Genome‐scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins

Pichia pastoris is used for commercial production of human therapeutic proteins, and genome‐scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N‐glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N‐glycosylated proteins was constructed. The current genome‐scale models of P. pastoris do not address native nor humanized N‐glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N‐glycosylation for recombinant protein production, but also an estimation of N‐glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N‐glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes. Biotechnol. Bioeng. 2016;113: 961–969. © 2015 Wiley Periodicals, Inc.