FEBS Lett. 2012 Jul 16;586(15):2177-83. doi: 10.1016/j.febslet.2012.02.008. Epub 2012 Feb 15.

Metabolomics methods for the synthetic biology of secondary metabolism.

FEBS letters

Quoc-Thai Nguyen, Maria E Merlo, Marnix H Medema, Andris Jankevics, Rainer Breitling, Eriko Takano

PMID: 22710183 DOI: 10.1016/j.febslet.2012.02.008

Abstract

Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or "awakening" of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent advances in DNA sequencing and synthesis to achieve unprecedented control over metabolic pathways. One of the indispensable tools in the synthetic biology toolbox is metabolomics, the global quantification of small biomolecules. This review illustrates the pivotal role of metabolomics for the synthetic microbiology of secondary metabolism, including its crucial role in novel compound discovery in microbes, the examination of side products of engineered metabolic pathways, as well as the identification of major bottlenecks for the overproduction of compounds of interest, especially in combination with metabolic modeling. We conclude by highlighting remaining challenges and recent technological advances that will drive metabolomics towards fulfilling its potential as a cornerstone technology of synthetic microbiology.

Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

MeSH terms

• Drug Discovery
• Metabolomics / methods
• Microbiology
• Models, Biological
• Synthetic Biology / methods

Publication Types

• Journal Article
• Research Support, Non-U.S. Gov't
• Review