Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris
Motivation: Genome-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...
| Autores: | , , |
|---|---|
| Tipo de documento: | artigo |
| Data de publicação: | 2016 |
| País: | España |
| Recursos: | Universitat Autònoma de Barcelona |
| Repositório: | Dipòsit Digital de Documents de la UAB |
| Idioma: | inglês |
| OAI Identifier: | oai:ddd.uab.cat:170620 |
| Acesso em linha: | https://ddd.uab.cat/record/170620 https://dx.doi.org/urn:doi:10.1371/journal.pone.0148031 |
| Access Level: | Acceso aberto |
| Palavra-chave: | Fatty acids Saccharomyces cerevisiae Glucose Metabolites Protein metabolism Pichia pastoris Recombinant proteins Metabolic pathways |
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Integration and Validation of the GenomeScale Metabolic Models of Pichia pastorisa Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy MetabolismTomàs Gamisans, Màrius|||0000-0002-6076-6716Ferrer, Pau|||0000-0002-5287-4127Albiol i Sala, Joan|||0000-0001-5626-429XFatty acidsSaccharomyces cerevisiaeGlucoseMetabolitesProtein metabolismPichia pastorisRecombinant proteinsMetabolic pathwaysMotivation: Genome-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. Results: In 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. 22016-01-0120162016-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/170620https://dx.doi.org/urn:doi:10.1371/journal.pone.0148031reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:1706202026-06-06T12:50:31Z |
| dc.title.none.fl_str_mv |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris a Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism |
| title |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris |
| spellingShingle |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris Tomàs Gamisans, Màrius|||0000-0002-6076-6716 Fatty acids Saccharomyces cerevisiae Glucose Metabolites Protein metabolism Pichia pastoris Recombinant proteins Metabolic pathways |
| title_short |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris |
| title_full |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris |
| title_fullStr |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris |
| title_full_unstemmed |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris |
| title_sort |
Integration and Validation of the GenomeScale Metabolic Models of Pichia pastoris |
| dc.creator.none.fl_str_mv |
Tomàs Gamisans, Màrius|||0000-0002-6076-6716 Ferrer, Pau|||0000-0002-5287-4127 Albiol i Sala, Joan|||0000-0001-5626-429X |
| author |
Tomàs Gamisans, Màrius|||0000-0002-6076-6716 |
| author_facet |
Tomàs Gamisans, Màrius|||0000-0002-6076-6716 Ferrer, Pau|||0000-0002-5287-4127 Albiol i Sala, Joan|||0000-0001-5626-429X |
| author_role |
author |
| author2 |
Ferrer, Pau|||0000-0002-5287-4127 Albiol i Sala, Joan|||0000-0001-5626-429X |
| author2_role |
author author |
| dc.subject.none.fl_str_mv |
Fatty acids Saccharomyces cerevisiae Glucose Metabolites Protein metabolism Pichia pastoris Recombinant proteins Metabolic pathways |
| topic |
Fatty acids Saccharomyces cerevisiae Glucose Metabolites Protein metabolism Pichia pastoris Recombinant proteins Metabolic pathways |
| description |
Motivation: Genome-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. Results: In 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. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2 2016-01-01 2016 2016-01-01 |
| dc.type.none.fl_str_mv |
Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
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article |
| dc.identifier.none.fl_str_mv |
https://ddd.uab.cat/record/170620 https://dx.doi.org/urn:doi:10.1371/journal.pone.0148031 |
| url |
https://ddd.uab.cat/record/170620 https://dx.doi.org/urn:doi:10.1371/journal.pone.0148031 |
| dc.language.none.fl_str_mv |
Inglés eng |
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Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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reponame:Dipòsit Digital de Documents de la UAB instname:Universitat Autònoma de Barcelona |
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Dipòsit Digital de Documents de la UAB |
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