1
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De Wannemaeker L, Mey F, Bervoets I, Ver Cruysse M, Baldwin GS, De Mey M. Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum. ACS Synth Biol 2023; 12:3591-3607. [PMID: 37981737 PMCID: PMC10729763 DOI: 10.1021/acssynbio.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/21/2023]
Abstract
In synthetic biology, Fluorescent reporters are frequently used to characterize the expression levels obtained from both genetic parts such as promoters and ribosome binding sites as well as from complex genetic circuits. To this end, plate readers offer an easy and high-throughput way of characterizing both the growth and fluorescence expression levels of cell cultures. However, despite the similar mode of action used in different devices, their output is not comparable due to intrinsic differences in their setup. Additionally, the generated output is expressed using arbitrary units, limiting reliable comparison of results to measurements taken within one single experiment using one specific plate reader, hampering the transferability of data across different plate readers and laboratories. This article presents an easy and accessible calibration method for transforming the device-specific output into a standardized output expressing the amount of fluorescence per well as a known equivalent fluorophore concentration per cell for fluorescent reporters spanning the visible light spectrum. This calibration method follows a 2-fold approach determining both the estimated number of cells and the equivalent chemical fluorophore concentration per well. It will contribute to the comparison of plate reader experiments between different laboratories across the world and will therefore greatly improve the reliability and exchange of both results and genetic parts between research groups.
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Affiliation(s)
- Lien De Wannemaeker
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Friederike Mey
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije
Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Michiel Ver Cruysse
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Geoff S. Baldwin
- Imperial
College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - Marjan De Mey
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
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2
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Lux MW, Strychalski EA, Vora GJ. Advancing reproducibility can ease the 'hard truths' of synthetic biology. Synth Biol (Oxf) 2023; 8:ysad014. [PMID: 38022744 PMCID: PMC10640854 DOI: 10.1093/synbio/ysad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/26/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Reproducibility has been identified as an outstanding challenge in science, and the field of synthetic biology is no exception. Meeting this challenge is critical to allow the transformative technological capabilities emerging from this field to reach their full potential to benefit the society. We discuss the current state of reproducibility in synthetic biology and how improvements can address some of the central shortcomings in the field. We argue that the successful adoption of reproducibility as a routine aspect of research and development requires commitment spanning researchers and relevant institutions via education, incentivization and investment in related infrastructure. The urgency of this topic pervades synthetic biology as it strives to advance fundamental insights and unlock new capabilities for safe, secure and scalable applications of biotechnology. Graphical Abstract.
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Affiliation(s)
- Matthew W Lux
- Research & Operations Directorate, U.S. Army Combat Capabilities Development Command Chemical Biological Center, APG, MD 21010, USA
| | - Elizabeth A Strychalski
- Cellular Engineering Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Gary J Vora
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA
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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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Collins L, Ponnazhagan S, Curiel DT. Synthetic Biology Design as a Paradigm Shift toward Manufacturing Affordable Adeno-Associated Virus Gene Therapies. ACS Synth Biol 2023; 12:17-26. [PMID: 36627108 PMCID: PMC9872172 DOI: 10.1021/acssynbio.2c00589] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Gene therapy has demonstrated enormous potential for changing how we combat disease. By directly engineering the genetic composition of cells, it provides a broad range of options for improving human health. Adeno-associated viruses (AAVs) represent a leading gene therapy vector and are expected to address a wide range of conditions in the coming decade. Three AAV therapies have already been approved by the FDA to treat Leber's congenital amaurosis, spinal muscular atrophy, and hemophilia B. Yet these therapies cost around $850,000, $2,100,000, and $3,500,000, respectively. Such prices limit the broad applicability of AAV gene therapy and make it inaccessible to most patients. Much of this problem arises from the high manufacturing costs of AAVs. At the same time, the field of synthetic biology has grown rapidly and has displayed a special aptitude for addressing biomanufacturing problems. Here, we discuss emerging efforts to apply synthetic biology design to decrease the price of AAV production, and we propose that such efforts could play a major role in making gene therapy much more widely accessible.
