Abstract
Lachancea kluyveri, a weak Crabtree positive yeast, has been extensively studied for its unique URC pyrimidine catabolism pathway. It produces more biomass than Saccharomyces cerevisiae due to the underlying weak Crabtree effect and resorts to fermentation only in oxygen limiting conditions that renders it as a suitable industrial host. The yeast also produces ethyl acetate as a major overflow metabolite in aerobic conditions. Here, we report the first genome-scale metabolic model, iPN730, of L. kluyveri comprising of 1235 reactions, 1179 metabolites, and 730 genes distributed in 8 compartments. The in silico viability in different media conditions and the growth characteristics in various carbon sources show good agreement with experimental data. Dynamic flux balance analysis describes the growth dynamics, substrate utilization and product formation kinetics in various oxygen-limited conditions. We have also demonstrated the effect of switching carbon sources on the production of ethyl acetate under varying oxygen uptake rates. A phenotypic phase plane analysis described the energetic cost penalty of ethyl acetate and ethanol production on the specific growth rate of L. kluyveri. We generated the context specific models of L. kluyveri growing on uracil or ammonium salts as the sole nitrogen source. Differential flux calculated using flux variability analysis helped us in highlighting pathways like purine, histidine, riboflavin and pyrimidine metabolism associated with uracil degradation. The genome-scale metabolic construction of L. kluyveri will provide a better understanding of metabolism behind ethyl acetate production as well as uracil catabolism (pyrimidine degradation) pathway. iPN730 is an addition to genome-scale metabolic models of non-conventional yeasts that will facilitate system-wide omics analysis to understand fungal metabolic diversity.
Highlights
Lachancea kluyveri, previously known as Saccharomyces kluyveri, is a weak Crabtree positive yeast that has been presented in numerous studies due to its quintessential metabolic p roperties[1,2,3]
Lachancea kluyveri NRRL-12651 strain was selected for the genome annotation due to the extensive experimental analysis that has been conducted on this organism with respect to ethyl acetate production and uracil degradation
The homology table generated from the BDBH algorithm for proteome comparison has been incorporated (Table S4, Supplementary Information). This can be used to predict possible duplication, inversion, deletion, insertion and synteny loci between the organisms i.e. L. kluyveri and S. cerevisiae.The details about the fungal templates used for reconstruction have been described in “Methods” section
Summary
Previously known as Saccharomyces kluyveri, is a weak Crabtree positive yeast that has been presented in numerous studies due to its quintessential metabolic p roperties[1,2,3]. The model yeast S. cerevisiae was the first choice among the eukaryotic organisms to be fully sequenced[11,12], and it is one of the conventional workhorses in cell factory engineering for bio-production of several compounds with various applications in c hemical13,14, food[15,16] and pharmaceutical industries[17] These models are widely being used for various biotechnological predictions and experimental designs. IMH805 has gene regulatory information making it a powerful model to analyze the coordination of metabolic pathways with gene circuits[23] This has begun the quest for exploring related yeast strains that can furnish novel phenotypes. It is the first attempt to develop a GEM for L. kluyveri through which we anticipate a better understanding of the metabolic routes in the organism and streamlining its industrial applications
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