1
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Salgado S, Hernández‐Herreros N, Prieto MA. Controlling the expression of heterologous genes in Bdellovibrio bacteriovorus using synthetic biology strategies. Microb Biotechnol 2024; 17:e14517. [PMID: 38934530 PMCID: PMC11209729 DOI: 10.1111/1751-7915.14517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Bdellovibrio bacteriovorus HD100 is an obligate predatory bacterium that preys upon Gram-negative bacteria. It has been proposed to be applied as a "living antibiotic" in several fields such as agriculture or even medicine, since it is able to prey upon bacterial pathogens. Its interesting lifestyle makes this bacterium very attractive as a microbial chassis for co-culture systems including two partners. A limitation to this goal is the scarcity of suitable synthetic biology tools for predator domestication. To fill this gap, we have firstly adapted the hierarchical assembly cloning technique Golden Standard (GS) to make it compatible with B. bacteriovorus HD100. The chromosomal integration of the Tn7 transposon's mobile element, in conjunction with the application of the GS technique, has allowed the systematic characterization of a repertoire of constitutive and inducible promoters, facilitating the control of the expression of heterologous genes in this bacterium. PJExD/EliR proved to be an exceptional promoter/regulator system in B. bacteriovorus HD100 when precise regulation is essential, while the synthetic promoter PBG37 showed a constitutive high expression. These genetic tools represent a step forward in the conversion of B. bacteriovorus into an amenable strain for microbial biotechnology approaches.
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Affiliation(s)
- Sergio Salgado
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyPolymer Biotechnology Group, Margarita Salas Center for Biological Research (CIB‐CSIC)MadridSpain
| | - Natalia Hernández‐Herreros
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyPolymer Biotechnology Group, Margarita Salas Center for Biological Research (CIB‐CSIC)MadridSpain
| | - M. Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyPolymer Biotechnology Group, Margarita Salas Center for Biological Research (CIB‐CSIC)MadridSpain
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2
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Trofimova E, Logel DY, Jaschke PR. An Improved Method for Eliminating or Creating Intragenic Bacterial Promoters. Methods Mol Biol 2024; 2760:199-207. [PMID: 38468090 DOI: 10.1007/978-1-0716-3658-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Recent advances in genomic refactoring have been hindered by the ever-present complication of internal or cryptic transcriptional regulation. Typical approaches to these features have been to randomize or perform mass alterations to the gene sequences thought to contain the regulatory motifs; however, this approach can cause problems by altering translational speeds, introducing long distance DNA-DNA interaction effects, and inducing RNA toxicity. Previously, we developed a rational design approach named COdon Restrained Promoter SilEncing (CORPSE) which takes externally identified promoter sequences and uses position-specific scoring matrices as proxy promoter strengths to make minimal changes to promoter sequences to disable their activity. Additionally, through inverting our system we were also able to modify weak internal promoters to increase their activity. In this chapter, we augment our previous process with the biophysical model Promoter Calculator v1.0 developed by LaFleur et al. to combine promoter identification and activity prediction, with our algorithm to silently modify promoter sequences, to provide more robust promoter elimination and creation.
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Affiliation(s)
- Ellina Trofimova
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
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3
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Demeester W, De Baets J, Duchi D, De Mey M, De Paepe B. MoBioS: Modular Platform Technology for High-Throughput Construction and Characterization of Tunable Transcriptional Biological Sensors. BIOSENSORS 2023; 13:590. [PMID: 37366955 DOI: 10.3390/bios13060590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
All living organisms have evolved and fine-tuned specialized mechanisms to precisely monitor a vast array of different types of molecules. These natural mechanisms can be sourced by researchers to build Biological Sensors (BioS) by combining them with an easily measurable output, such as fluorescence. Because they are genetically encoded, BioS are cheap, fast, sustainable, portable, self-generating and highly sensitive and specific. Therefore, BioS hold the potential to become key enabling tools that stimulate innovation and scientific exploration in various disciplines. However, the main bottleneck in unlocking the full potential of BioS is the fact that there is no standardized, efficient and tunable platform available for the high-throughput construction and characterization of biosensors. Therefore, a modular, Golden Gate-based construction platform, called MoBioS, is introduced in this article. It allows for the fast and easy creation of transcription factor-based biosensor plasmids. As a proof of concept, its potential is demonstrated by creating eight different, functional and standardized biosensors that detect eight diverse molecules of industrial interest. In addition, the platform contains novel built-in features to facilitate fast and efficient biosensor engineering and response curve tuning.
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Affiliation(s)
- Wouter Demeester
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Jasmine De Baets
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Dries Duchi
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Brecht De Paepe
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
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4
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A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae. Synth Syst Biotechnol 2022; 7:657-663. [PMID: 35224233 PMCID: PMC8857431 DOI: 10.1016/j.synbio.2022.02.001] [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: 10/31/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/22/2022] Open
Abstract
The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.
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5
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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] [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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6
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Logel DY, Trofimova E, Jaschke PR. Codon-Restrained Method for Both Eliminating and Creating Intragenic Bacterial Promoters. ACS Synth Biol 2022; 11:689-699. [PMID: 35043622 DOI: 10.1021/acssynbio.1c00359] [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: 11/28/2022]
Abstract
Future applications of synthetic biology will require refactored genetic sequences devoid of internal regulatory elements within coding sequences. These regulatory elements include cryptic and intragenic promoters, which may constitute up to a third of the predicted Escherichia coli promoters. The promoter activity is dependent on the structural interaction of core bases with a σ factor. Rational engineering can be used to alter key promoter element nucleotides interacting with σ factors and eliminate downstream transcriptional activity. In this paper, we present codon-restrained promoter silencing (CORPSE), a system for removing intragenic promoters. CORPSE exploits the DNA-σ factor structural relationship to disrupt σ70 promoters embedded within gene coding sequences with a minimum of synonymous codon changes. Additionally, we present an inverted CORPSE system, iCORPSE, which can create highly active promoters within a gene sequence while not perturbing the function of the modified gene.
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Affiliation(s)
- Dominic Y. Logel
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2109, New South Wales, Australia
| | - Ellina Trofimova
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2109, New South Wales, Australia
| | - Paul R. Jaschke
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2109, New South Wales, Australia
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7
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Garagounis C, Delkis N, Papadopoulou KK. Unraveling the roles of plant specialized metabolites: using synthetic biology to design molecular biosensors. THE NEW PHYTOLOGIST 2021; 231:1338-1352. [PMID: 33997999 DOI: 10.1111/nph.17470] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 05/25/2023]
Abstract
Plants are a rich source of specialized metabolites with a broad range of bioactivities and many applications in human daily life. Over the past decades significant progress has been made in identifying many such metabolites in different plant species and in elucidating their biosynthetic pathways. However, the biological roles of plant specialized metabolites remain elusive and proposed functions lack an identified underlying molecular mechanism. Understanding the roles of specialized metabolites frequently is hampered by their dynamic production and their specific spatiotemporal accumulation within plant tissues and organs throughout a plant's life cycle. In this review, we propose the employment of strategies from the field of Synthetic Biology to construct and optimize genetically encoded biosensors that can detect individual specialized metabolites in a standardized and high-throughput manner. This will help determine the precise localization of specialized metabolites at the tissue and single-cell levels. Such information will be useful in developing complete system-level models of specialized plant metabolism, which ultimately will demonstrate how the biosynthesis of specialized metabolites is integrated with the core processes of plant growth and development.
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Affiliation(s)
- Constantine Garagounis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Nikolaos Delkis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
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8
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Roy S, Radivojevic T, Forrer M, Marti JM, Jonnalagadda V, Backman T, Morrell W, Plahar H, Kim J, Hillson N, Garcia Martin H. Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering. Front Bioeng Biotechnol 2021; 9:612893. [PMID: 33634086 PMCID: PMC7902046 DOI: 10.3389/fbioe.2021.612893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Biology has changed radically in the past two decades, growing from a purely descriptive science into also a design science. The availability of tools that enable the precise modification of cells, as well as the ability to collect large amounts of multimodal data, open the possibility of sophisticated bioengineering to produce fuels, specialty and commodity chemicals, materials, and other renewable bioproducts. However, despite new tools and exponentially increasing data volumes, synthetic biology cannot yet fulfill its true potential due to our inability to predict the behavior of biological systems. Here, we showcase a set of computational tools that, combined, provide the ability to store, visualize, and leverage multiomics data to predict the outcome of bioengineering efforts. We show how to upload, visualize, and output multiomics data, as well as strain information, into online repositories for several isoprenol-producing strain designs. We then use these data to train machine learning algorithms that recommend new strain designs that are correctly predicted to improve isoprenol production by 23%. This demonstration is done by using synthetic data, as provided by a novel library, that can produce credible multiomics data for testing algorithms and computational tools. In short, this paper provides a step-by-step tutorial to leverage these computational tools to improve production in bioengineered strains.