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Affiliation(s)
- Logan
Thrasher Collins
- Department
of Biomedical Engineering, Washington University
in St. Louis, 4950 Childrens Place, St. Louis, Missouri 63110, United
States
| | - Selvarangan Ponnazhagan
- Department
of Pathology, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, Alabama 35233, United States
| | - David T. Curiel
- Department
of Biomedical Engineering, Washington University
in St. Louis, 4950 Childrens Place, St. Louis, Missouri 63110, United
States,Department
of Radiation Oncology, Washington University
in St. Louis, 4950 Childrens
Place, St. Louis, Missouri 63110, United States,
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5
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Menke MJ, Behr AS, Rosenthal K, Linke D, Kockmann N, Bornscheuer UT, Dörr M. Development of an Ontology for Biocatalysis. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Marian J. Menke
- University of Greifswald Dept. of Biotechnology & Enzyme Catalysis Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Alexander S. Behr
- TU Dortmund University Department of Biochemical and Chemical Engineering Laboratory of Equipment Design Emil-Figge-Strasse 68 44227 Dortmund Germany
| | - Katrin Rosenthal
- TU Dortmund University Department of Biochemical and Chemical Engineering Chair for Bioprocess Engineering Emil-Figge-Strasse 66 44227 Dortmund Germany
| | - David Linke
- Leibniz-Institut für Katalyse e. V. Albert-Einstein-Strasse 29A 18059 Rostock Germany
| | - Norbert Kockmann
- TU Dortmund University Department of Biochemical and Chemical Engineering Laboratory of Equipment Design Emil-Figge-Strasse 68 44227 Dortmund Germany
| | - Uwe T. Bornscheuer
- University of Greifswald Dept. of Biotechnology & Enzyme Catalysis Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Mark Dörr
- University of Greifswald Dept. of Biotechnology & Enzyme Catalysis Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
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6
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Li J, Jamieson WD, Dimitriou P, Xu W, Rohde P, Martinac B, Baker M, Drinkwater BW, Castell OK, Barrow DA. Building programmable multicompartment artificial cells incorporating remotely activated protein channels using microfluidics and acoustic levitation. Nat Commun 2022; 13:4125. [PMID: 35840619 PMCID: PMC9287423 DOI: 10.1038/s41467-022-31898-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/06/2022] [Indexed: 01/25/2023] Open
Abstract
Intracellular compartments are functional units that support the metabolism within living cells, through spatiotemporal regulation of chemical reactions and biological processes. Consequently, as a step forward in the bottom-up creation of artificial cells, building analogous intracellular architectures is essential for the expansion of cell-mimicking functionality. Herein, we report the development of a droplet laboratory platform to engineer complex emulsion-based, multicompartment artificial cells, using microfluidics and acoustic levitation. Such levitated models provide free-standing, dynamic, definable droplet networks for the compartmentalisation of chemical species. Equally, they can be remotely operated with pneumatic, heating, and magnetic elements for post-processing, including the incorporation of membrane proteins; alpha-hemolysin; and mechanosensitive channel of large-conductance. The assembly of droplet networks is three-dimensionally patterned with fluidic input configurations determining droplet contents and connectivity, whilst acoustic manipulation can be harnessed to reconfigure the droplet network in situ. The mechanosensitive channel can be repeatedly activated and deactivated in the levitated artificial cell by the application of acoustic and magnetic fields to modulate membrane tension on demand. This offers possibilities beyond one-time chemically mediated activation to provide repeated, non-contact, control of membrane protein function. Collectively, this expands our growing capability to program and operate increasingly sophisticated artificial cells as life-like materials.
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Affiliation(s)
- Jin Li
- School of Engineering, Cardiff University, The Parade, Cardiff, CF24 3AA, UK.
| | - William D Jamieson
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Ave, Cardiff, CF10 3NB, UK
| | | | - Wen Xu
- Cardiff Business School, Cardiff University, Aberconway Building, Colum Dr, Cardiff, CF10 3EU, UK
| | - Paul Rohde
- Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool St, Darlinhurst, NSW, 2010, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool St, Darlinhurst, NSW, 2010, Australia.,School of Clinical Medicine, UNSW, Sydney, NSW, 2052, Australia
| | - Matthew Baker
- School of Biotechnology and Biomolecular Science, UNSW, Sydney, NSW, 2052, Australia
| | - Bruce W Drinkwater
- Department of Mechanical Engineering, University of Bristol, University Walk, Bristol, BS8 1TR, UK.
| | - Oliver K Castell
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Ave, Cardiff, CF10 3NB, UK.
| | - David A Barrow
- School of Engineering, Cardiff University, The Parade, Cardiff, CF24 3AA, UK.
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7
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Update on the Development of Toehold Switch-Based Approach for Molecular Diagnostic Tests of COVID-19. J Nucleic Acids 2022; 2022:7130061. [PMID: 35586794 PMCID: PMC9110250 DOI: 10.1155/2022/7130061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
A high volume of diagnostic tests is needed during the coronavirus disease 2019 (COVID-19) pandemic to obtain representative results. These results can help to design and implement effective policies to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis using current gold standard methods, i.e., real-time quantitative PCR (RT-qPCR), is challenging, especially in areas with limited trained personnel and health-related infrastructure. The toehold switch-based diagnostic system is a promising alternative method for detecting SARS-CoV-2 that has advantages such as inexpensive cost per testing, rapid, and highly sensitive and specific analysis. Moreover, the system can be applied to paper-based platforms, simplifying the distribution and utilization in low-resource settings. This review provides insight into the development of toehold switch-based diagnostic devices as the most recent methods for detecting SARS-CoV-2.
