In silico deletion of PtsG gene in Escherichia coli genome-scale model predicts increased succinate production from glycerol.
Systems metabolic engineering and in silico analyses are necessary to study gene knockout candidate for enhanced succinic acid production by Escherichia coli. Metabolically engineered E. coli has been reported to produce succinate from glucose and glycerol. However, investigation on in silico deletion of ptsG/b1101 gene in E. coli from glycerol using minimization of metabolic adjustment algorithm with the OptFlux software platform has not yet been elucidated. Herein we report what is to our knowledge the first direct predicted increase in succinate production following in silico deletion of the ptsG gene in E. coli GEM from glycerol with the OptFlux software platform. The result indicates that the deletion of this gene in E. coli GEM predicts increased succinate production that is 20% higher than the wild-type control model. Hence, the mutant model maintained a growth rate that is 77% of the wild-type parent model. It was established that knocking out of the ptsG/b1101 gene in E. coli using glucose as substrate enhanced succinate production, but the exact mechanism of this effect is still obscure. This study informs other studies that the deletion of ptsG/b1101 gene in E. coli GEM predicted increased succinate production, enabling a model-driven experimental inquiry and/or novel biological discovery on the underground metabolic role of this gene in E. coli central metabolism in relation to increasing succinate production when glycerol is the substrate.
a Faculty of Biosciences and Medical Engineering, Bioinformatics Research Group (BIRG), Biosciences & Health Sciences Department , Universiti Teknologi Malaysia , Skudai , Malaysia.
Bashir Sajo
BS
Mienda
a Faculty of Biosciences and Medical Engineering, Bioinformatics Research Group (BIRG), Biosciences & Health Sciences Department , Universiti Teknologi Malaysia , Skudai , Malaysia.
Mohd Shahir
MS
Shamsir
D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D017353:Gene Deletion; D055786:Gene Knockout Techniques; D005990:Glycerol / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D013386:Succinates / Q000378:metabolism*
D013386:Succinates; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C031629:phosphoenolpyruvate-glucose phosphotransferase; D005990:Glycerol
Escherichia coli genome-scale model; OptFlux; Phosphatetransferase system (ptsG); gene deletion; glycerol; prediction; succinate production