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Affiliation(s)
- Somtirtha Roy
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States
| | - Tijana Radivojevic
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Mark Forrer
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States.,Sandia National Laboratories, Biomaterials and Biomanufacturing, Livermore, CA, United States
| | - Jose Manuel Marti
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Vamshi Jonnalagadda
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States
| | - Tyler Backman
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - William Morrell
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States.,Sandia National Laboratories, Biomaterials and Biomanufacturing, Livermore, CA, United States
| | - Hector Plahar
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, United States.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nathan Hillson
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Hector Garcia Martin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States.,BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
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10
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Tas H, Amara A, Cueva ME, Bongaerts N, Calvo‐Villamañán A, Hamadache S, Vavitsas K. Are synthetic biology standards applicable in everyday research practice? Microb Biotechnol 2020; 13:1304-1308. [PMID: 32567248 PMCID: PMC7415368 DOI: 10.1111/1751-7915.13612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/30/2020] [Indexed: 12/27/2022] Open
Abstract
The issue of standardization in synthetic biology is a recurring one. As a discipline that incorporates engineering principles into biological designs, synthetic biology needs effective ways to communicate results and allow different researchers (both academic and industrial) to build upon previous results and improve on existing designs. An aspect that is left out of the discussions, especially when they happen at the level of academic and industrial consortia or policymaking, is whether or not standards are applicable or even useful in everyday research practice. In this caucus article, we examine this particular issue with the hope of including it in the standardization discussions agenda and provide insights into a topic that synthetic biology researchers experience daily.
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Affiliation(s)
- Huseyin Tas
- Systems and Synthetic Biology ProgramSpanish National Center for Biotechnology (CNB‐CSIC)MadridSpain
| | - Adam Amara
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterUK
| | - Miguel E. Cueva
- SynthSys, CSEC and School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Nadine Bongaerts
- Center for Research and Interdisciplinarity (CRI)Université de ParisINSERM U1284ParisFrance
| | | | - Samir Hamadache
- Department of BiochemistrySchulich School of Medicine and DentistryWestern UniversityLondonONCanada
| | - Konstantinos Vavitsas
- Department of BiologyNational and Kapodistrian University of AthensPanepistimioupolisAthens15784Greece
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11
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Vazquez‐Vilar M, Gandía M, García‐Carpintero V, Marqués E, Sarrion‐Perdigones A, Yenush L, Polaina J, Manzanares P, Marcos JF, Orzaez D. Multigene Engineering by GoldenBraid Cloning: From Plants to Filamentous Fungi and Beyond. ACTA ACUST UNITED AC 2020; 130:e116. [DOI: 10.1002/cpmb.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Mónica Gandía
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Victor García‐Carpintero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Eric Marqués
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | | | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Julio Polaina
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Paloma Manzanares
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Jose F. Marcos
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
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12
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Belén Paredes M, Eugenia Sulen M. An overview of synthetic biology. BIONATURA 2020. [DOI: 10.21931/rb/2020.05.01.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Synthetic Biology is the combination of basic sciences with engineering. The aim of Synthetic Biology is to create, design, and redesign biological systems and devices to understand biological processes and to achieve useful and sophisticated functionalities to improve human welfare. When the engineering community took part in the discussion for the definition of Synthetic Biology, the idea of extraction and reassembly of “biological parts” along with the principles of abstraction, modularity, and standardization was introduced. Genetic Engineering is one of the many essential tools for synthetic biology, and even though they share the DNA manipulation basis and approach to intervene in the complexity of molecular biology, they differ in many aspects, and the two terms should not be used interchangeably. Some of the applications that have already been done by Synthetic Biology include the production of 1,4-butanediol (BDO), the antimalarial drug artemisinin, and the anticancer compound taxol. The potential of Synthetic Biology to design new genomes without immediate biological ancestry has raised ontological, political, economic, and ethical concerns based on the possibility that synthetic biology may be intrinsically unethical.
