OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization

Anthony P. Burgard, Priti Pharkya, Costas D. Maranas

Research output: Contribution to journalArticle

722 Citations (Scopus)

Abstract

The advent of genome-scale models of metabolism has laid the foundation for the development of computational procedures for suggesting genetic manipulations that lead to overproduction. In this work, the computational OptKnock framework is introduced for suggesting gene deletion strategies leading to the over-production of chemicals or biochemicals in E. coli. This is accomplished by ensuring that a drain towards growth resources (i.e., carbon, redox potential, and energy) must be accompanied, due to stoichiometry, by the production of a desired product. Computational results for gene deletions for succinate, lactate, and 1,3-propanediol (PDO) production are in good agreement with mutant strains published in the literature. While some of the suggested deletion strategies are straightforward and involve eliminating competing reaction pathways, many others suggest complex and nonintuitive mechanisms of compensating for the removed functionalities. Finally, the OptKnock procedure, by coupling biomass formation with chemical production, hints at a growth selection/adaptation system for indirectly evolving overproducing mutants.

Original languageEnglish (US)
Pages (from-to)647-657
Number of pages11
JournalBiotechnology and bioengineering
Volume84
Issue number6
DOIs
StatePublished - Dec 20 2003

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Gene Knockout Techniques
Gene Deletion
Genes
Succinic Acid
Growth
Biomass
Oxidation-Reduction
Lactic Acid
Carbon
Genome
Escherichia coli
Metabolism
Stoichiometry
1,3-propanediol

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology

Cite this

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OptKnock : A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization. / Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D.

In: Biotechnology and bioengineering, Vol. 84, No. 6, 20.12.2003, p. 647-657.

Research output: Contribution to journalArticle

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