{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Pdf":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001.pdf"],"Svg":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001.svg"],"Owl":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001-biopax2.owl","https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001-biopax3.owl"],"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001_url.xml","https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001_urn.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001.xpp","https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001.sci","https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001.png","https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001.vcml","https://www.ebi.ac.uk/biomodels/model/download/MODEL1011080001?filename=MODEL1011080001.m"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Lukas Endler"],"curationStatus":["Non-curated"],"levelVersion":["L2V3"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL1011080001"],"publication_pubmed":["20543878"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Gonzalez2010 N pharaonis metabolism"],"publication_year":["2010"],"submissionId":["MODEL1011080001"],"modelFlag":["Non Kinetic"],"publication_authors":["Orland Gonzalez, Tanja Oberwinkler, Locedie Mansueto, F Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt"],"first_author":["Orland Gonzalez"],"publication":["20543878,\n                            Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment.. 6, 6.\n                            Department of Membrane Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany. gonzalez@bio.ifi.lmu.de"],"submitter_mail":["lukas@ebi.ac.uk"],"submitter_affiliation":["EMBL-EBI"],"pubmed_abstract":["Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment."],"pubmed_title":["Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis."],"pubmed_authors":["Gonzalez Orland O, Oberwinkler Tanja T, Mansueto Locedie L, Pfeiffer Friedhelm F, Mendoza Eduardo E, Zimmer Ralf R, Oesterhelt Dieter D"],"description_synonyms":["biochemical pathways, extent, scale tissue, Metabolic Process, D-jun/Jra, Public Sectors, Esters, determination, AP-1, d-jun, postnatal development, NetrinA, AUTSX5, Metabolic Concepts, ethanoate, D430049E23Rik, growth and development, CSMF, NOVH, jra, CCN3, QM, Productivity, SKIP3, Personal, halite, Carbon-12, ionic compounds, p65-interacting inhibitor of NF-kappa-B, Concepts, Msal-1, Impacts, Metabolism Concept, Environmental Impacts, Public Enterprise, Phenomenon, fs(1)M104, Junc, C, me75, Elkh, Genomes, catabolism, entire life cycle, plant peltate hair, l(2)IA109, 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pathways, multicellular organism metabolic process, Metabolic Process, biodegradation, growth pattern, Metabolic, degradation, Process, catabolism, Processes, non-developmental growth, postnatal development, metabolism resulting in cell growth, postnatal growth, Metabolic Concepts, Metabolic Concept, growth and development, metabolic process resulting in cell growth, Metabolic Processes, Concept, Metabolic Phenomena, Natronobacterium pharaonis, development, Metabolism Concepts, Metabolism, Phenomena, Concepts, biotransformation, secretion, Halobacterium pharaonis., Metabolism Concept, Phenomenon, growth, Metabolism Phenomena, Catabolism, metabolism, Metabolic Phenomenon, Anabolism"],"additional_accession":[]},"is_claimable":false,"name":"Gonzalez2010_N_pharaonis_metabolism","description":"\n      \n        This is metabolic network reconstruction of      Natronomonas pharaonis\n          described in the article      \n        Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis.\n        \n          Gonzalez O, Oberwinkler T, Mansueto L, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D.      PLoS Comput Biol.\n          2010 Jun 3;6(6):e1000799. PMID:      20543878\n          , DOI:      e1000799. doi:10.1371/journal.pcbi.1000799\n    \n    Abstract:      \n          Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment.      \n  This model was downloaded from the supplemetary materials to the article. To make this file valid SBML, some minor changes had to be done. The reaction Test_sink and empty lists were removed.\n  This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.      \n          To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to      CC0 Public Domain Dedication\n          for more information.      In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..      \n          To cite BioModels Database, please use:      Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.\n\n\n","dates":{"last_modification":"2010-11-08","publication":"2005-01-01","submission":"2010-11-08"},"accession":"MODEL1011080001","cross_references":{"pubmed":["20543878"],"biomodels__db":["MODEL1011080001"],"go":["GO:0040008"],"taxonomy":["2257"]}}