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13
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Kelly CL, Harris AWK, Steel H, Hancock EJ, Heap JT, Papachristodoulou A. Synthetic negative feedback circuits using engineered small RNAs. Nucleic Acids Res 2019; 46:9875-9889. [PMID: 30212900 PMCID: PMC6182179 DOI: 10.1093/nar/gky828] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
Negative feedback is known to enable biological and man-made systems to perform reliably in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have primarily relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA molecules that can inhibit translation of target messenger RNAs (mRNAs). In this work, we modelled, built and validated two synthetic negative feedback circuits that use rationally-designed sRNAs for the first time. The first circuit builds upon the well characterised tet-based autorepressor, incorporating an externally-inducible sRNA to tune the effective feedback strength. This allows more precise fine-tuning of the circuit output in contrast to the sigmoidal, steep input–output response of the autorepressor alone. In the second circuit, the output is a transcription factor that induces expression of an sRNA, which inhibits translation of the mRNA encoding the output, creating direct, closed-loop, negative feedback. Analysis of the noise profiles of both circuits showed that the use of sRNAs did not result in large increases in noise. Stochastic and deterministic modelling of both circuits agreed well with experimental data. Finally, simulations using fitted parameters allowed dynamic attributes of each circuit such as response time and disturbance rejection to be investigated.
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Affiliation(s)
- Ciarán L Kelly
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK.,Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Andreas W K Harris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Edward J Hancock
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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14
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Vecchioni S, Capece MC, Toomey E, Nguyen L, Ray A, Greenberg A, Fujishima K, Urbina J, Paulino-Lima IG, Pinheiro V, Shih J, Wessel G, Wind SJ, Rothschild L. Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology. Sci Rep 2019; 9:6942. [PMID: 31061396 PMCID: PMC6502794 DOI: 10.1038/s41598-019-43316-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/25/2019] [Indexed: 12/28/2022] Open
Abstract
DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag+-mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag+-C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11-50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag+-C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.
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Affiliation(s)
- Simon Vecchioni
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
| | - Mark C Capece
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Emily Toomey
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Le Nguyen
- School of Engineering, Brown University, Providence, RI, 02912, USA
| | - Austin Ray
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alissa Greenberg
- Department of History, Stanford University, Stanford, CA, 94305, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Jesica Urbina
- Geology, Minerals, Energy, & Geophysics Science Center, U.S. Geological Survey, Menlo Park, CA, 94025, USA
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Ivan G Paulino-Lima
- Blue Marble Space Institute of Science, NASA Ames Research Center, Planetary Systems Branch, Moffett Field, CA, 94035-0001, USA
| | - Vitor Pinheiro
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Joseph Shih
- Department of Natural Sciences and Mathematics, University of Saint Mary, Leavenworth, KS, 66048, USA
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA
| | - Lynn Rothschild
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA.
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Davies JA. Real-World Synthetic Biology: Is It Founded on an Engineering Approach, and Should It Be? Life (Basel) 2019; 9:life9010006. [PMID: 30621107 PMCID: PMC6463249 DOI: 10.3390/life9010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/20/2018] [Accepted: 12/29/2018] [Indexed: 12/22/2022] Open
Abstract
Authors often assert that a key feature of 21st-century synthetic biology is its use of an 'engineering approach'; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey of synthetic biology projects that have reached, or are near to, commercial application outside laboratories shows that they showed very few of these attributes. Instead, they featured much trial and error, and the use of specialized, custom components and assays. What is more, consideration of the special features of living systems suggest that a conventional engineering approach will often not be helpful. The article concludes that the engineering approach may be useful in some projects, but it should not be used to define or constrain synthetic biological endeavour, and that in fact the conventional engineering has more to gain by expanding and embracing more biological ways of working.
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Affiliation(s)
- Jamie A Davies
- UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK.
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16
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Vazquez-Vilar M, Orzaez D, Patron N. DNA assembly standards: Setting the low-level programming code for plant biotechnology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:33-41. [PMID: 29907307 DOI: 10.1016/j.plantsci.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Synthetic Biology is defined as the application of engineering principles to biology. It aims to increase the speed, ease and predictability with which desirable changes and novel traits can be conferred to living cells. The initial steps in this process aim to simplify the encoding of new instructions in DNA by establishing low-level programming languages for biology. Together with advances in the laboratory that allow multiple DNA molecules to be efficiently assembled together into a desired order in a single step, this approach has simplified the design and assembly of multigene constructs and has even facilitated the automated construction of synthetic chromosomes. These advances and technologies are now being applied to plants, for which there are a growing number of software and wetware tools for the design, construction and delivery of DNA molecules and for the engineering of endogenous genes. Here we review the efforts of the past decade that have established synthetic biology workflows and tools for plants and discuss the constraints and bottlenecks of this emerging field.
