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Systems metabolic engineering: Genome‐scale models and beyond

Systems metabolic engineering: Genome‐scale models and beyond The advent of high throughput genome‐scale bioinformatics has led to an exponential increase in available cellular system data. Systems metabolic engineering attempts to use data‐driven approaches – based on the data collected with high throughput technologies – to identify gene targets and optimize phenotypical properties on a systems level. Current systems metabolic engineering tools are limited for predicting and defining complex phenotypes such as chemical tolerances and other global, multigenic traits. The most pragmatic systems‐based tool for metabolic engineering to arise is the in silico genome‐scale metabolic reconstruction. This tool has seen wide adoption for modeling cell growth and predicting beneficial gene knockouts, and we examine here how this approach can be expanded for novel organisms. This review will highlight advances of the systems metabolic engineering approach with a focus on de novo development and use of genome‐scale metabolic reconstructions for metabolic engineering applications. We will then discuss the challenges and prospects for this emerging field to enable model‐based metabolic engineering. Specifically, we argue that current state‐of‐the‐art systems metabolic engineering techniques represent a viable first step for improving product yield that still must be followed by combinatorial techniques or random strain mutagenesis to achieve optimal cellular systems. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Biotechnology Journal Wiley

Systems metabolic engineering: Genome‐scale models and beyond

Biotechnology Journal , Volume 5 (7) – Jul 1, 2010

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References (110)

Publisher
Wiley
Copyright
Copyright © 2010 Wiley Subscription Services, Inc., A Wiley Company
ISSN
1860-6768
eISSN
1860-7314
DOI
10.1002/biot.200900247
pmid
20151446
Publisher site
See Article on Publisher Site

Abstract

The advent of high throughput genome‐scale bioinformatics has led to an exponential increase in available cellular system data. Systems metabolic engineering attempts to use data‐driven approaches – based on the data collected with high throughput technologies – to identify gene targets and optimize phenotypical properties on a systems level. Current systems metabolic engineering tools are limited for predicting and defining complex phenotypes such as chemical tolerances and other global, multigenic traits. The most pragmatic systems‐based tool for metabolic engineering to arise is the in silico genome‐scale metabolic reconstruction. This tool has seen wide adoption for modeling cell growth and predicting beneficial gene knockouts, and we examine here how this approach can be expanded for novel organisms. This review will highlight advances of the systems metabolic engineering approach with a focus on de novo development and use of genome‐scale metabolic reconstructions for metabolic engineering applications. We will then discuss the challenges and prospects for this emerging field to enable model‐based metabolic engineering. Specifically, we argue that current state‐of‐the‐art systems metabolic engineering techniques represent a viable first step for improving product yield that still must be followed by combinatorial techniques or random strain mutagenesis to achieve optimal cellular systems.

Journal

Biotechnology JournalWiley

Published: Jul 1, 2010

Keywords: ; ;

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