Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

Abstract Background Lachancea kluyveri , a weak Crabtree positive yeast, has been extensively studied for the unique URC pyrimidine catabolism it harbours. It produces more biomass than Saccharomyces cerevisiae due to the underlying Crabtree effect and resorts to fermentation only in oxygen limiting conditions that makes it suitable host for industrial scale protein production. Ethyl acetate, an important industrial chemical, has been demonstrated to be a major overflow metabolite during aerobic batch cultivation with a specific rate of 0.12 g per g dry weight per hour. Here, we attempted to reconstruct the metabolism of the yeast from the genome to better explain the observed phenotypes and aid further hypothesis generation. Results We report the first genome-scale metabolic model, iPN730, using Build Fungal Model in KBase workspace. The inconsistencies in the model were manually corrected using literature and published datasets. The model comprises of 1235 reactions, 1179 metabolites and 730 genes distributed in 8 compartments. The in silico viability and the growth rates in various carbon sources show good agreement. The gene essentiality of the metabolic model also performs well in comparison to experimental data confirmed by statistical analysis. Dynamic flux balance analysis describes the growth dynamics, substrate utilization and product formation kinetics in various oxygen limited conditions. The URC pyrimidine degradation pathway incorporated into the model enables it to grow on uracil or urea as the sole nitrogen source. Conclusion The genome-scale metabolic construction of L. kluyveri provides better understanding of metabolism, particularly that of pyrimidine metabolism and ethyl acetate production. Metabolic flux analysis using the model will enable hypotheses generation to gain deeper understanding of metabolism in weakly Crabtree positive yeast.