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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

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. (PI), Breitling, R. (CoI) & Hollywood, K. (CoI)
1/07/16 → 30/06/20
Project: Research
Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals
Scrutton, N. (PI), Azapagic, A. (CoI), Balmer, A. (CoI), Barran, P. (CoI), Breitling, R. (CoI), Delneri, D. (CoI), Dixon, N. (CoI), Faulon, J.-L. (CoI), Flitsch, S. (CoI), Goble, C. (CoI), Goodacre, R. (CoI), Hay, S. (CoI), Kell, D. (CoI), Leys, D. (CoI), Lloyd, J. (CoI), Lockyer, N. (CoI), Martin, P. (CoI), Micklefield, J. (CoI), Munro, A. (CoI), Pedrosa Mendes, P. (CoI), Randles, S. (CoI), Salehi Yazdi, F. (CoI), Shapira, P. (CoI), Takano, E. (CoI), Turner, N. (CoI) & Winterburn, J. (CoI)
14/11/14 → 13/05/20
Project: Research
Innovative routes to monoterpene hydrocarbons and their high value derivatives
Scrutton, N. (PI), Breitling, R. (CoI), Gardiner, J. (CoI), Hay, S. (CoI), Leys, D. (CoI), Pedrosa Mendes, P. (CoI) & Takano, E. (CoI)
1/11/14 → 30/04/20
Project: Research

Cite this

@article{8aa90f8a6d7441ad8d4a3089cac8b365,

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

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",

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

year = "2016",

doi = "10.1039/C6NP00018E",

language = "English",

volume = "33",

pages = "925--932",

journal = "Natural Product Reports",

issn = "0265-0568",

publisher = "Royal Society of Chemistry",

}

TY - JOUR

T1 - Bioinformatics for the synthetic biology of natural products: Integrating across the Design–Build–Test cycle

AU - Carbonell, Pablo

AU - Currin, Andrew

AU - Jervis, Adrian

AU - Rattray, Nicholas

AU - Swainston, Neil

AU - Yan, Cunyu

AU - Takano, Eriko

AU - Breitling, Rainer

PY - 2016

Y1 - 2016

N2 - 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

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

U2 - 10.1039/C6NP00018E

DO - 10.1039/C6NP00018E

M3 - Article

SN - 0265-0568

VL - 33

SP - 925

EP - 932

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

UN SDGs

Access to Document

Fingerprint

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