depth summary of biological containment systems for micro-organisms published to date, including the production of a genetic firewall through genome recoding and physical containment of microbes using auxotrophies, regulation of essential genes, and expression of toxic genes. The level of containment required to consider a transgenic organism suitable for deployment is discussed, as well as standards of practice for developing new containment systems.
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Affiliation(s)
- Finn Stirling
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA.
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Tellechea-Luzardo J, Winterhalter C, Widera P, Kozyra J, de Lorenzo V, Krasnogor N. Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering. ACS Synth Biol 2020; 9:536-545. [PMID: 32078768 DOI: 10.1021/acssynbio.9b00400] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
As DNA sequencing and synthesis become cheaper and more easily accessible, the scale and complexity of biological engineering projects is set to grow. Yet, although there is an accelerating convergence between biotechnology and digital technology, a deficit in software and laboratory techniques diminishes the ability to make biotechnology more agile, reproducible, and transparent while, at the same time, limiting the security and safety of synthetic biology constructs. To partially address some of these problems, this paper presents an approach for physically linking engineered cells to their digital footprint-we called it digital twinning. This enables the tracking of the entire engineering history of a cell line in a specialized version control system for collaborative strain engineering via simple barcoding protocols.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne NE4 5TG, U.K
| | - Charles Winterhalter
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne NE4 5TG, U.K
| | - Paweł Widera
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne NE4 5TG, U.K
| | - Jerzy Kozyra
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne NE4 5TG, U.K
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne NE4 5TG, U.K
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Conde-Pueyo N, Vidiella B, Sardanyés J, Berdugo M, Maestre FT, de Lorenzo V, Solé R. Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome. Life (Basel) 2020; 10:E14. [PMID: 32050455 PMCID: PMC7175242 DOI: 10.3390/life10020014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022] Open
Abstract
What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems capable of persisting in closed environments? Can synthetic communities be created to thrive on planets different from ours? These and other questions pervade major future developments within synthetic biology. The goal of engineering ecosystems is plagued with all kinds of technological, scientific and ethic problems. In this paper, we consider the requirements for terraformation, i.e., for changing a given environment to make it hospitable to some given class of life forms. Although the standard use of this term involved strategies for planetary terraformation, it has been recently suggested that this approach could be applied to a very different context: ecological communities within our own planet. As discussed here, this includes multiple scales, from the gut microbiome to the entire biosphere.
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Affiliation(s)
- Nuria Conde-Pueyo
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
| | - Blai Vidiella
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Campus UAB Edifici C, 08193 Bellaterra, Barcelona, Spain;
- Barcelona Graduate School of Mathematics (BGSMath), Campus UAB Edifici C, 08193 Bellaterra, Barcelona, Spain
| | - Miguel Berdugo
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio “Ramon Margalef”, Universidad de Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain;
| | - Fernando T. Maestre
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio “Ramon Margalef”, Universidad de Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain;
| | - Victor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Schmidt M. A metric space for semantic containment: Towards the implementation of genetic firewalls. Biosystems 2019; 185:104015. [PMID: 31408698 DOI: 10.1016/j.biosystems.2019.104015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022]
Abstract
Analysing or engineering the genetic code has mainly been considered as an approach to reduce or increase the mutational robustness of the genetic code, i.e. the error tolerance in DNA mutations, or to enable the incorporation of non-canonical amino acids. The approach of "semantic containment", however, is less interested in altering the mutational tolerance of the standard code, but to create synthetic alternative genetic codes that limit or all together impede horizontal gene transfer between a natural and genomically recoded organisms (GRO). A major claim or conjecture of semantic containment is: "the farther, the safer", meaning, the less similarity there is between two codes, the less chance of a horizontal gene transfer, and the stronger the genetic firewall. So far, no metrics were available to measure and quantify the "genetic distance" between different genetic codes. Such a metric, however, is iis paramount to allow the experimental testing and evaluation of the validity of semantic biocontainment for the first time. Here, we introduce a metric space to measure exactly the distance (dissimilarity) between different genetic codes, in order to provide a framework to evaluate the relation between distance and strength of a genetic firewall. Results are presented that incorporate bespoken metrics when producing alternative genetic codes according to predefined goals, specifications and limitations. Finally, as an outlook, implications and challenges for genetic firewall(s) are discussed for dual- and multi-code systems.
