UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction

Xi Wang; Liang Yu; Shulin Chen

doi:10.1016/j.meteno.2017.08.001

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UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction

Journal article

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UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction

Xi Wang, Liang Yu and Shulin Chen

Metabolic engineering communications, Vol.5(C), pp.54-59

12/2017

DOI: https://doi.org/10.1016/j.meteno.2017.08.001

Handle:

https://hdl.handle.net/2376/110987

PMCID: PMC5699525

PMID: 29188184

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Abstract

COBRA toolbox

Gene overexpression strategy

Targeted overproduction

Rational pathway design

Metabolic Engineering

Overexpression of key genes is a basic strategy for overproducing target products via metabolic engineering. Traditionally, identifying those key genes/pathways largely relies on the knowledge of biochemistry and bioinformatics. In this study, a modeling tool named UP Finder was developed to facilitate the rapid identification of gene overexpression strategies. It was based on the COBRA toolbox under MATLAB environment. All the key gene/pathway targets are identified in one click after simply loading a Systems Biology Markup Language model and specifying a metabolite as the targeted product. The outputs are also quantitatively ranked to show the preference for determining overexpression strategies in pathway design. Analysis examples for overproducing lycopene precursor in Escherichia coli and fatty acyl-ACP in the cyanobacterium Synechocystis sp. PCC 6803 by the UP Finder showed high degree of agreement with the reported key genes in the literatures. fx1 • A modeling interface is developed for identifying gene overexpression targets. • It evaluates the yield contribution for each overexpression candidate. • The outputs are ranked to show the preference for determining strategies.

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Title: UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction
Creators: Xi Wang - Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA
Liang Yu - Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA
Shulin Chen - Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA
Publication Details: Metabolic engineering communications, Vol.5(C), pp.54-59
Academic Unit: Biological Systems Engineering, Department of
Publisher: Elsevier
Identifiers: 99900583058501842
Language: English
Resource Type: Journal article