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8
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Maithani D, Sharma A, Gangola S, Choudhary P, Bhatt P. Insights into applications and strategies for discovery of microbial bioactive metabolites. Microbiol Res 2022; 261:127053. [DOI: 10.1016/j.micres.2022.127053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 03/12/2022] [Accepted: 04/26/2022] [Indexed: 10/25/2022]
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9
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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10
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Otto M, Skrekas C, Gossing M, Gustafsson J, Siewers V, David F. Expansion of the Yeast Modular Cloning Toolkit for CRISPR-Based Applications, Genomic Integrations and Combinatorial Libraries. ACS Synth Biol 2021; 10:3461-3474. [PMID: 34860007 PMCID: PMC8689691 DOI: 10.1021/acssynbio.1c00408] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 01/04/2023]
Abstract
Standardisation of genetic parts has become a topic of increasing interest over the last decades. The promise of simplifying molecular cloning procedures, while at the same time making them more predictable and reproducible has led to the design of several biological standards, one of which is modular cloning (MoClo). The Yeast MoClo toolkit provides a large library of characterised genetic parts combined with a comprehensive and flexible assembly strategy. Here we aimed to (1) simplify the adoption of the standard by providing a simple design tool for including new parts in the MoClo library, (2) characterise the toolkit further by demonstrating the impact of a BglII site in promoter parts on protein expression, and (3) expand the toolkit to enable efficient construction of gRNA arrays, marker-less integration cassettes and combinatorial libraries. These additions make the toolkit more applicable for common engineering tasks and will further promote its adoption in the yeast biological engineering community.
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Affiliation(s)
- Maximilian Otto
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Christos Skrekas
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Michael Gossing
- Discovery
Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg SE-43150, Sweden
| | - Johan Gustafsson
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Wallenberg
Center for Protein Research, Chalmers University
of Technology, Gothenburg SE-41296, Sweden
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Florian David
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
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11
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Schladt T, Engelmann N, Kubaczka E, Hochberger C, Koeppl H. Automated Design of Robust Genetic Circuits: Structural Variants and Parameter Uncertainty. ACS Synth Biol 2021; 10:3316-3329. [PMID: 34807573 PMCID: PMC8689692 DOI: 10.1021/acssynbio.1c00193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Genetic design automation
methods for combinational circuits often
rely on standard algorithms from electronic design automation in their
circuit synthesis and technology mapping. However, those algorithms
are domain-specific and are hence often not directly suitable for
the biological context. In this work we identify aspects of those
algorithms that require domain-adaptation. We first demonstrate that
enumerating structural variants for a given Boolean specification
allows us to find better performing circuits and that stochastic gate
assignment methods need to be properly adjusted in order to find the
best assignment. Second, we present a general circuit scoring scheme
that accounts for the limited accuracy of biological device models
including the variability across cells and show that circuits selected
according to this score exhibit higher robustness with respect to
parametric variations. If gate characteristics in a library are just
given in terms of intervals, we provide means to efficiently propagate
signals through such a circuit and compute corresponding scores. We
demonstrate the novel design approach using the Cello gate library
and 33 logic functions that were synthesized and implemented in vivo
recently (Nielsen, A., et al., Science, 2016, 352 (6281), DOI: 10.1126/science.aac7341). Across this set of functions, 32 of them can be improved by simply
considering structural variants yielding performance gains of up to
7.9-fold, whereas 22 of them can be improved with gains up to 26-fold
when selecting circuits according to the novel robustness score. We
furthermore report on the synergistic combination of the two proposed
improvements.
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Affiliation(s)
- Tobias Schladt
- Department of Electrical Engineering and Information Technology, TU Darmstadt, Darmstadt 64283, Germany
| | - Nicolai Engelmann
- Department of Electrical Engineering and Information Technology, TU Darmstadt, Darmstadt 64283, Germany
| | - Erik Kubaczka
- Department of Electrical Engineering and Information Technology, TU Darmstadt, Darmstadt 64283, Germany
| | - Christian Hochberger
- Department of Electrical Engineering and Information Technology, TU Darmstadt, Darmstadt 64283, Germany
| | - Heinz Koeppl
- Department of Electrical Engineering and Information Technology, TU Darmstadt, Darmstadt 64283, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt 64283, Germany
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12
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Range J, Halupczok C, Lohmann J, Swainston N, Kettner C, Bergmann FT, Weidemann A, Wittig U, Schnell S, Pleiss J. EnzymeML-a data exchange format for biocatalysis and enzymology. FEBS J 2021; 289:5864-5874. [PMID: 34890097 DOI: 10.1111/febs.16318] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/15/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
EnzymeML is an XML-based data exchange format that supports the comprehensive documentation of enzymatic data by describing reaction conditions, time courses of substrate and product concentrations, the kinetic model, and the estimated kinetic constants. EnzymeML is based on the Systems Biology Markup Language, which was extended by implementing the STRENDA Guidelines. An EnzymeML document serves as a container to transfer data between experimental platforms, modeling tools, and databases. EnzymeML supports the scientific community by introducing a standardized data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An application programming interface in Python supports the integration of software tools for data acquisition, data analysis, and publication. The feasibility of a seamless data flow using EnzymeML is demonstrated by creating an EnzymeML document from a structured spreadsheet or from a STRENDA DB database entry, by kinetic modeling using the modeling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO-RK.