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Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code. J Theor Biol 2019; 464:21-32. [DOI: 10.1016/j.jtbi.2018.12.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023]
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Whitford CM, Dymek S, Kerkhoff D, März C, Schmidt O, Edich M, Droste J, Pucker B, Rückert C, Kalinowski J. Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. J Biol Eng 2018; 12:13. [PMID: 30123321 PMCID: PMC6090650 DOI: 10.1186/s13036-018-0105-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer. MAIN BODY Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system. CONCLUSION Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.
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Affiliation(s)
| | - Saskia Dymek
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Denise Kerkhoff
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Camilla März
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Olga Schmidt
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Maximilian Edich
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julian Droste
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Boas Pucker
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Present address: Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Christian Rückert
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
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de Lorenzo V. Evolutionary tinkering vs. rational engineering in the times of synthetic biology. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:18. [PMID: 30099657 PMCID: PMC6087506 DOI: 10.1186/s40504-018-0086-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
Synthetic biology is not only a contemporary reformulation of the recombinant DNA technologies of the last 30 years, combined with descriptive language imported from electrical and industrial engineering. It is also a new way to interpret living systems and a statement of intent for the use and reprogramming of biological objects for human benefit. In this context, the notion of designer biology is often presented as opposed to natural selection following the powerful rationale formulated by François Jacob on evolution-as-tinkering. The onset of synthetic biology opens a different perspective by leaving aside the question about the evolutionary origin of biological phenomena and focusing instead on the relational logic and the material properties of the corresponding components that make biological system work as they do. Once a functional challenge arises, the solution space for the problem is not homogeneous but it has attractors that can be accessed either through random exploration (as evolution does) or rational design (as engineers do). Although these two paths (i.e. evolution and engineering) are essentially different, they can lead to solutions to specific mechanistic bottlenecks that frequently coincide or converge-and one can easily help to understand and improve the other. Alas, productive discussions on these matters are often contaminated by ideological preconceptions that prevent adoption of the engineering metaphor to understand and ultimately reshape living systems-as ambitioned by synthetic biology. Yet, some possible ways to overcome the impasse are feasible. In parallel to Monod's evolutionary paradox of teleo-logy (finality/purpose) vs. teleo-nomy (appearance of finality/purpose), a mechanistic paradox could be entertained between techno-logy (rational engineering) vs techno-nomy (appearance of rational engineering), all for the sake of understanding the relational logic that enables live systems to function as physico-chemical entities in time and space. This article thus proposes a radical vision of synthetic biology through the lens of the engineering metaphor.
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Affiliation(s)
- Víctor de Lorenzo
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, 28049, Madrid, Spain.
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The evolving interface between synthetic biology and functional metagenomics. Nat Chem Biol 2018; 14:752-759. [DOI: 10.1038/s41589-018-0100-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
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Solé RV, Montañez R, Duran-Nebreda S, Rodriguez-Amor D, Vidiella B, Sardanyés J. Population dynamics of synthetic terraformation motifs. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180121. [PMID: 30109068 PMCID: PMC6083676 DOI: 10.1098/rsos.180121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/22/2018] [Indexed: 05/23/2023]
Abstract
Ecosystems are complex systems, currently experiencing several threats associated with global warming, intensive exploitation and human-driven habitat degradation. Because of a general presence of multiple stable states, including states involving population extinction, and due to the intrinsic nonlinearities associated with feedback loops, collapse in ecosystems could occur in a catastrophic manner. It has been recently suggested that a potential path to prevent or modify the outcome of these transitions would involve designing synthetic organisms and synthetic ecological interactions that could push these endangered systems out of the critical boundaries. In this paper, we investigate the dynamics of the simplest mathematical models associated with four classes of ecological engineering designs, named Terraformation motifs (TMs). These TMs put in a nutshell different ecological strategies. In this context, some fundamental types of bifurcations pervade the systems' dynamics. Mutualistic interactions can enhance persistence of the systems by means of saddle-node bifurcations. The models without cooperative interactions show that ecosystems achieve restoration through transcritical bifurcations. Thus, our analysis of the models allows us to define the stability conditions and parameter domains where these TMs must work.
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Affiliation(s)
- Ricard V. Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolitiva, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003 Barcelona, Spain
- Santa Fe Institute 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Raúl Montañez
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolitiva, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003 Barcelona, Spain
| | - Salva Duran-Nebreda
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolitiva, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003 Barcelona, Spain
| | - Daniel Rodriguez-Amor
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolitiva, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003 Barcelona, Spain
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Blai Vidiella
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolitiva, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003 Barcelona, Spain
| | - Josep Sardanyés
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Institut de Biologia Evolitiva, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003 Barcelona, Spain
- Centre de Recerca Matemàtica, Edifici C, Campus de Bellaterra, 08193, Bellaterra, Barcelona, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Edifici C, Campus de Bellaterra, 08193, Bellaterra, Barcelona, Spain
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Schmidt M, Pei L, Budisa N. Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:301-315. [PMID: 28567486 DOI: 10.1007/10_2016_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.
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Affiliation(s)
- Markus Schmidt
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria.
| | - Lei Pei
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria
| | - Nediljko Budisa
- AK Biokatalyse, Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
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de Lorenzo V, Schmidt M. Biological standards for the Knowledge-Based BioEconomy: What is at stake. N Biotechnol 2018; 40:170-180. [DOI: 10.1016/j.nbt.2017.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023]
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18
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Agostini F, Völler J, Koksch B, Acevedo‐Rocha CG, Kubyshkin V, Budisa N. Biocatalysis with Unnatural Amino Acids: Enzymology Meets Xenobiology. Angew Chem Int Ed Engl 2017; 56:9680-9703. [DOI: 10.1002/anie.201610129] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Federica Agostini
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Jan‐Stefan Völler
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | | | - Vladimir Kubyshkin
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
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19
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Rampley CPN, Davison PA, Qian P, Preston GM, Hunter CN, Thompson IP, Wu LJ, Huang WE. Development of SimCells as a novel chassis for functional biosensors. Sci Rep 2017; 7:7261. [PMID: 28775370 PMCID: PMC5543166 DOI: 10.1038/s41598-017-07391-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/28/2017] [Indexed: 01/31/2023] Open
Abstract
This work serves as a proof-of-concept for bacterially derived SimCells (Simple Cells), which contain the cell machinery from bacteria and designed DNA (or potentially a simplified genome) to instruct the cell to carry out novel, specific tasks. SimCells represent a reprogrammable chassis without a native chromosome, which can host designed DNA to perform defined functions. In this paper, the use of Escherichia coli MC1000 ∆minD minicells as a non-reproducing chassis for SimCells was explored, as demonstrated by their ability to act as sensitive biosensors for small molecules. Highly purified minicells derived from E. coli strains containing gene circuits for biosensing were able to transduce the input signals from several small molecules (glucarate, acrylate and arabinose) into the production of green fluorescent protein (GFP). A mathematical model was developed to fit the experimental data for induction of gene expression in SimCells. The intracellular ATP level was shown to be important for SimCell function. A purification and storage protocol was developed to prepare SimCells which could retain their functions for an extended period of time. This study demonstrates that SimCells are able to perform as ‘smart bioparticles’ controlled by designed gene circuits.
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Affiliation(s)
- Cordelia P N Rampley
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, Oxford, United Kingdom
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Ling Juan Wu
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom.
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20
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de Lorenzo V. Synthetic microbiology: from analogy to methodology. Microb Biotechnol 2017; 10:1264-1266. [PMID: 28745463 PMCID: PMC5609264 DOI: 10.1111/1751-7915.12786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/01/2017] [Indexed: 01/26/2023] Open
Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Cantoblanco-Madrid, Spain
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21
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Biokatalyse mit nicht‐natürlichen Aminosäuren: Enzymologie trifft Xenobiologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610129] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Howard J, Murashov V, Schulte P. Synthetic biology and occupational risk. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2017; 14:224-236. [PMID: 27754800 DOI: 10.1080/15459624.2016.1237031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Synthetic biology is an emerging interdisciplinary field of biotechnology that involves applying the principles of engineering and chemical design to biological systems. Biosafety professionals have done an excellent job in addressing research laboratory safety as synthetic biology and gene editing have emerged from the larger field of biotechnology. Despite these efforts, risks posed by synthetic biology are of increasing concern as research procedures scale up to industrial processes in the larger bioeconomy. A greater number and variety of workers will be exposed to commercial synthetic biology risks in the future, including risks to a variety of workers from the use of lentiviral vectors as gene transfer devices. There is a need to review and enhance current protection measures in the field of synthetic biology, whether in experimental laboratories where new advances are being researched, in health care settings where treatments using viral vectors as gene delivery systems are increasingly being used, or in the industrial bioeconomy. Enhanced worker protection measures should include increased injury and illness surveillance of the synthetic biology workforce; proactive risk assessment and management of synthetic biology products; research on the relative effectiveness of extrinsic and intrinsic biocontainment methods; specific safety guidance for synthetic biology industrial processes; determination of appropriate medical mitigation measures for lentiviral vector exposure incidents; and greater awareness and involvement in synthetic biology safety by the general occupational safety and health community as well as by government occupational safety and health research and regulatory agencies.
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Affiliation(s)
- John Howard
- a National Institute for Occupational Safety and Health , Washington, DC
| | - Vladimir Murashov
- a National Institute for Occupational Safety and Health , Washington, DC
| | - Paul Schulte
- a National Institute for Occupational Safety and Health , Washington, DC
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23
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Torres L, Krüger A, Csibra E, Gianni E, Pinheiro VB. Synthetic biology approaches to biological containment: pre-emptively tackling potential risks. Essays Biochem 2016; 60:393-410. [PMID: 27903826 PMCID: PMC5264511 DOI: 10.1042/ebc20160013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022]
Abstract
Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs.
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Affiliation(s)
- Leticia Torres
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - Antje Krüger
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Eszter Csibra
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Edoardo Gianni
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Vitor B Pinheiro
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
- Birkbeck, Department of Biological Sciences, University of London, Malet Street, WC1E 7HX, U.K
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24
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de Lorenzo V, Marlière P, Solé R. Bioremediation at a global scale: from the test tube to planet Earth. Microb Biotechnol 2016; 9:618-25. [PMID: 27489146 PMCID: PMC4993180 DOI: 10.1111/1751-7915.12399] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 12/19/2022] Open
Abstract
Planet Earth's biosphere has evolved over billions of years as a balanced bio‐geological system ultimately sustained by sunpower and the large‐scale cycling of elements largely run by the global environmental microbiome. Humans have been part of this picture for much of their existence. But the industrial revolution started in the XIX century and the subsequent advances in medicine, chemistry, agriculture and communications have impacted such balances to an unprecedented degree – and the problem has nothing but exacerbated in the last 20 years. Human overpopulation, industrial growth along with unsustainable use of natural resources have driven many sites and perhaps the planetary ecosystem as a whole, beyond recovery by spontaneous natural means, even if the immediate causes could be stopped. The most conspicuous indications of such a state of affairs include the massive change in land use, the accelerated increase in the levels of greenhouse gases, the frequent natural disasters associated to climate change and the growing non‐recyclable waste (e.g. plastics and recalcitrant chemicals) that we release to the Environment. While the whole planet is afflicted at a global scale by chemical pollution and anthropogenic emissions, the ongoing development of systems and synthetic biology, metagenomics, modern chemistry and some key concepts from ecological theory allow us to tackle this phenomenal challenge and propose large‐scale interventions aimed at reversing and even improving the situation. This involves (i) identification of key reactions or processes that need to be re‐established (or altogether created) for ecosystem reinstallation, (ii) implementation of such reactions in natural or designer hosts able to self‐replicate and deliver the corresponding activities when/where needed in a fashion guided by sound ecological modelling, (iii) dispersal of niche‐creating agents at a global scale and (iv) containment, monitoring and risk assessment of the whole process.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain
| | | | - Ricard Solé
- ICREA-Complex Systems Laboratory, Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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25
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Schmidt JC. Prospective Technology Assessment of Synthetic Biology: Fundamental and Propaedeutic Reflections in Order to Enable an Early Assessment. SCIENCE AND ENGINEERING ETHICS 2016; 22:1151-1170. [PMID: 26160061 DOI: 10.1007/s11948-015-9673-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
Synthetic biology is regarded as one of the key technosciences of the future. The goal of this paper is to present some fundamental considerations to enable procedures of a technology assessment (TA) of synthetic biology. To accomplish such an early "upstream" assessment of a not yet fully developed technology, a special type of TA will be considered: Prospective TA (ProTA). At the center of ProTA are the analysis and the framing of "synthetic biology," including a characterization and assessment of the technological core. The thesis is that if there is any differentia specifica giving substance to the umbrella term "synthetic biology," it is the idea of harnessing self-organization for engineering purposes. To underline that we are likely experiencing an epochal break in the ontology of technoscientific systems, this new type of technology is called "late-modern technology." -I start this paper by analyzing the three most common visions of synthetic biology. Then I argue that one particular vision deserves more attention because it underlies the others: the vision of self-organization. I discuss the inherent limits of this new type of late-modern technology in the attempt to control and monitor possible risk issues. I refer to Hans Jonas' ethics and his early anticipation of the risks of a novel type of technology. I end by drawing conclusions for the approach of ProTA towards an early societal shaping of synthetic biology.
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Affiliation(s)
- Jan Cornelius Schmidt
- Department of Social Sciences, Darmstadt University of Applied Sciences, Haardtring 100, 64295, Darmstadt, Germany.
