Metabolic flux analysis of recombinant Pichia pastoris growing on different glycerol/methanol mixtures by iterative fitting of NMR-derived (13)C-labelling data from proteinogenic amino acids

Abstract

The yeast Pichia pastoris has emerged as one of the most promising yeast cell factories for the production of heterologous proteins. The readily available genetic tools and the ease of high-cell density cultivations using methanol or glycerol/methanol mixtures are among the key factors for this development. Previous studies have shown that the use of mixed feeds of glycerol and methanol seem to alleviate the metabolic burden derived from protein production, allowing for higher specific and volumetric process productivities. However, initial studies of glycerol/methanol co-metabolism in P. pastoris by classical metabolic flux analyses using (13)C-derived Metabolic Flux Ratio (METAFoR) constraints were hampered by the reduced labelling information obtained when using C3:C1 substrate mixtures in relation to the conventional C6 substrate, that is, glucose. In this study, carbon flux distributions through the central metabolic pathways in glycerol/methanol co-assimilation conditions have been further characterised using biosynthetically directed fractional (13)C labelling. In particular, metabolic flux distributions were obtained under 3 different glycerol/methanol ratios and growth rates by iterative fitting of NMR-derived (13)C-labelling data from proteinogenic amino acids using the software tool (13)CFlux2. Specifically, cells were grown aerobically in chemostat cultures fed with 80:20, 60:40 and 40:60 (w:w) glycerol/methanol mixtures at two dilutions rates (0.05 hour(-1) and 0.16 hour(-1)), allowing to obtain additional data (biomass composition and extracellular fluxes) to complement pre-existing datasets. The performed (13)C-MFA reveals a significant redistribution of carbon fluxes in the central carbon metabolism as a result of the shift in the dilution rate, while the ratio of carbon sources has a lower impact on carbon flux distribution in cells growing at the same dilution rate. At low growth rate, the percentage of methanol directly dissimilated to CO2 ranges between 50% and 70%. At high growth rate the methanol is completely dissimilated to CO2 by the direct pathway, in the two conditions of highest methanol content.

Keywords: 1,3-Diphophoglycerate; 13dpg; 2-phosphoglycerate; 3-phosphoglycerate; ACALD; ACCoA; Acetalehyde; Acetyl coenzyme; BFD; Biomass formation; CER; CGly; CHOR; CIT; CO(2) Exchange Rate; Citrate; DHA; DHAP; DHF; Dihydrofolate; Dihydroxyacetone; Dihydroxyacetone phosphate; E4P; ETC; Eritrose-4-phosphate; FBP; FOR; FUM; Form; Formaldehyde; Fru6P; Fructose-1,6-biphosphate; Fructose-6-phosphate; Fully labelled Glycerol; FullyGly; Fumarate; G1P: SUCCoA; GA3P; GA3P(per); Glc6P; Glucose-6-phosphate; Glyceraldehyde-3-phosphate; Glyceraldehyde-3-phosphate peroxisome; ICIT; Inorganic phosphate; Inorganic pyrophosphate; Isocitrate; Ketovalerate; Kval; MAL; MTHF; Malate; Methanol; Methylenetetrahydrofolate; Metoh; MetohL; MetohN; NMR; Nuclear Magnetic Resonance; OAA; OUR; Oxaloacetate; Oxigen Uptake Rate; PG2; PG3; PPP; PPi; PRPP; Pep; Phosphoenolpyruvate; Phosphoribosyl Pirophosphate; Pi; Pyr; Pyruvate; ROL; Rhizopus oryzae lipase; Rib5P; Ribose-5-phosphate; Ribulose-5-phosphate; Rul5P; SUCC; Sed7P; Sedoheptulose-7-phosphate; Succinate; Succinyl coenzyme A; THF; Tetrahydrofolate; X(bio); Xul5P; Xylulose-5-phosphate; biosynthetically directed fractional; chorismate; electron transfer chain; formate; labelled Methanol; n.d.; non labelled Methanol; non-labelled Glycerol; not determined; pentose phosphate pathway; sd; sem; standard deviation; standard error of the mean; α-ketoglutarate; αKG.