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Affiliation(s)
- Jan Range
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Colin Halupczok
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Jens Lohmann
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Neil Swainston
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, UK
| | | | | | | | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies, Germany
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
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13
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Juteršek M, Dolinar M. A chimeric vector for dual use in cyanobacteria and Escherichia coli, tested with cystatin, a nonfluorescent reporter protein. PeerJ 2021; 9:e12199. [PMID: 34760347 PMCID: PMC8571960 DOI: 10.7717/peerj.12199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022] Open
Abstract
Background Developing sustainable autotrophic cell factories depends heavily on the availability of robust and well-characterized biological parts. For cyanobacteria, these still lag behind the more advanced E. coli toolkit. In the course of previous protein expression experiments with cyanobacteria, we encountered inconveniences in working with currently available RSF1010-based shuttle plasmids, particularly due to their low biosafety and low yields of recombinant proteins. We also recognized some drawbacks of the commonly used fluorescent reporters, as quantification can be affected by the intrinsic fluorescence of cyanobacteria. To overcome these drawbacks, we envisioned a new chimeric vector and an alternative reporter that could be used in cyanobacterial synthetic biology and tested them in the model cyanobacterium Synechocystis sp. PCC 6803. Methods We designed the pMJc01 shuttle plasmid based on the broad host range RSFmob-I replicon. Standard cloning techniques were used for vector construction following the RFC10 synthetic biology standard. The behavior of pMJC01 was tested with selected regulatory elements in E. coli and Synechocystis sp. PCC 6803 for the biosynthesis of the established GFP reporter and of a new reporter protein, cystatin. Cystatin activity was assayed using papain as a cognate target. Results With the new vector we observed a significantly higher GFP expression in E. coli and Synechocystis sp. PCC 6803 compared to the commonly used RSF1010-based pPMQAK1. Cystatin, a cysteine protease inhibitor, was successfully expressed with the new vector in both E. coli and Synechocystis sp. PCC 6803. Its expression levels allowed quantification comparable to the standardly used fluorescent reporter GFPmut3b. An important advantage of the new vector is its improved biosafety due to the absence of plasmid regions encoding conjugative transfer components. The broadhost range vector pMJc01 could find application in synthetic biology and biotechnology of cyanobacteria due to its relatively small size, stability and ease of use. In addition, cystatin could be a useful reporter in all cell systems that do not contain papain-type proteases and inhibitors, such as cyanobacteria, and provides an alternative to fluorescent reporters or complements them.
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Affiliation(s)
- Mojca Juteršek
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.,Current Affiliation: National Institute of Biology, Ljubljana, Slovenia
| | - Marko Dolinar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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14
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Raman K, Sinha H, Vickers CE, Nikel PI. Synthetic biology beyond borders. Microb Biotechnol 2021; 14:2254-2256. [PMID: 34792854 PMCID: PMC8601182 DOI: 10.1111/1751-7915.13966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 10/22/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Karthik Raman
- Department of BiotechnologyCentre for Integrative Biology and Systems Medicine (IBSE)Indian Institute of Technology MadrasChennaiIndia
| | - Himanshu Sinha
- Department of BiotechnologyCentre for Integrative Biology and Systems Medicine (IBSE)Indian Institute of Technology MadrasChennaiIndia
| | - Claudia E. Vickers
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organization (CSIRO)Dutton ParkAustralia
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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15
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Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
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Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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16
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Mey F, Clauwaert J, Van Huffel K, Waegeman W, De Mey M. Improving the performance of machine learning models for biotechnology: The quest for deus ex machina. Biotechnol Adv 2021; 53:107858. [PMID: 34695560 DOI: 10.1016/j.biotechadv.2021.107858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022]
Abstract
Machine learning is becoming an integral part of the Design-Build-Test-Learn cycle in biotechnology. Machine learning models learn from collected datasets such as omics data and predict a defined outcome, which has led to both production improvements and predictive tools in the field. Robust prediction of the behavior of microbial cell factories and production processes not only greatly increases our understanding of the function of such systems, but also provides significant savings of development time. However, many pitfalls when modeling biological data - bad fit, noisy data, model instability, low data quantity and imbalances in the data - cause models to suffer in their performance. Here we provide an accessible, in-depth analysis on the problems created by these pitfalls, as well as means of their detection and mediation, with a focus on supervised learning. Assessing the state of the art, we show that, currently, in-depth analyses of model performance are often absent and must be improved. This review provides a toolbox for the analysis of model robustness and performance, and simultaneously proposes a standard for the community to facilitate future work. It is further accompanied by an interactive online tutorial on the discussed issues.
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Affiliation(s)
- Friederike Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Jim Clauwaert
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
| | - Kirsten Van Huffel
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000 Ghent, Belgium.