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26
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Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements. Cell Syst 2016; 3:199-207. [PMID: 27426981 DOI: 10.1016/j.cels.2016.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 05/06/2016] [Accepted: 06/17/2016] [Indexed: 11/21/2022]
Abstract
Horizontally transferred genetic elements such as viruses and conjugative plasmids move DNA between organisms, increasing genetic diversity but destabilizing engineered biological systems. Here, we used a genomically recoded Escherichia coli strain lacking UAG stop codons and the recognition protein release factor 1 to study how an alternative genetic code influences horizontally transferred genetic element propagation. The alternative genetic code conferred resistance to multiple viruses (λ, M13, P1, MS2) at titers up to 10(11) PFU/ml and impaired conjugative plasmids (F and RK2) up to 10(5)-fold. By recoding UAG codons to UAA in viruses and plasmids, we restored viral infectivity and conjugative function. Propagating viruses on a mixed community of cells with standard and alternative genetic codes reduced viral titer, and over time viruses adapted to the alternative genetic code. This work demonstrates that altering the genetic code broadly obstructs the propagation of horizontally transferred genetic elements and supports the use of genomic recoding as a strategy to stabilize engineered biological systems.
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27
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Schmidt M, de Lorenzo V. Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms. Curr Opin Biotechnol 2016; 38:90-6. [PMID: 26874261 DOI: 10.1016/j.copbio.2016.01.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 12/14/2022]
Abstract
Synthetic Biology (SynBio) has brought up again questions on the environmental fate of microorganisms carrying genetic modifications. The growing capacity of editing genomes for deployment of man-made programs opens unprecedented biotechnological opportunities. But the same exacerbate concerns regarding fortuitous or deliberate releases to the natural medium. Most approaches to tackle these worries involve endowing SynBio agents with containment devices for halting horizontal gene transfer and survival of the live agents only at given times and places. Genetic circuits and trophic restraint schemes have been proposed to this end in the pursuit of complete containment. The most promising include adoption of alternative genetic codes and/or dependency on xenobiotic amino acids and nucleotides. But the field has to still overcome serious bottlenecks.
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Affiliation(s)
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain.
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28
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Abstract
Active containment systems are a major tool for reducing the uncertainty associated with the introduction of monocultures, genetically engineered or not, into target habitats for a large number of biotechnological applications (e.g., bioremediation, bioleaching, biopesticides, biofuels, biotransformations, live vaccines, etc.). While biological containment reduces the survival of the introduced organism outside the target habitat and/or upon completion of the projected task, gene containment strategies reduce the lateral spread of the key genetic determinants to indigenous microorganisms. In fundamental research, suicide circuits become relevant tools to address the role of gene transfer, mainly plasmid transfer, in evolution and how this transfer contributes to genome plasticity and to the rapid adaptation of microbial communities to environmental changes. Many lethal functions and regulatory circuits have been used and combined to design efficient containment systems. As many new genomes are being sequenced, novel lethal genes and regulatory elements are available, e.g., new toxin-antitoxin modules, and they could be used to increase further the current containment efficiencies and to expand containment to other organisms. Although the current containment systems can increase the predictability of genetically modified organisms in the environment, containment will never be absolute, due to the existence of mutations that lead to the appearance of surviving subpopulations. In this sense, orthogonal systems (xenobiology) appear to be the solution for setting a functional genetic firewall that will allow absolute containment of recombinant organisms.
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29
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Promising applications of synthetic biology – and how to avoid their potential pitfalls. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-658-10988-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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30
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Kato Y. An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system. PeerJ 2015; 3:e1247. [PMID: 26401457 PMCID: PMC4579030 DOI: 10.7717/peerj.1247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/27/2015] [Indexed: 12/31/2022] Open
Abstract
Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8) per 105 cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3.
