Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions

An optimization-based procedure for studying the response of metabolic netw orks after gene knockouts or additions is introduced and applied to a linea r flux balance analysis (FBA) Escherichia coli model. Both the gene additio n problem of optimally selecting which foreign genes to recombine into E. c oli, as well as the gene deletion problem of removing a given number of exi sting ones, are formulated as mixed-integer optimization problems using bin ary 0-1 variables. The developed modeling and optimization framework is tes ted by investigating the effect of gene deletions on biomass production and addressing the maximum theoretical production of the 20 amino acids for ae robic growth on glucose and acetate substrates. In the gene deletion study, the smallest gene set necessary to achieve maximum biomass production in E . coli is determined for aerobic growth on glucose. The subsequent gene kno ckout analysis indicates that biomass production decreases monotonically, r endering the metabolic network incapable of growth after only 18 gene delet ions. In the gene addition study, the E. coli flux balance model is augment ed with 3,400 non-E. coli reactions from the KEGG database to form a multis pecies model. This model is referred to as the Universal model. This study reveals that the maximum theoretical production of six amino acids could be improved by the addition of only one or two genes to the native amino acid production pathway of E. coli, even though the model could choose from 3,4 00 foreign reaction candidates. Specifically, manipulation of the arginine production pathway showed the most promise with 8.75% and 9.05% predicted i ncreases with the addition of genes for growth on glucose and acetate, resp ectively. The mechanism of all suggested enhancements is either by: 1) impr oving the energy efficiency and/or 2) increasing the carbon conversion effi ciency of the production route. (C) 2001 John Wiley & Sons, Inc.