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17
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Lammens EM, Boon M, Grimon D, Briers Y, Lavigne R. SEVAtile: a standardised DNA assembly method optimised for Pseudomonas. Microb Biotechnol 2021; 15:370-386. [PMID: 34651450 PMCID: PMC8719830 DOI: 10.1111/1751-7915.13922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/29/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022] Open
Abstract
To meet the needs of synthetic biologists, DNA assembly methods have transformed from simple 'cut-and-paste' procedures to highly advanced, standardised assembly techniques. Implementing these standardised DNA assembly methods in biotechnological research conducted in non-model hosts, including Pseudomonas putida and Pseudomonas aeruginosa, could greatly benefit reproducibility and predictability of experimental results. SEVAtile is a Type IIs-based assembly approach, which enables the rapid and standardised assembly of genetic parts - or tiles - to create genetic circuits in the established SEVA-vector backbone. Contrary to existing DNA assembly methods, SEVAtile is an easy and straightforward method, which is compatible with any vector, both SEVA- and non-SEVA. To prove the efficiency of the SEVAtile method, a three-vector system was successfully generated to independently co-express three different proteins in P. putida and P. aeruginosa. More specifically, one of the vectors, pBGDes, enables genomic integration of assembled circuits in the Tn7 landing site, while self-replicatory vectors pSTDesX and pSTDesR enable inducible expression from the XylS/Pm and RhaRS/PrhaB expression systems, respectively. Together, we hope these vector systems will support research in both the microbial SynBio and Pseudomonas field.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
| | - Dennis Grimon
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, Gent, 9000, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, Gent, 9000, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
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18
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Collins LT, Curiel DT. Synthetic Biology Approaches for Engineering Next-Generation Adenoviral Gene Therapies. ACS NANO 2021; 15:13970-13979. [PMID: 34415739 DOI: 10.1021/acsnano.1c04556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Synthetic biology centers on the design and modular assembly of biological parts so as to construct artificial biological systems. Over the past decade, synthetic biology has blossomed into a highly productive field, yielding advances in diverse areas such as neuroscience, cell-based therapies, and chemical manufacturing. Similarly, the field of gene therapy has made enormous strides both in proof-of-concept studies and in the clinical setting. One viral vector of increasing interest for gene therapy is the adenovirus (Ad). A major part of the Ad's increasing momentum comes from synthetic biology approaches to Ad engineering. Convergence of gene therapy and synthetic biology has enhanced Ad vectors by mitigating Ad toxicity in vivo, providing precise Ad tropisms, and incorporating genetic circuits to make smart therapies which adapt to environmental stimuli. Synthetic biology engineering of Ad vectors may lead to superior gene delivery and editing platforms which could find applications in a wide range of therapeutic contexts.
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Affiliation(s)
- Logan Thrasher Collins
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - David T Curiel
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63110, United States
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
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19
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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20
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Moškon M, Komac R, Zimic N, Mraz M. Distributed biological computation: from oscillators, logic gates and switches to a multicellular processor and neural computing applications. Neural Comput Appl 2021. [DOI: 10.1007/s00521-021-05711-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Schuster LA, Reisch CR. A plasmid toolbox for controlled gene expression across the Proteobacteria. Nucleic Acids Res 2021; 49:7189-7202. [PMID: 34125913 PMCID: PMC8266580 DOI: 10.1093/nar/gkab496] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Controlled gene expression is fundamental for the study of gene function and our ability to engineer bacteria. However, there is currently no easy-to-use genetics toolbox that enables controlled gene expression in a wide range of diverse species. To facilitate the development of genetics systems in a fast, easy, and standardized manner, we constructed and tested a plasmid assembly toolbox that will enable the identification of well-regulated promoters in many Proteobacteria and potentially beyond. Each plasmid is composed of four categories of genetic parts (i) the origin of replication, (ii) resistance marker, (iii) promoter-regulator and (iv) reporter. The plasmids can be efficiently assembled using ligation-independent cloning, and any gene of interest can be easily inserted in place of the reporter. We tested this toolbox in nine different Proteobacteria and identified regulated promoters with over fifty-fold induction range in eight of these bacteria. We also constructed variant libraries that enabled the identification of promoter-regulators with varied expression levels and increased inducible fold change relative to the original promoter. A selection of over 50 plasmids, which contain all of the toolbox's genetic parts, are available for community use and will enable easy construction and testing of genetics systems in both model and non-model bacteria.
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Affiliation(s)
- Layla A Schuster
- Dept. of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Christopher R Reisch
- Dept. of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32603, USA
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22
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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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23
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McCarthy J. Engineering and standardization of posttranscriptional biocircuitry in Saccharomyces cerevisiae. Integr Biol (Camb) 2021; 13:210-220. [PMID: 34270725 DOI: 10.1093/intbio/zyab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022]
Abstract
This short review considers to what extent posttranscriptional steps of gene expression can provide the basis for novel control mechanisms and procedures in synthetic biology and biotechnology. The term biocircuitry is used here to refer to functionally connected components comprising DNA, RNA or proteins. The review begins with an overview of the diversity of devices being developed and then considers the challenges presented by trying to engineer more scaled-up systems. While the engineering of RNA-based and protein-based circuitry poses new challenges, the resulting 'toolsets' of components and novel mechanisms of operation will open up multiple new opportunities for synthetic biology. However, agreed procedures for standardization will need to be placed at the heart of this expanding field if the full potential benefits are to be realized.