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Affiliation(s)
- Yusuke Kato
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences , Tsukuba, Ibaraki , Japan
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31
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Affiliation(s)
- Kristin Hagen
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Margret Engelhard
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Georg Toepfer
- Center for Literary and Cultural Research Berlin, Berlin, Germany
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32
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Schindler D, Waldminghaus T. Synthetic chromosomes. FEMS Microbiol Rev 2015; 39:871-91. [DOI: 10.1093/femsre/fuv030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
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33
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34
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Ravikumar A, Liu CC. Biocontainment through Reengineered Genetic Codes. Chembiochem 2015; 16:1149-51. [DOI: 10.1002/cbic.201500157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Indexed: 11/10/2022]
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35
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Gallagher RR, Patel JR, Interiano AL, Rovner AJ, Isaacs FJ. Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Res 2015; 43:1945-54. [PMID: 25567985 PMCID: PMC4330353 DOI: 10.1093/nar/gku1378] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/20/2014] [Accepted: 12/20/2014] [Indexed: 12/29/2022] Open
Abstract
Genetically modified organisms (GMOs) are commonly used to produce valuable compounds in closed industrial systems. However, their emerging applications in open clinical or environmental settings require enhanced safety and security measures. Intrinsic biocontainment, the creation of bacterial hosts unable to survive in natural environments, remains a major unsolved biosafety problem. We developed a new biocontainment strategy containing overlapping 'safeguards'-engineered riboregulators that tightly control expression of essential genes, and an engineered addiction module based on nucleases that cleaves the host genome-to restrict viability of Escherichia coli cells to media containing exogenously supplied synthetic small molecules. These multilayered safeguards maintain robust growth in permissive conditions, eliminate persistence and limit escape frequencies to <1.3 × 10(-12). The staged approach to safeguard implementation revealed mechanisms of escape and enabled strategies to overcome them. Our safeguarding strategy is modular and employs conserved mechanisms that could be extended to clinically or industrially relevant organisms and undomesticated species.
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Affiliation(s)
- Ryan R Gallagher
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jaymin R Patel
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Alexander L Interiano
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Alexis J Rovner
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
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36
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Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ. Recoded organisms engineered to depend on synthetic amino acids. Nature 2015; 518:89-93. [PMID: 25607356 PMCID: PMC4590768 DOI: 10.1038/nature14095] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 11/17/2014] [Indexed: 01/21/2023]
Abstract
Genetically modified organisms (GMOs) are increasingly used in research and industrial systems to produce high-value pharmaceuticals, fuels, and chemicals1. Genetic isolation and intrinsic biocontainment would provide essential biosafety measures to secure these closed systems and enable safe applications of GMOs in open systems2,3, which include bioremediation4 and probiotics5. Although safeguards have been designed to control cell growth by essential gene regulation6, inducible toxin switches7, and engineered auxotrophies8, these approaches are compromised by cross-feeding of essential metabolites, leaked expression of essential genes, or genetic mutations9,10. Here, we describe the construction of a series of genomically recoded organisms (GROs)11 whose growth is restricted by the expression of multiple essential genes that depend on exogenously supplied synthetic amino acids (sAAs). We introduced a Methanocaldococcus jannaschii tRNA:aminoacyl-tRNA synthetase (aaRS) pair into the chromosome of a GRO that lacks all TAG codons and release factor 1, endowing this organism with the orthogonal translational components to convert TAG into a dedicated sense codon for sAAs. Using multiplex automated genome engineering (MAGE)12, we introduced in-frame TAG codons into 22 essential genes, linking their expression to the incorporation of synthetic phenylalanine-derived amino acids. Of the 60 sAA-dependent variants isolated, a notable strain harboring 3 TAG codons in conserved functional residues13 of MurG, DnaA and SerS and containing targeted tRNA deletions maintained robust growth and exhibited undetectable escape frequencies upon culturing ∼1011 cells on solid media for seven days or in liquid media for 20 days. This is a significant improvement over existing biocontainment approaches2,3,6-10. We constructed synthetic auxotrophs dependent on sAAs that were not rescued by cross-feeding in environmental growth assays. These auxotrophic GROs possess alternate genetic codes that impart genetic isolation by impeding horizontal gene transfer11 and now depend on the use of synthetic biochemical building blocks, advancing orthogonal barriers between engineered organisms and the environment.
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Affiliation(s)
- Alexis J Rovner
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Adrian D Haimovich
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Spencer R Katz
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Zhe Li
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Michael W Grome
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Brandon M Gassaway
- 1] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA [2] Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520, USA
| | - Miriam Amiram
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jaymin R Patel
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Ryan R Gallagher
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jesse Rinehart
- 1] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA [2] Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520, USA
| | - Farren J Isaacs
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
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37
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Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, Gregg CJ, Stoddard BL, Church GM. Biocontainment of genetically modified organisms by synthetic protein design. Nature 2015; 518:55-60. [PMID: 25607366 DOI: 10.1038/nature14121] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
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Affiliation(s)
- Daniel J Mandell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marc J Lajoie
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Program in Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Michael T Mee
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Ryo Takeuchi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Gleb Kuznetsov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Julie E Norville
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher J Gregg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - George M Church
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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38
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Synthetic Biology as Late-Modern Technology. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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39
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Abstract
Computational protein design, a process that searches for mutants with desired improved properties, plays a central role in the conception of many synthetic biology devices including biosensors, bioproduction, or regulation circuits. To that end, a rational workflow for computational protein design is described here consisting of (a) searching in the sequence, structure or chemical spaces for the desired function and associated protein templates; (b) finding the list of potential hot regions to mutate in the parent proteins; and (c) performing in silico screening of mutants with predicted improved properties.
