ArticlePloS one2016
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Systematic optimization ofEngineering microbiology · 2026Review
- Metabolic engineering ofApplied and environmental microbiology · 2026Review
- High-Throughput StationaryMethods in molecular biology (Clifton, N.J.) · 2026Article
- Characterising the metabolic rewiring of extremely slow growing Komagataella phaffii.Microbial biotechnology · 2024Article
- Pichia pastoris growth-coupled heme biosynthesis analysis using metabolic modelling.Scientific reports · 2023Article
- High throughputMicrobial cell factories · 2023Article
- merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models.Nucleic acids research · 2022Article
- Advances in Cell Engineering of theMetabolites · 2022Review
- Aerobic Utilization of Methanol for Microbial Growth and Production.Advances in biochemical engineering/biotechnology · 2022Article
- Benchmarking recombinant Pichia pastoris for 3-hydroxypropionic acid production from glycerol.Microbial biotechnology · 2021Article
- Inclusion of maintenance energy improves the intracellular flux predictions of CHO.PLoS computational biology · 2021Article
- Development of synthetic biology tools to engineerSynthetic and systems biotechnology · 2021Review
- Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species.FEMS yeast research · 2021Article
- Genome-scale metabolic reconstruction of the non-model yeastMetabolic engineering communications · 2020Article
- Redox Engineering by Ectopic Overexpression of NADH Kinase in Recombinant Pichia pastoris (Applied and environmental microbiology · 2020Article
- Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain.Biotechnology and bioengineering · 2020Article
- Contextualized genome-scale model unveils high-order metabolic effects of the specific growth rate and oxygenation level in recombinantMetabolic engineering communications · 2019Article
- Bioproduction of the Recombinant Sweet Protein Thaumatin: Current State of the Art and Perspectives.Frontiers in microbiology · 2019Review
- COMetabolic engineering communications · 2018Article
- Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources.Microbial biotechnology · 2018Article
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3 authors.
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Abstract
motivationGenome-scale metabolic models (GEMs) are tools that allow predicting a phenotype from a genotype under certain environmental conditions. GEMs have been developed in the last ten years for a broad range of organisms, and are used for multiple purposes such as discovering new properties of metabolic networks, predicting new targets for metabolic engineering, as well as optimizing the cultivation conditions for biochemicals or recombinant protein production. Pichia pastoris is one of the most widely used organisms for heterologous protein expression. There are different GEMs for this methylotrophic yeast of which the most relevant and complete in the published literature are iPP668, PpaMBEL1254 and iLC915. However, these three models differ regarding certain pathways, terminology for metabolites and reactions and annotations. Moreover, GEMs for some species are typically built based on the reconstructed models of related model organisms. In these cases, some organism-specific pathways could be missing or misrepresented.
resultsIn order to provide an updated and more comprehensive GEM for P. pastoris, we have reconstructed and validated a consensus model integrating and merging all three existing models. In this step a comprehensive review and integration of the metabolic pathways included in each one of these three versions was performed. In addition, the resulting iMT1026 model includes a new description of some metabolic processes. Particularly new information described in recently published literature is included, mainly related to fatty acid and sphingolipid metabolism, glycosylation and cell energetics. Finally the reconstructed model was tested and validated, by comparing the results of the simulations with available empirical physiological datasets results obtained from a wide range of experimental conditions, such as different carbon sources, distinct oxygen availability conditions, as well as producing of two different recombinant proteins. In these simulations, the iMT1026 model has shown a better performance than the previous existing models.
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