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

Pablo Carbonell; Andrew Currin; Adrian J. Jervis; Nicholas J. W. 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,

*^a Andrew Currin,^a Adrian J. Jervis,^a Nicholas J. W. Rattray,^a Neil Swainston,^a Cunyu Yan,^a Eriko Takano*^a and Rainer Breitling^a

Author affiliations

* Corresponding authors

^a Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
E-mail: pablo.carbonell@manchester.ac.uk, eriko.takano@manchester.ac.uk

Abstract

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.

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

This article is part of the themed collection: Synthetic Biology and Bioinformatics

Article information

https://doi.org/10.1039/C6NP00018E

Article type

Highlight

Submitted

05 Feb 2016

First published

17 May 2016

This article is Open Access

Download Citation

Nat. Prod. Rep., 2016,33, 925-932

Permissions

Request permissions

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

P. Carbonell, A. Currin, A. J. Jervis, N. J. W. Rattray, N. Swainston, C. Yan, E. Takano and R. Breitling, Nat. Prod. Rep., 2016, 33, 925 DOI: 10.1039/C6NP00018E

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

Natural Product Reports

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

Abstract

Article information

Download Citation

Permissions

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

Social activity

Search articles by author

Spotlight

Advertisements