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Guazzaroni ME, Silva-Rocha R, Ward RJ. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. Microb Biotechnol 2014; 8:52-64. [PMID: 25123225 PMCID: PMC4321373 DOI: 10.1111/1751-7915.12146] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/22/2014] [Accepted: 06/28/2014] [Indexed: 11/28/2022] Open
Abstract
There is a growing demand for enzymes with improved catalytic performance or tolerance to process-specific parameters, and biotechnology plays a crucial role in the development of biocatalysts for use in industry, agriculture, medicine and energy generation. Metagenomics takes advantage of the wealth of genetic and biochemical diversity present in the genomes of microorganisms found in environmental samples, and provides a set of new technologies directed towards screening for new catalytic activities from environmental samples with potential biotechnology applications. However, biased and low level of expression of heterologous proteins in Escherichia coli together with the use of non-optimal cloning vectors for the construction of metagenomic libraries generally results in an extremely low success rate for enzyme identification. The bottleneck arising from inefficient screening of enzymatic activities has been addressed from several perspectives; however, the limitations related to biased expression in heterologous hosts cannot be overcome by using a single approach, but rather requires the synergetic implementation of multiple methodologies. Here, we review some of the principal constraints regarding the discovery of new enzymes in metagenomic libraries and discuss how these might be resolved by using synthetic biology methods.
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Lan WS, Lu TK, Qin ZF, Shi XJ, Wang JJ, Hu YF, Chen B, Zhu YH, Liu Z. Genetically modified microorganism Spingomonas paucimobilis UT26 for simultaneously degradation of methyl-parathion and γ-hexachlorocyclohexane. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:840-850. [PMID: 24648032 DOI: 10.1007/s10646-014-1224-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/06/2014] [Indexed: 06/03/2023]
Abstract
Bioremediation of pesticide residues by bacteria is an efficient and environmentally friendly method to deal with environmental pollution. In this study, a genetically modified microorganism (GMM) named UT26XEGM was constructed by introducing a parathion hydrolase gene into an initially γ-hexachlorocyclohexane (γ-HCH) degrading bacterium Spingomonas paucimobilis UT26. In order to reduce its potential risk of gene escaping into the environment for the public concern on biosafety, a suicide system was also designed that did not interfere with the performance of the GMM until its physiological function was activated by specific signal. The system was designed with circuiting suicide cassettes consisting of killing genes gef and ecoRIR from Escherichia coli controlled by Pm promoter and the xylS gene. The cell viability and original degradation characteristics were not affected by the insertion of exogenous genes. The novel GMM was capable of degrading methyl-parathion and γ-HCH simultaneously. In laboratory scale testing, the recombinant bacteria were successfully applied to the bioremediation of mixed pesticide residues with the activity of self-destruction after 3-methylbenzoate induction.
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Affiliation(s)
- Wen S Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, Animal & Plant Inspection and Quarantine Technical Center, Shenzhen Entry-Exit Inspection and Quarantine Bureau, 1011 Fuqiang Road, Shenzhen, 518045, People's Republic of China,
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43
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Fesenko E, Edwards R. Plant synthetic biology: a new platform for industrial biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1927-37. [PMID: 24638901 DOI: 10.1093/jxb/eru070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Thirty years after the production of the first generation of genetically modified plants we are now set to move into a new era of recombinant crop technology through the application of synthetic biology to engineer new and complex input and output traits. The use of synthetic biology technologies will represent more than incremental additions of transgenes, but rather the directed design of completely new metabolic pathways, physiological traits, and developmental control strategies. The need to enhance our ability to improve crops through new engineering capability is now increasingly pressing as we turn to plants not just for food, but as a source of renewable feedstocks for industry. These accelerating and diversifying demands for new output traits coincide with a need to reduce inputs and improve agricultural sustainability. Faced with such challenges, existing technologies will need to be supplemented with new and far-more-directed approaches to turn valuable resources more efficiently into usable agricultural products. While these objectives are challenging enough, the use of synthetic biology in crop improvement will face public acceptance issues as a legacy of genetically modified technologies in many countries. Here we review some of the potential benefits of adopting synthetic biology approaches in improving plant input and output traits for their use as industrial chemical feedstocks, as linked to the rapidly developing biorefining industry. Several promising technologies and biotechnological targets are identified along with some of the key regulatory and societal challenges in the safe and acceptable introduction of such technology.
