Bioinformatics for the synthetic biology of natural products: Integrating across the Design–Build–Test cycle

Pablo Carbonell; Andrew Currin; Adrian Jervis; Nicholas Rattray; Neil Swainston; Cunyu Yan; Eriko Takano; Rainer Breitling

doi:10.1039/C6NP00018E

Bioinformatics for the synthetic biology of natural products: Integrating across the Design–Build–Test cycle

Pablo Carbonell, Andrew Currin, Adrian Jervis, Nicholas Rattray, Neil Swainston, Cunyu Yan, Eriko Takano, Rainer Breitling

Research output: Contribution to journal › Article › peer-review

Abstract

Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted

Original language	English
Pages (from-to)	925-932
Journal	Natural Product Reports
Volume	33
Early online date	17 May 2016
DOIs	https://doi.org/10.1039/C6NP00018E
Publication status	Published - 2016

Research Beacons, Institutes and Platforms

Manchester Institute of Biotechnology

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10.1039/C6NP00018ELicence: CC BY

Japan Partnering Award: Application of MS-Imaging and Metabolomics in Synthetic Biology Based Strain Improvement of Industrially Important Microbes
Takano, E., Breitling, R. & Hollywood, K.
1/07/16 → 30/06/20
Project: Research
Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals
Scrutton, N., Azapagic, A., Balmer, A., Barran, P., Breitling, R., Delneri, D., Dixon, N., Faulon, J., Flitsch, S., Goble, C., Goodacre, R., Hay, S., Kell, D., Leys, D., Lloyd, J., Lockyer, N., Martin, P., Micklefield, J., Munro, A., Pedrosa Mendes, P., Randles, S., Salehi Yazdi, F., Shapira, P., Takano, E., Turner, N. & Winterburn, J.
14/11/14 → 13/05/20
Project: Research
Innovative routes to monoterpene hydrocarbons and their high value derivatives
Scrutton, N., Breitling, R., Gardiner, J., Hay, S., Leys, D., Pedrosa Mendes, P. & Takano, E.
1/11/14 → 30/04/20
Project: Research

Cite this

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author = "Pablo Carbonell and Andrew Currin and Adrian Jervis and Nicholas Rattray and Neil Swainston and Cunyu Yan and Eriko Takano and Rainer Breitling",

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AU - Carbonell, Pablo

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AU - Yan, Cunyu

AU - Takano, Eriko

AU - Breitling, Rainer

PY - 2016

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AB - Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted

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DO - 10.1039/C6NP00018E

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JO - Natural Product Reports

JF - Natural Product Reports

ER -

Bioinformatics for the synthetic biology of natural products: Integrating across the Design–Build–Test cycle

Abstract

Research Beacons, Institutes and Platforms

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Projects

Japan Partnering Award: Application of MS-Imaging and Metabolomics in Synthetic Biology Based Strain Improvement of Industrially Important Microbes

Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals

Innovative routes to monoterpene hydrocarbons and their high value derivatives

Cite this