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Affiliation(s)
- John McCarthy
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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24
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Di Blasi R, Marbiah MM, Siciliano V, Polizzi K, Ceroni F. A call for caution in analysing mammalian co-transfection experiments and implications of resource competition in data misinterpretation. Nat Commun 2021; 12:2545. [PMID: 33953169 PMCID: PMC8099865 DOI: 10.1038/s41467-021-22795-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 02/08/2023] Open
Abstract
Transient transfections are routinely used in basic and synthetic biology studies to unravel pathway regulation and to probe and characterise circuit designs. As each experiment has a component of intrinsic variability, reporter gene expression is usually normalized with co-delivered genes that act as transfection controls. Recent reports in mammalian cells highlight how resource competition for gene expression leads to biases in data interpretation, with a direct impact on co-transfection experiments. Here we define the connection between resource competition and transient transfection experiments and discuss possible alternatives. Our aim is to raise awareness within the community and stimulate discussion to include such considerations in future experimental designs, for the development of better transfection controls.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Masue M Marbiah
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Velia Siciliano
- Synthetic and Systems Biology lab for Biomedicine, Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples (ITA), Italy
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK. .,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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25
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David F, Davis AM, Gossing M, Hayes MA, Romero E, Scott LH, Wigglesworth MJ. A Perspective on Synthetic Biology in Drug Discovery and Development-Current Impact and Future Opportunities. SLAS DISCOVERY 2021; 26:581-603. [PMID: 33834873 DOI: 10.1177/24725552211000669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The global impact of synthetic biology has been accelerating, because of the plummeting cost of DNA synthesis, advances in genetic engineering, growing understanding of genome organization, and explosion in data science. However, much of the discipline's application in the pharmaceutical industry remains enigmatic. In this review, we highlight recent examples of the impact of synthetic biology on target validation, assay development, hit finding, lead optimization, and chemical synthesis, through to the development of cellular therapeutics. We also highlight the availability of tools and technologies driving the discipline. Synthetic biology is certainly impacting all stages of drug discovery and development, and the recognition of the discipline's contribution can further enhance the opportunities for the drug discovery and development value chain.
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Affiliation(s)
- Florian David
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew M Davis
- Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Michael Gossing
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Hayes
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elvira Romero
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Louis H Scott
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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26
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Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits. Methods Mol Biol 2021; 2229:1-40. [PMID: 33405215 DOI: 10.1007/978-1-0716-1032-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Qualitative modeling approaches are promising and still underexploited tools for the analysis and design of synthetic circuits. They can make predictions of circuit behavior in the absence of precise, quantitative information. Moreover, they provide direct insight into the relation between the feedback structure and the dynamical properties of a network. We review qualitative modeling approaches by focusing on two specific formalisms, Boolean networks and piecewise-linear differential equations, and illustrate their application by means of three well-known synthetic circuits. We describe various methods for the analysis of state transition graphs, discrete representations of the network dynamics that are generated in both modeling frameworks. We also briefly present the problem of controlling synthetic circuits, an emerging topic that could profit from the capacity of qualitative modeling approaches to rapidly scan a space of design alternatives.
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27
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Daley SK, Cordell GA. Natural Products, the Fourth Industrial Revolution, and the Quintuple Helix. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211003029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The profound interconnectedness of the sciences and technologies embodied in the Fourth Industrial Revolution is discussed in terms of the global role of natural products, and how that interplays with the development of sustainable and climate-conscious practices of cyberecoethnopharmacolomics within the Quintuple Helix for the promotion of a healthier planet and society.
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Affiliation(s)
| | - Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
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28
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Food synthetic biology-driven protein supply transition: From animal-derived production to microbial fermentation. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Wang B, Yang H, Sun J, Dou C, Huang J, Guo FB. BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts. Front Microbiol 2021; 12:593979. [PMID: 33552037 PMCID: PMC7858672 DOI: 10.3389/fmicb.2021.593979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/04/2021] [Indexed: 01/25/2023] Open
Abstract
Synthetic biology seeks to create new biological parts, devices, and systems, and to reconfigure existing natural biological systems for custom-designed purposes. The standardized BioBrick parts are the foundation of synthetic biology. The incomplete and flawed metadata of BioBrick parts, however, are a major obstacle for designing genetic circuit easily, quickly, and accurately. Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related literature. Moreover, BioMaster is also a user-friendly platform for retrieval and analyses of relevant information on BioBrick parts.
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Affiliation(s)
- Beibei Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Huayi Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jianan Sun
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Chuhao Dou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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30
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Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
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Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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31
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Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host. Non-model bacteria offer unique and versatile metabolisms for synthetic biology. In this Perspective, the authors explore the limited availability of well-characterised biological parts in these species and argue that bacteriophages represent a diverse trove of orthogonal parts.
