BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000.cellmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000.xpphttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1612130000?filename=MODEL1612130000.vcmlprimaryOK200Màrius Tomàs-GamisansNon-curatedL2V1https://www.ebi.ac.uk/biomodels/MODEL161213000029160039falseBioModelsSBMLModelsP. pastoris model iMT1026 v32018MODEL1612130000Non KineticMàrius Tomàs-Gamisans, Pau Ferrer, Joan AlbiolMàrius Tomàs-Gamisans29160039, The methylotrophic yeast Pichia pastoris (Komagataella spp.) is widely used as cell factory for recombinant protein production. In the past recent years, important breakthroughs in the systems-level quantitative analysis of its physiology have been achieved. This wealth of information has allowed the development of genome-scale metabolic models, which make new approaches possible for host cell and bioprocess engineering. Nevertheless, the predictive accuracy of the previous consensus model required to be upgraded and validated with new experimental data sets for P. pastoris growing on glycerol or methanol as sole carbon sources, two of the most relevant substrates for this cell factory. In this study, we have characterized P. pastoris growing in chemostat cultures using glycerol or methanol as sole carbon sources over a wide range of growth rates, thereby providing physiological data on the effect of growth rate and culture conditions on biomass macromolecular and elemental composition. In addition, these data sets were used to improve the performance of the P. pastoris consensus genomic-scale metabolic model iMT1026. Thereupon, new experimentally determined bounds, including the representation of biomass composition for these growth conditions, have been incorporated. As a result, here, we present version 3 (v3.0) of the consensus P. pastoris genome-scale metabolic model as an update of the iMT1026 model. The v3.0 model was validated for growth on glycerol and methanol as sole carbon sources, demonstrating improved prediction capabilities over an extended substrate range including two biotechnologically relevant carbon sources.. 1, 11. Department of Chemical Biological and Environmental Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.marius.tomas@gmail.comUniversitat Autònoma de BarcelonaThe methylotrophic yeast Pichia pastoris (Komagataella spp.) is widely used as cell factory for recombinant protein production. In the past recent years, important breakthroughs in the systems-level quantitative analysis of its physiology have been achieved. This wealth of information has allowed the development of genome-scale metabolic models, which make new approaches possible for host cell and bioprocess engineering. Nevertheless, the predictive accuracy of the previous consensus model required to be upgraded and validated with new experimental data sets for P. pastoris growing on glycerol or methanol as sole carbon sources, two of the most relevant substrates for this cell factory. In this study, we have characterized P. pastoris growing in chemostat cultures using glycerol or methanol as sole carbon sources over a wide range of growth rates, thereby providing physiological data on the effect of growth rate and culture conditions on biomass macromolecular and elemental composition. In addition, these data sets were used to improve the performance of the P. pastoris consensus genomic-scale metabolic model iMT1026. Thereupon, new experimentally determined bounds, including the representation of biomass composition for these growth conditions, have been incorporated. As a result, here, we present version 3 (v3.0) of the consensus P. pastoris genome-scale metabolic model as an update of the iMT1026 model. The v3.0 model was validated for growth on glycerol and methanol as sole carbon sources, demonstrating improved prediction capabilities over an extended substrate range including two biotechnologically relevant carbon sources.Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources.Tomàs-Gamisans Màrius M, Ferrer Pau P, Albiol Joan JDesc, DESCR., Description, Descriptive, Descriptor, description, Product Description/Appearancescale tissue, d230, single-organism developmental process, determination, H-PAST, Carbon 12., postnatal development, peltate hair, number, baker's yeast, Gene, dTAFII250, Methyl, growth and development, CH3OH, carbon, protein, Development, broad, protein-containing complex, Methylalkohol, EfW1, Komagataella pastoris (Guilliermond) Y.Yamada et al., presence, Saccharomyces italicus, signal peptide peptidase activity, dmTAF[[II]]230, Glycerine, Background, glycyl alcohol, IMP1, Propanetriol, dmTAF1, Carbon-12, Taf230, yeast, Consensus, Trihydroxypropane, Cultural, Gene Products, T18E12.21, 1, 2, Wood Alcohol, PAST, protein aggregate, ATSPP, lager beer yeast, wood alcohol, Backgrounds, TAF250, 3-Propanetriol, study, C, Taf200, ethnicity, DmelCG6525, Oelsuess, T18E12_21, dTAF[[II]]250, TFIID TAF250, Genomes, Pichia pastoris, cel, cell, plant peltate hair, Glycerin, Saccharomyes cerevisiae, Taf1p, Cultural Relativisms, Saccharomyces uvarum var. melibiosus, FBgn0082831, dTAF250, Kohlenstoff, PSENL3, Candida robusta, Zygosaccharomyces pastoris, glycerolum, Saccharomyces capensis, wood naphtha, H13, Carbon, dJ324O17.1, Customs, HPAST1, Consensus Development, Sodium Methoxide, culture, brewer's yeast, TAF, Pichia pastoris (Guillierm.) Phaff, close to, Glyceritol, dTAF[[II]]230, TAF[[II]]250, wide/broad, Alcohol, signal peptide peptidase, protein complex, Glyzerin, PSL3, SPPL1, IMPAS-1, Proteins, Spp, SPP, TAF200, l(3)84Ab, Methyl alcohol, BG:DS00004.13, function, TAFII-250, Cultural Backgrounds, TAF250/230, carbone, Saccaromyces cerevisiae, Cell, dTAF230, near to, carbono, Sccharomyces cerevisiae, development, Vitreous, count in organism, TAFII250, Cultural Background, native protein, Cultures, p230, Protein, chemical analysis, glycerol, TAF[[II]]250/230, spp, TFIID, Sodium, MeOH, scales, Carbinol, carbinol, Saccharomyces oviformis, Taf[[II]]250, 3-Trihydroxypropane, Yeast, Gro, TAF[[II]]230, scale, Cultural Beliefs, glycerine, growth pattern, Engineerings, 6C, non-developmental growth, postnatal growth, TAF[II]250, whole genome, PAST1, CG17603, TAF[[II]], Carbon 12, Protein Gene Products, Gene Proteins, Wood, Vitreous Carbon, wide, DmelCG17603, Taf250, MSTP086, Biomasses, SR3-5, approaches, spirit of wood, wood spirit, vicinity of, carbonium, CG6525, Relativisms, assay, IMPAS, Relativism, Cultural Relativism, growth, Methyl Alcohol, TAF230, Methoxide, TAF1Glyceritol, scale tissue, Alcohol, Carbon 12., Glyzerin, peltate hair, postnatal development, Methyl alcohol, Methyl, growth and development, CH3OH, carbon, Methylalkohol, carbone, carbono, development, Vitreous, Glycerine, glycyl alcohol, Propanetriol, Carbon-12, Trihydroxypropane, glycerol, 1, Wood Alcohol, 2, Sodium, MeOH, scales, Carbinol, wood alcohol, carbinol, 3-Propanetriol, 3-Trihydroxypropane, C, Gro, Oelsuess, scale, Genomes, growth pattern, glycerine, non-developmental growth, 6C, plant peltate hair, Glycerin, postnatal growth, whole genome, Wood, Kohlenstoff, Vitreous Carbon, glycerolum, wood naphtha, spirit of wood, wood spirit, Carbon, carbonium, Sodium Methoxide, growth, Methyl Alcohol, MethoxidefalseP. pastoris model iMT1026 v3No description2018-11-192018-11-192016-12-13MODEL161213000029160039MODEL1612130000