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Affiliation(s)
- Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Spain.
| | - Nicola Patron
- Department of Engineering Biology, The Earlham Institute, Norwich Research Park, Norfolk, NR1 7UZ, UK.
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17
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Borg Y, Grigonyte AM, Boeing P, Wolfenden B, Smith P, Beaufoy W, Rose S, Ratisai T, Zaikin A, Nesbeth DN. Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering. PeerJ 2016; 4:e2031. [PMID: 27441104 PMCID: PMC4941783 DOI: 10.7717/peerj.2031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/20/2016] [Indexed: 11/20/2022] Open
Abstract
Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists' efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15-20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global 'do-it-yourself' research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrick(TM) standard and finally, (iii) that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools. Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrick(TM) formatted plasmid. Results. All species were stable over 11 weeks of glycerol cryopreservation, sensitive to 17 µg/mL chloramphenicol and resistant to transformation using the conditions and plasmids tested. An incubator-shaker device, 'UCLHack-12' was assembled and used to cultivate sufficient quantity of Oceanobulbus indolifexcells to enable isolation of the anf1 gene and its subcloning into a plasmid to generate the BioBrick(TM) BBa_K729016. Conclusion.The process of 'de-skilling' biomolecular techniques, particularly for relatively under-investigated organisms, is still on-going. However, our successful cell growth and DNA manipulation experiments serve to indicate the types of capabilities that are now available to citizen scientists. Science democratised in this way can make a positive contribution to the debate around the use of bio-geoengineering to address oceanic pollution or climate change.
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Affiliation(s)
- Yanika Borg
- Department of Biochemical Engineering, University College London, United Kingdom.,Department of Mathematics, University College London, London, United Kingdom
| | | | | | | | | | | | - Simon Rose
- London BioHackspace, London, United Kingdom
| | | | - Alexey Zaikin
- Department of Mathematics, University College London, London, United Kingdom.,Institute for Women's Health, University College London, London, United Kingdom
| | - Darren N Nesbeth
- Department of Biochemical Engineering, University College London, United Kingdom
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18
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Templar A, Woodhouse S, Keshavarz-Moore E, Nesbeth DN. Influence of Pichia pastoris cellular material on polymerase chain reaction performance as a synthetic biology standard for genome monitoring. J Microbiol Methods 2016; 127:111-122. [PMID: 27211507 DOI: 10.1016/j.mimet.2016.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 05/09/2016] [Accepted: 05/16/2016] [Indexed: 02/08/2023]
Abstract
Advances in synthetic genomics are now well underway in yeasts due to the low cost of synthetic DNA. These new capabilities also bring greater need for quantitating the presence, loss and rearrangement of loci within synthetic yeast genomes. Methods for achieving this will ideally; i) be robust to industrial settings, ii) adhere to a global standard and iii) be sufficiently rapid to enable at-line monitoring during cell growth. The methylotrophic yeast Pichia pastoris (P. pastoris) is increasingly used for industrial production of biotherapeutic proteins so we sought to answer the following questions for this particular yeast species. Is time-consuming DNA purification necessary to obtain accurate end-point polymerase chain reaction (e-pPCR) and quantitative PCR (qPCR) data? Can the novel linear regression of efficiency qPCR method (LRE qPCR), which has properties desirable in a synthetic biology standard, match the accuracy of conventional qPCR? Does cell cultivation scale influence PCR performance? To answer these questions we performed e-pPCR and qPCR in the presence and absence of cellular material disrupted by a mild 30s sonication procedure. The e-pPCR limit of detection (LOD) for a genomic target locus was 50pg (4.91×10(3) copies) of purified genomic DNA (gDNA) but the presence of cellular material reduced this sensitivity sixfold to 300pg gDNA (2.95×10(4) copies). LRE qPCR matched the accuracy of a conventional standard curve qPCR method. The presence of material from bioreactor cultivation of up to OD600=80 did not significantly compromise the accuracy of LRE qPCR. We conclude that a simple and rapid cell disruption step is sufficient to render P. pastoris samples of up to OD600=80 amenable to analysis using LRE qPCR which we propose as a synthetic biology standard.
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Affiliation(s)
- Alexander Templar
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, United Kingdom
| | - Stefan Woodhouse
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, United Kingdom
| | - Eli Keshavarz-Moore
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, United Kingdom
| | - Darren N Nesbeth
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, United Kingdom.
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19
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Kelwick R, Bowater L, Yeoman KH, Bowater RP. Promoting microbiology education through the iGEM synthetic biology competition. FEMS Microbiol Lett 2015; 362:fnv129. [DOI: 10.1093/femsle/fnv129] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2015] [Indexed: 12/14/2022] Open
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20
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Kushwaha M, Salis HM. A portable expression resource for engineering cross-species genetic circuits and pathways. Nat Commun 2015; 6:7832. [PMID: 26184393 PMCID: PMC4518296 DOI: 10.1038/ncomms8832] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/16/2015] [Indexed: 12/24/2022] Open
Abstract
Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology and metabolic engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables circuits and pathways to reuse the same genetic parts, while functioning similarly across diverse organisms. Our engineered system combines mixed feedback control loops and cross-species translation signals to autonomously self-regulate expression of an orthogonal polymerase without host-specific promoters, achieving nontoxic and tuneable gene expression in diverse Gram-positive and Gram-negative bacteria. Combining 50 characterized system variants with mechanistic modelling, we show how the cross-species expression resource's dynamics, capacity and toxicity are controlled by the control loops' architecture and feedback strengths. We also demonstrate one application of the resource by reusing the same genetic parts to express a biosynthesis pathway in both model and non-model hosts. Organism-specific genetic parts are often used to express circuits and pathways, limiting their portability. Here the authors engineer a cross-species expression resource, without using host-specific parts, to control protein and pathway expression in non-model bacteria.
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Affiliation(s)
- Manish Kushwaha
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard M Salis
- 1] Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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21
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Software-assisted stacking of gene modules using GoldenBraid 2.0 DNA-assembly framework. Methods Mol Biol 2015; 1284:399-420. [PMID: 25757784 DOI: 10.1007/978-1-4939-2444-8_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GoldenBraid (GB) is a modular DNA assembly technology for plant multigene engineering based on type IIS restriction enzymes. GB speeds up the assembly of transcriptional units from standard genetic parts and facilitates the stacking of several genes within the same T-DNA in few days. GBcloning is software-assisted with a set of online tools. The GBDomesticator tool assists in the adaptation of DNA parts to the GBstandard. The combination of GB-adapted parts to build new transcriptional units is assisted by the GB TU Assembler tool. Finally, the assembly of multigene modules is simulated by the GB Binary Assembler. All the software tools are available at www.gbcloning.org . Here, we describe in detail the assembly methodology to create a multigene construct with three transcriptional units for polyphenol metabolic engineering in plants.
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22
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Patil M, Dhar PK. A Brief Introduction to Synthetic Biology. SYSTEMS AND SYNTHETIC BIOLOGY 2015. [DOI: 10.1007/978-94-017-9514-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol 2014; 2:61. [PMID: 25538939 PMCID: PMC4259112 DOI: 10.3389/fbioe.2014.00061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/14/2014] [Indexed: 11/17/2022] Open
Abstract
Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology.
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Affiliation(s)
- Andreas Dräger
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Cognitive Systems, Center for Bioinformatics Tübingen (ZBIT), Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
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24
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Mustard J, Levin M. Bioelectrical Mechanisms for Programming Growth and Form: Taming Physiological Networks for Soft Body Robotics. Soft Robot 2014. [DOI: 10.1089/soro.2014.0011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Jessica Mustard
- Department of Biology and Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts
| | - Michael Levin
- Department of Biology and Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts
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25
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Radeck J, Kraft K, Bartels J, Cikovic T, Dürr F, Emenegger J, Kelterborn S, Sauer C, Fritz G, Gebhard S, Mascher T. The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis. J Biol Eng 2013; 7:29. [PMID: 24295448 PMCID: PMC4177231 DOI: 10.1186/1754-1611-7-29] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/12/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Standardized and well-characterized genetic building blocks are a prerequisite for the convenient and reproducible assembly of novel genetic modules and devices. While numerous standardized parts exist for Escherichia coli, such tools are still missing for the Gram-positive model organism Bacillus subtilis. The goal of this study was to develop and thoroughly evaluate such a genetic toolbox. RESULTS We developed five BioBrick-compatible integrative B. subtilis vectors by deleting unnecessary parts and removing forbidden restriction sites to allow cloning in BioBrick (RFC10) standard. Three empty backbone vectors with compatible resistance markers and integration sites were generated, allowing the stable chromosomal integration and combination of up to three different devices in one strain. In addition, two integrative reporter vectors, based on the lacZ and luxABCDE cassettes, were BioBrick-adjusted, to enable β-galactosidase and luciferase reporter assays, respectively. Four constitutive and two inducible promoters were thoroughly characterized by quantitative, time-resolved measurements. Together, these promoters cover a range of more than three orders of magnitude in promoter strength, thereby allowing a fine-tuned adjustment of cellular protein amounts. Finally, the Bacillus BioBrick Box also provides five widely used epitope tags (FLAG, His10, cMyc, HA, StrepII), which can be translationally fused N- or C-terminally to any protein of choice. CONCLUSION Our genetic toolbox contains three compatible empty integration vectors, two reporter vectors and a set of six promoters, two of them inducible. Furthermore, five different epitope tags offer convenient protein handling and detection. All parts adhere to the BioBrick standard and hence enable standardized work with B. subtilis. We believe that our well-documented and carefully evaluated Bacillus BioBrick Box represents a very useful genetic tool kit, not only for the iGEM competition but any other BioBrick-based project in B. subtilis.
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Affiliation(s)
- Jara Radeck
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Korinna Kraft
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Julia Bartels
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Tamara Cikovic
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Franziska Dürr
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Jennifer Emenegger
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Simon Kelterborn
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Christopher Sauer
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany.,Present affiliation: Institute of Cell and Molecular Biosciences, Newcastle University, Centre for Bacterial Cell Biology, Richardson Road, NE2 4AX Newcastle upon Tyne, UK
| | - Georg Fritz
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany.,Ludwig-Maximilians-University Munich, Arnold Sommerfeld Center for Theoretical Physics, Theresienstr. 37, D-80333 München, Germany
| | - Susanne Gebhard
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Thorsten Mascher
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
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Porcar M, Latorre A, Moya A. What Symbionts Teach us about Modularity. Front Bioeng Biotechnol 2013; 1:14. [PMID: 25023877 PMCID: PMC4090905 DOI: 10.3389/fbioe.2013.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/22/2013] [Indexed: 11/13/2022] Open
Abstract
The main goal of Synthetic Biology (SB) is to apply engineering principles to biotechnology in order to make life easier to engineer. These engineering principles include modularity: decoupling of complex systems into smaller, orthogonal sub-systems that can be used in a range of different applications. The successful use of modules in engineering is expected to be reproduced in synthetic biological systems. But the difficulties experienced up to date with SB approaches question the short-term feasibility of designing life. Considering the “engineerable” nature of life, here we discuss the existence of modularity in natural living systems, particularly in symbiotic interactions, and compare the behavior of such systems, with those of engineered modules. We conclude that not only is modularity present but it is also common among living structures, and that symbioses are a new example of module-like sub-systems having high similarity with modularly designed ones. However, we also detect and stress fundamental differences between man-made and biological modules. Both similarities and differences should be taken into account in order to adapt SB design to biological laws.
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Affiliation(s)
- Manuel Porcar
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Fundació General de la Universitat de València , València , Spain
| | - Amparo Latorre
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - Salud Pública , València , Spain
| | - Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - Salud Pública , València , Spain
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27
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Systems metabolic engineering in an industrial setting. Appl Microbiol Biotechnol 2013; 97:2319-26. [DOI: 10.1007/s00253-013-4738-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
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Abstract
Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. We highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of microbial ecosystem engineering. We argue that simply engineering individual microbes will lead to fragile homogenous populations that are difficult to sustain, especially in highly heterogeneous and unpredictable environments. Instead, engineered microbial ecosystems are likely to be more robust and able to achieve complex tasks at the spatial and temporal resolution needed for truly programmable biology.
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Affiliation(s)
- Michael T Mee
- Department of Biomedical Engineering, Boston University, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Harris H Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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