Genome‐scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production

Abstract

The methylotrophic yeast Pichia pastoris has gained much attention during the last decade as a platform for producing heterologous recombinant proteins of pharmaceutical importance, due to its ability to reproduce post-translational modification similar to higher eukaryotes. With the recent release of the full genome sequence for P. pastoris, in-depth study of its functions has become feasible. Here we present the first reconstruction of the genome-scale metabolic model of the eukaryote P. pastoris type strain DSMZ 70382, PpaMBEL1254, consisting of 1254 metabolic reactions and 1147 metabolites compartmentalized into eight different regions to represent organelles. Additionally, equations describing the production of two heterologous proteins, human serum albumin and human superoxide dismutase, were incorporated. The protein-producing model versions of PpaMBEL1254 were then analyzed to examine the impact on oxygen limitation on protein production.

Process development for the obtention and use of recombinant glycosidases: expression, modelling and immobilisation

“…Genomic scale models have also been developed (Chung et al, 2010;Sohn et al, 2010), but their high complexity makes it difficult to use them for control and monitorisation purposes.…”

“…Quantitative prediction based on the use of lumped biochemical equations has been shown to be inaccurate, possibly due to its large sensitivity to the measured fluxes (Carinhas et al, 2011). More detailed models that consider induction, transcription and translation phenomena can be used, but these become necessarily protein-specific (Chung et al, 2010;Çelik et al, 2010;Sohn et al, 2010).…”

“…(iii) to include stoichiometric equations representing transcription, amino acid formation and translation (Chung et al, 2010;Sohn et al, 2010).…”

“…However, several genome scale models have been published (Chung et al, 2010;Sohn et al, 2010) and it should be expected the whole set of metabolic reactions for P. pastoris to be available soon. In this way, the current constraint based model can be extended to represent P.…”

“…More detailed models considering induction, proteolysis, transcription and translation phenomena have also been used in this context, but these are necessarily proteinspecific (Chung et al, 2010;Çelik et al, 2010;Sohn et al, 2010) or require extensive parameter fitting (Mendoza-Muñoz et al, 2008).…”