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32
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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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33
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Decoene T, De Maeseneire SL, De Mey M. Modulating transcription through development of semi-synthetic yeast core promoters. PLoS One 2019; 14:e0224476. [PMID: 31689317 PMCID: PMC6830820 DOI: 10.1371/journal.pone.0224476] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023] Open
Abstract
Altering gene expression regulation by promoter engineering is a very effective way to fine-tune heterologous pathways in eukaryotic hosts. Typically, pathway building approaches in yeast still use a limited set of long, native promoters. With the today’s introduction of longer and more complex pathways, an expansion of this synthetic biology toolbox is necessary. In this study we elucidated the core promoter structure of the well-characterized yeast TEF1 promoter and determined the minimal length needed for sufficient protein expression. Furthermore, this minimal core promoter sequence was used for the creation of a promoter library covering different expression strengths. This resulted in a group of short, 69 bp promoters with an 8.0-fold expression range. One exemplar had a two and four times higher expression compared to the native CYC1 and ADH1 promoter, respectively. Additionally, as it was described that the protein expression range could be broadened by upstream activating sequences (UASs), we integrated earlier described single and multiple short, synthetic UASs in front of the strongest yeast core promoter. This approach resulted to further variation in protein expression and an overall promoter library spanning a 20-fold activity range and covering a length from 69 bp to maximally 129 bp. Furthermore, the robustness of this library was assessed on three alternative carbon sources besides glucose. As such, the suitability of short yeast core promoters for metabolic engineering applications on different media, either in an individual context or combined with UAS elements, was demonstrated.
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Affiliation(s)
- Thomas Decoene
- Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Sofie L. De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Ghent University, Coupure links, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
- * E-mail:
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El Karoui M, Hoyos-Flight M, Fletcher L. Future Trends in Synthetic Biology-A Report. Front Bioeng Biotechnol 2019; 7:175. [PMID: 31448268 PMCID: PMC6692427 DOI: 10.3389/fbioe.2019.00175] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/08/2019] [Indexed: 11/20/2022] Open
Abstract
Leading researchers working on synthetic biology and its applications gathered at the University of Edinburgh in May 2018 to discuss the latest challenges and opportunities in the field. In addition to the potential socio-economic benefits of synthetic biology, they also examined the ethics and security risks arising from the development of these technologies. Speakers from industry, academia and not-for-profit organizations presented their vision for the future of the field and provided guidance to funding and regulatory bodies to ensure that synthetic biology research is carried out responsibly and can realize its full potential. This report aims to capture the collective views and recommendations that emerged from the discussions that took place. The meeting was held under the Chatham House Rule (i.e., a private invite-only meeting where comments can be freely used but not attributed) to promote open discussion; the findings and quotes included in the report are therefore not attributed to individuals. The goal of the meeting was to identify research priorities and bottlenecks. It also provided the opportunity to discuss how best to manage risk and earn public acceptance of this emerging and disruptive technology.
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Affiliation(s)
- Meriem El Karoui
- SynthSys-Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Monica Hoyos-Flight
- Innogen Institute, School of Social and Political Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Liz Fletcher
- SynthSys-Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Urquiza-García U, Zieliński T, Millar AJ. Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs. Synth Biol (Oxf) 2019; 4:ysz016. [PMID: 31423466 PMCID: PMC6690502 DOI: 10.1093/synbio/ysz016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 12/25/2022] Open
Abstract
Synthetic biology aims to introduce engineering principles into biology, for example, the construction of biological devices by assembling previously-characterized, functional parts. This approach demands new resources for cataloging and sharing biological components and designs, in order to accelerate the design-build-test-learn cycle. We evaluated two free, open source software platforms for managing synthetic biology data: Joint Bioenergy Institute-Inventory of Composable Elements (JBEI-ICE) and SynBioHub. We analyzed the systems from the perspective of experimental biology research groups in academia, which seek to incorporate the repositories into their synthetic biology workflow. Here, we define the minimal requirements for a repository in this context and develop three usage scenarios, where we then examine the two platforms: (i) supporting the synthetic biology design-build-test-learn cycle, (ii) batch deposit of existing designs into the repository and (iii) discovery and reuse of designs from the repository. Our evaluation of JBEI-ICE and SynBioHub provides an insight into the current state of synthetic biology resources, might encourage their wider adoption and should guide future development to better meet the needs of this user group.
