Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary ¹³C flux analysis

Abstract

Background: Several studies have shown that the utilization of mixed carbon feeds instead of methanol as sole carbon source is beneficial for protein production with the methylotrophic yeast Pichia pastoris. In particular, growth under mixed feed conditions appears to alleviate the metabolic burden related to stress responses triggered by protein overproduction and secretion. Yet, detailed analysis of the metabolome and fluxome under mixed carbon source metabolizing conditions are missing. To obtain a detailed flux distribution of central carbon metabolism, including the pentose phosphate pathway under methanol-glucose conditions, we have applied metabolomics and instationary ¹³C flux analysis in chemostat cultivations.

Results: Instationary ¹³C-based metabolic flux analysis using GC-MS and LC-MS measurements in time allowed for an accurate mapping of metabolic fluxes of glycolysis, pentose phosphate and methanol assimilation pathways. Compared to previous results from NMR-derived stationary state labelling data (proteinogenic amino acids, METAFoR) more fluxes could be determined with higher accuracy. Furthermore, using a thermodynamic metabolic network analysis the metabolite measurements and metabolic flux directions were validated. Notably, the concentration of several metabolites of the upper glycolysis and pentose phosphate pathway increased under glucose-methanol feeding compared to the reference glucose conditions, indicating a shift in the thermodynamic driving forces. Conversely, the extracellular concentrations of all measured metabolites were lower compared with the corresponding exometabolome of glucose-grown P. pastoris cells.The instationary ¹³C flux analysis resulted in fluxes comparable to previously obtained from NMR datasets of proteinogenic amino acids, but allowed several additional insights. Specifically, i) in vivo metabolic flux estimations were expanded to a larger metabolic network e.g. by including trehalose recycling, which accounted for about 1.5% of the glucose uptake rate; ii) the reversibility of glycolytic/gluconeogenesis, TCA cycle and pentose phosphate pathways reactions was estimated, revealing a significant gluconeogenic flux from the dihydroxyacetone phosphate/glyceraldehydes phosphate pool to glucose-6P. The origin of this finding could be carbon recycling from the methanol assimilatory pathway to the pentose phosphate pool. Additionally, high exchange fluxes of oxaloacetate with aspartate as well as malate indicated amino acid pool buffering and the activity of the malate/Asp shuttle; iii) the ratio of methanol oxidation vs utilization appeared to be lower (54 vs 79% assimilated methanol directly oxidized to CO₂).

Conclusions: In summary, the application of instationary ¹³C-based metabolic flux analysis to P. pastoris provides an experimental framework with improved capabilities to explore the regulation of the carbon and energy metabolism of this yeast, particularly for the case of methanol and multicarbon source metabolism.

Figure 1

Dynamics of mass isotopomers distribution of metabolites in P. pastoris chemostat cultures after switching to ¹³C-labeled substrates. Experimental data points are represented as solid circles. Solid lines reflect the simulation with the best flux estimation using the extended metabolic model (see Additional file 2). Dashed lines reflect the simulation with the best flux estimation using the metabolic model previously defined by [22].

Figure 2

Thermodynamic analysis of the P. pastoris reaction network, (a) Thermodynamically feasible concentration range of the measured metabolites and expected ranges of the non measured ones. The white bars represent a priori considered metabolite ranges, the light grey bars (measured metabolites) and the green bars (unmeasured metabolites) show the corrected values after performing a network-embedded thermodynamic (NET) analysis. In case of detection of a significant metabolite quantification error, the original measurement (red bar) and concentration ranges before and after the NET analysis are shown together. (b) Transformed Gibbs energy of the cytosolic reactions of the central carbon metabolism of P. pastoris growing on glucose-methanol.

Figure 3

Intracellular concentrations of P. pastoris cells growing on glucose-methanol. (a) Central carbon intermediates (b), Amino acids (c) Cometabolites and Nucleotides. Concentrations are given in μmol/g_CDW.

Figure 4

Metabolic flux distribution based on ¹³C flux analysis using the extended metabolic model. The flux values are given in μmol/g_CDW/h. The upper value represents the net flux (in direction of the arrow), the lower value (on blue background) reflects the backward flux (absolute). All fluxes are also listed in Additional file 6.