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Background   Pichia stipitis  and  Pichia pastoris  have long been investigated due to their native abilities to metabolize every sugar from lignocellulose and to modulate methanol consumption, respectively. The latter has been driving the production of several recombinant proteins. As a result, significant advances in their biochemical knowledge, as well as in genetic engineering and fermentation methods have been generated. The release of their genome sequences has allowed systems level research.    Results  In this work, genome-scale metabolic models (GEMs) of  P. stipitis  (iSS884) and  P. pastoris  (iLC915) were reconstructed. iSS884 includes 1332 reactions, 922 metabolites, and 4 compartments. iLC915 contains 1423 reactions, 899 metabolites, and 7 compartments. Compared with the previous GEMs of  P. pastoris , PpaMBEL1254 and iPP668, iLC915 contains more genes and metabolic functions, as well as improved predictive capabilities. Simulations of physiological responses for the growth of both yeasts on selected carbon sources using iSS884 and iLC915 closely reproduced the experimental data. Additionally, the iSS884 model was used to predict ethanol production from xylose at different oxygen uptake rates. Simulations with iLC915 closely reproduced the effect of oxygen uptake rate on physiological states of  P. pastoris  expressing a recombinant protein. The potential of  P. stipitis  for the conversion of xylose and glucose into ethanol using reactors in series, and of  P. pastoris  to produce recombinant proteins using mixtures of methanol and glycerol or sorbitol are also discussed.    Conclusions  In conclusion the first GEM of  P. stipitis  (iSS884) was reconstructed and validated. The expanded version of the  P. pastoris  GEM, iLC915, is more complete and has improved capabilities over the existing models. Both GEMs are useful frameworks to explore the versatility of these yeasts and to capitalize on their biotechnological potentials.

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials