COMPARATIVE FLUX BALANCE ANALYSES OF SERINE ALKALINE PROTEASE OVERPRODUCTION IN Bacillus subtilis AT GENOME AND SMALL SCALE

Year 2023, , 8 - 18, 30.01.2023

Pınar Kocabaş

https://doi.org/10.18036/estubtdc.1184733

Abstract

The aim of this work is to conduct flux balance analysis of serine alkaline protease overproduction in Bacillus subtilis using enzyme-constrained genome scale model and to compare the results with fluxes obtained by a smaller, bioreaction based model. Fluxes of the enzyme constraint genome scale model were calculated using CobraToolbox v3.0 and compared with those of bioreaction based model for the specific growth rate of zero. Active reaction number first increased and then remained constant with specific growth rate for enzyme constrained genome scale model. SAP synthesis flux increased with the decrease in specific growth rate for both models. TCA cycle was active for both models, but with lower fluxes for enzyme-constrained genome scale model. Anaplerotic reactions were active only for bioreaction based model. Glycolysis pathway fluxes were active for enzyme-constrained genome scale model, meanwhile gluconeogenesis pathway fluxes were active for bioreaction based model. Oxidative pentose phosphate pathway was inactive for both models and generally higher pentose phosphate pathway fluxes were obtained with bioreaction based model. The fluxes towards amino acid synthesis pathways and serine alkaline protease synthesis were higher with bioreaction based model. Since TCA cycle fluxes were lower with enzyme constrained genome scale model, ATP synthesis was lower with enzyme constrained genome scale model compared to bioreaction based model. For both models, active pathways were the same for TCA cycle, pentose phosphate pathway, amino acid synthesis pathways except glycolysis pathway. The results showed that bioreaction based model gave more sound results compared to enzyme constrained genome scale model since gluconeogenesis should be active with the carbon source of citrate.

Keywords

Enzyme constrained genome scale metabolic model, Metabolic flux analysis, Bioreaction-based model

COMPARATIVE FLUX BALANCE ANALYSES OF SERINE ALKALINE PROTEASE OVERPRODUCTION IN Bacillus subtilis AT GENOME AND SMALL SCALE

Abstract

This work aims to conduct flux balance analysis of serine alkaline protease overproduction in Bacillus subtilis using enzyme-constrained genome scale model and to compare the results with fluxes obtained from a smaller, bioreaction-based model. Fluxes of the enzyme constraint genome scale model were calculated using CobraToolbox v3.0 and compared with those of bioreaction-based model for the specific growth rate of zero. The active reaction number first increased and then remained constant with specific growth rate for enzyme constrained genome scale model. The SAP synthesis flux increased with a decrease in specific growth rate for both models. The TCA cycle was active for both models, but with lower fluxes for enzyme-constrained genome scale model. Anaplerotic reactions were active only for bioreaction-based model. Glycolysis pathway fluxes were active for enzyme-constrained genome scale model, meanwhile gluconeogenesis pathway fluxes were active for bioreaction-based model. Oxidative pentose phosphate pathway was inactive for both models and generally higher pentose phosphate pathway fluxes were obtained using bioreaction-based model. The fluxes toward amino acid synthesis pathways and serine alkaline protease synthesis were higher with bioreaction-based model. Since TCA cycle fluxes were lower with enzyme constrained genome scale model, ATP synthesis was lower with enzyme constrained genome scale model compared to bioreaction-based model. For both models, active pathways were the same for TCA cycle, pentose phosphate pathway, amino acid synthesis pathways except glycolysis pathway. The results showed that bioreaction-based model gave more sound results compared to enzyme constrained genome scale model since gluconeogenesis should be active with the carbon source of citrate.

Keywords

Enzyme constrained genome scale metabolic model, Metabolic flux analysis, Bioreaction-based model

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