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

Covering: 2000 to 2016 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 pr...

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Autores principales: Carbonell, Pablo, Currin, Andrew, Jervis, Adrian J., Rattray, Nicholas J. W., Swainston, Neil, Yan, Cunyu, Takano, Eriko, Breitling, Rainer
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Royal Society of Chemistry 2016
Materias:
Chemistry
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063057/
https://www.ncbi.nlm.nih.gov/pubmed/27185383
http://dx.doi.org/10.1039/c6np00018e
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author Carbonell, Pablo
Currin, Andrew
Jervis, Adrian J.
Rattray, Nicholas J. W.
Swainston, Neil
Yan, Cunyu
Takano, Eriko
Breitling, Rainer
author_facet Carbonell, Pablo
Currin, Andrew
Jervis, Adrian J.
Rattray, Nicholas J. W.
Swainston, Neil
Yan, Cunyu
Takano, Eriko
Breitling, Rainer
author_sort Carbonell, Pablo
collection PubMed
description Covering: 2000 to 2016 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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spelling pubmed-50630572016-10-19 Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle Carbonell, Pablo Currin, Andrew Jervis, Adrian J. Rattray, Nicholas J. W. Swainston, Neil Yan, Cunyu Takano, Eriko Breitling, Rainer Nat Prod Rep Chemistry Covering: 2000 to 2016 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. Royal Society of Chemistry 2016-08-01 2016-05-17 /pmc/articles/PMC5063057/ /pubmed/27185383 http://dx.doi.org/10.1039/c6np00018e Text en This journal is © The Royal Society of Chemistry 2016 http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution 3.0 Unported License (http://creativecommons.org/licenses/by/3.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Chemistry
Carbonell, Pablo
Currin, Andrew
Jervis, Adrian J.
Rattray, Nicholas J. W.
Swainston, Neil
Yan, Cunyu
Takano, Eriko
Breitling, Rainer
Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle
title Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle
title_full Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle
title_fullStr Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle
title_full_unstemmed Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle
title_short Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle
title_sort bioinformatics for the synthetic biology of natural products: integrating across the design–build–test cycle
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063057/
https://www.ncbi.nlm.nih.gov/pubmed/27185383
http://dx.doi.org/10.1039/c6np00018e
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