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Affiliation(s)
- Elena Fesenko
- Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK
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Abstract
Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.
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Affiliation(s)
- Christina M. Agapakis
- Department of Molecular,
Cell and Developmental Biology and Art
- Science Center, University of California, Los Angeles, Los Angeles, California 90095, United States of America
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Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ. Genomically recoded organisms expand biological functions. Science 2013; 342:357-60. [PMID: 24136966 PMCID: PMC4924538 DOI: 10.1126/science.1241459] [Citation(s) in RCA: 600] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We describe the construction and characterization of a genomically recoded organism (GRO). We replaced all known UAG stop codons in Escherichia coli MG1655 with synonymous UAA codons, which permitted the deletion of release factor 1 and reassignment of UAG translation function. This GRO exhibited improved properties for incorporation of nonstandard amino acids that expand the chemical diversity of proteins in vivo. The GRO also exhibited increased resistance to T7 bacteriophage, demonstrating that new genetic codes could enable increased viral resistance.
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Affiliation(s)
- Marc J. Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexis J. Rovner
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daniel B. Goodman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical Engineering and Medical Physics, Harvard–Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - Adrian D. Haimovich
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Gleb Kuznetsov
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Harris H. Wang
- Department of Systems Biology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Joshua A. Mosberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph M. Jacobson
- Center for Bits and Atoms, MIT, Cambridge, MA 02139, USA
- MIT Media Lab, MIT, Cambridge, MA 02139, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
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46
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Wright O, Stan GB, Ellis T. Building-in biosafety for synthetic biology. Microbiology (Reading) 2013; 159:1221-1235. [DOI: 10.1099/mic.0.066308-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Oliver Wright
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
| | - Guy-Bart Stan
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
| | - Tom Ellis
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
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47
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Moe-Behrens GHG, Davis R, Haynes KA. Preparing synthetic biology for the world. Front Microbiol 2013; 4:5. [PMID: 23355834 PMCID: PMC3554958 DOI: 10.3389/fmicb.2013.00005] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/04/2013] [Indexed: 11/21/2022] Open
Abstract
Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or “living devices.” As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety.
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48
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Guan ZJ, Schmidt M, Pei L, Wei W, Ma KP. Biosafety Considerations of Synthetic Biology in the International Genetically Engineered Machine (iGEM) Competition. Bioscience 2013. [DOI: 10.1525/bio.2013.63.1.7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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49
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From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 2012; 29:273-9. [PMID: 23219343 PMCID: PMC3642372 DOI: 10.1016/j.tig.2012.11.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 10/14/2012] [Accepted: 11/01/2012] [Indexed: 11/21/2022]
Abstract
A central undertaking in synthetic biology (SB) is the quest for the 'minimal genome'. However, 'minimal sets' of essential genes are strongly context-dependent and, in all prokaryotic genomes sequenced to date, not a single protein-coding gene is entirely conserved. Furthermore, a lack of consensus in the field as to what attributes make a gene truly essential adds another aspect of variation. Thus, a universal minimal genome remains elusive. Here, as an alternative to defining a minimal genome, we propose that the concept of gene persistence can be used to classify genes needed for robust long-term survival. Persistent genes, although not ubiquitous, are conserved in a majority of genomes, tend to be expressed at high levels, and are frequently located on the leading DNA strand. These criteria impose constraints on genome organization, and these are important considerations for engineering cells and for creating cellular life-like forms in SB.
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50
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Abstract
In the past decade, systems biology has revealed great metabolic and regulatory complexity even in seemingly simple microbial systems. Metabolic engineering aims to control this complexity in order to establish sustainable and economically viable production routes for valuable chemicals. Recent advances in systems-level data generation and modeling of cellular metabolism and regulation together with tremendous progress in synthetic biology will provide the tools to put biotechnologists on the fast track for implementing novel production processes. Great potential lies in the reduction of cellular complexity by orthogonalization of metabolic modules. Here, we review recent advances that will eventually enable metabolic engineers to predict, design, and build streamlined microbial cell factories with reduced time and effort.
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Affiliation(s)
- Joerg Mampel
- B.R.A.I.N. AG (Biotechnology Research and Information Network), Darmstaedter Strasse 34-36, D-64673 Zwingenberg, Germany.
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