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Affiliation(s)
- Uriel Urquiza-García
- SynthSys and School of Biological Sciences, C. H. Waddington Building, University of Edinburgh, King's Buildings, Edinburgh, UK.,Institute for Molecular Plant Sciences, D. Rutherford Building, University of Edinburgh, King's Buildings, Edinburgh, UK
| | - Tomasz Zieliński
- SynthSys and School of Biological Sciences, C. H. Waddington Building, University of Edinburgh, King's Buildings, Edinburgh, UK
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, C. H. Waddington Building, University of Edinburgh, King's Buildings, Edinburgh, UK
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Santos-Merino M, Singh AK, Ducat DC. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. Front Bioeng Biotechnol 2019; 7:33. [PMID: 30873404 PMCID: PMC6400836 DOI: 10.3389/fbioe.2019.00033] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/05/2019] [Indexed: 01/25/2023] Open
Abstract
Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Amit K. Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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Jessop-Fabre MM, Sonnenschein N. Improving Reproducibility in Synthetic Biology. Front Bioeng Biotechnol 2019; 7:18. [PMID: 30805337 PMCID: PMC6378554 DOI: 10.3389/fbioe.2019.00018] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/24/2019] [Indexed: 12/01/2022] Open
Abstract
Synthetic biology holds great promise to deliver transformative technologies to the world in the coming years. However, several challenges still remain to be addressed before it can deliver on its promises. One of the most important issues to address is the lack of reproducibility within research of the life sciences. This problem is beginning to be recognised by the community and solutions are being developed to tackle the problem. The recent emergence of automated facilities that are open for use by researchers (such as biofoundries and cloud labs) may be one of the ways that synthetic biologists can improve the quality and reproducibility of their work. In this perspective article, we outline these and some of the other technologies that are currently being developed which we believe may help to transform how synthetic biologists approach their research activities.
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Affiliation(s)
- Mathew M Jessop-Fabre
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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Exley K, Reynolds CR, Suckling L, Chee SM, Tsipa A, Freemont PS, McClymont D, Kitney RI. Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway. J Biol Eng 2019; 13:8. [PMID: 30675181 PMCID: PMC6339355 DOI: 10.1186/s13036-019-0141-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/07/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The automation of modular cloning methodologies permits the assembly of many genetic designs. Utilising characterised biological parts aids in the design and redesign of genetic pathways. The characterisation information held on datasheets can be used to determine whether a biological part meets the design requirements. To manage the design of genetic pathways, researchers have turned to modelling-based computer aided design software tools. RESULT An automated workflow has been developed for the design and build of heterologous metabolic pathways. In addition, to demonstrate the powers of electronic datasheets we have developed software which can transfer part information from a datasheet to the Design of Experiment software JMP. To this end we were able to use Design of Experiment software to rationally design and test randomised samples from the design space of a lycopene pathway in E. coli. This pathway was optimised by individually modulating the promoter strength, RBS strength, and gene order targets. CONCLUSION The use of standardised and characterised biological parts will empower a design-oriented synthetic biology for the forward engineering of heterologous expression systems. A Design of Experiment approach streamlines the design-build-test cycle to achieve optimised solutions in biodesign. Developed automated workflows provide effective transfer of information between characterised information (in the form of datasheets) and DoE software.
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Affiliation(s)
- Kealan Exley
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Christopher Robert Reynolds
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Lorna Suckling
- Department of Bioengineering, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
| | - Soo Mei Chee
- Department of Bioengineering, Imperial College London, London, UK
- SynbiCITE, Imperial College London, London, UK
| | - Argyro Tsipa
- Department of Bioengineering, Imperial College London, London, UK
- SynbiCITE, Imperial College London, London, UK
| | - Paul S. Freemont
- SynbiCITE, Imperial College London, London, UK
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
| | | | - Richard Ian Kitney
- Department of Bioengineering, Imperial College London, London, UK
- SynbiCITE, Imperial College London, London, UK
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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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Nora LC, Westmann CA, Martins‐Santana L, Alves LDF, Monteiro LMO, Guazzaroni M, Silva‐Rocha R. The art of vector engineering: towards the construction of next-generation genetic tools. Microb Biotechnol 2019; 12:125-147. [PMID: 30259693 PMCID: PMC6302727 DOI: 10.1111/1751-7915.13318] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/20/2022] Open
Abstract
When recombinant DNA technology was developed more than 40 years ago, no one could have imagined the impact it would have on both society and the scientific community. In the field of genetic engineering, the most important tool developed was the plasmid vector. This technology has been continuously expanding and undergoing adaptations. Here, we provide a detailed view following the evolution of vectors built throughout the years destined to study microorganisms and their peculiarities, including those whose genomes can only be revealed through metagenomics. We remark how synthetic biology became a turning point in designing these genetic tools to create meaningful innovations. We have placed special focus on the tools for engineering bacteria and fungi (both yeast and filamentous fungi) and those available to construct metagenomic libraries. Based on this overview, future goals would include the development of modular vectors bearing standardized parts and orthogonally designed circuits, a task not fully addressed thus far. Finally, we present some challenges that should be overcome to enable the next generation of vector design and ways to address it.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - Luana de Fátima Alves
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - María‐Eugenia Guazzaroni
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Rafael Silva‐Rocha
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
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Farny NG. A Vision for Teaching the Values of Synthetic Biology. Trends Biotechnol 2018; 36:1097-1100. [DOI: 10.1016/j.tibtech.2018.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 01/01/2023]
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