biostudies-otherUnknown9Judith A.H. WodkeMolecular systems biology653Mycoplasma pneumoniaehttps://www.ebi.ac.uk/biostudies/studies/MODEL1301290000biostudies-other23549481Judith A.H. WodkefalseWodke2013 - Genome-scale constraint-based model of M.pneumoniae energy metabolism (iJW145)<notes xmlns="http://www.sbml.org/sbml/level2"> <body xmlns="http://www.w3.org/1999/xhtml"> <div class="dc:title">Wodke2013 - Genome-scale constraint-based model of M.pneumoniae energy metabolism (iJW145)</div> <div class="dc:description"> <p>A new genome-scale metabolic reconstruction of M.pneumoniae is used in combination with external metabolite measurement and protein abundance measurements to quantitatively explore the energy metabolism of this genome-reduce human pathogen.</p> </div> <div class="dc:bibliographicCitation"> <p>This model is described in the article:</p> <div class="bibo:title"> <a href="http://identifiers.org/pubmed/23549481" title="Access to this publication">Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling.</a> </div> <div class="bibo:authorList">Wodke JA, Puchałka J, Lluch-Senar M, Marcos J, Yus E, Godinho M, Gutiérrez-Gallego R, dos Santos VA, Serrano L, Klipp E, Maier T.</div> <div class="bibo:Journal">Mol Syst Biol. 2013;9:653.</div> <p>Abstract:</p> <div class="bibo:abstract"> <p>Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint-based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time-dependent changes, albeit using a static model. By performing an in silico knock-out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms.</p> </div> </div> <div class="dc:publisher"> <p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a> and identifiedby: <a href="http://identifiers.org/biomodels.db/MODEL1301290000">MODEL1301290000</a> . </p> <p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resourcefor published quantitative kinetic models</a> . </p> </div> <div class="dc:license"> <p>To the extent possible under law, all copyright and related orneighbouring rights to this encoded model have been dedicated to the publicdomain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public DomainDedication</a> for more information. </p> </div></body></notes>2013-01-29T00:00:00Z2025-07-15T09:30:37.777Z2025-03-30T21:24:47.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-07-0643-13-0365-08-220398-34-985-61-0902-04-5372-75-859-56-371-00-161-90-5491-97-462-49-73884-47-715978-08-2987-78-061-19-869-65-858-68-458-98-054-47-7496-65-12800-34-265-47-470-47-356-65-559-67-656-84-8590-55-673-22-3653-63-4951-77-9135-16-060802-29-174-79-3964-26-158-61-772-89-9146-91-81032-65-11927-31-785-32-560-18-42056-98-62564-35-4147-85-356-73-564-19-7979-92-07444-29-379-33-496-26-464-18-6940-69-265-46-373-40-556-81-54033-27-67782-44-72646-35-77540-64-956-85-9118-00-350-81-7124-38-929908-03-050-89-5951-78-0107-73-363-39-8961-07-958-05-973-32-5591-57-172-18-4488-69-784-52-666-22-82226-71-356-86-07664-38-2146-14-556-40-673-24-52466-09-358-96-852-90-483-88-53672-15-97664-41-786-01-11053-73-2365-07-159-30-363-68-33432-99-36027-13-072-19-565-71-4138-08-94300-28-17722-84-163-91-217989-41-2958-09-856-87-1154-87-02956-16-356-41-7133-89-156-45-19007-49-2590-54-563-38-766-72-858-97-9585-18-22646-71-1127-17-3146-17-8CHEBI:29157CHEBI:29156CHEBI:29159CHEBI:29158CHEBI:28862CHEBI:29153CHEBI:29152CHEBI:29155CHEBI:29154CHEBI:16635CHEBI:15428CHEBI:16643CHEBI:17732CHEBI:16761CHEBI:18385CHEBI:17053CHEBI:17295CHEBI:17172CHEBI:28850CHEBI:29265CHEBI:9532CHEBI:16988CHEBI:16624CHEBI:9533CHEBI:15414CHEBI:17713CHEBI:17835CHEBI:18019CHEBI:16753CHEBI:15422CHEBI:17962CHEBI:17720CHEBI:16870CHEBI:16991CHEBI:16077CHEBI:16750CHEBI:18132CHEBI:16192CHEBI:422CHEBI:16977CHEBI:16858CHEBI:16857CHEBI:18009CHEBI:18367CHEBI:18366CHEBI:33563CHEBI:15638CHEBI:15635CHEBI:15637CHEBI:17821CHEBI:15763CHEBI:16975CHEBI:18359CHEBI:16298CHEBI:15640CHEBI:16174CHEBI:28542CHEBI:15351CHEBI:17895CHEBI:15354CHEBI:35366CHEBI:18066CHEBI:15350CHEBI:16680CHEBI:1989CHEBI:29186CHEBI:29185CHEBI:29182CHEBI:17517CHEBI:29181CHEBI:29184CHEBI:29183CHEBI:15468CHEBI:29180CHEBI:16436CHEBI:15346CHEBI:16311CHEBI:15343CHEBI:18050CHEBI:29179CHEBI:29178CHEBI:29175CHEBI:29174CHEBI:29177CHEBI:29176CHEBI:17748CHEBI:29171CHEBI:29170CHEBI:16899CHEBI:29173CHEBI:29052CHEBI:29172CHEBI:17754CHEBI:15698CHEBI:16541CHEBI:17196CHEBI:17191CHEBI:47013CHEBI:29168CHEBI:29167CHEBI:29169CHEBI:29164CHEBI:29163CHEBI:29166CHEBI:29165CHEBI:16526CHEBI:29160CHEBI:29162CHEBI:29161CHEBI:16414CHEBI:17621CHEBI:17985CHEBI:17622CHEBI:44897CHEBI:18035CHEBI:15946CHEBI:15824CHEBI:18304CHEBI:17694CHEBI:16240CHEBI:16908CHEBI:16905CHEBI:16108CHEBI:16349CHEBI:17568CHEBI:16235CHEBI:17203CHEBI:16238CHEBI:15940CHEBI:16474CHEBI:16110CHEBI:17562CHEBI:17561CHEBI:16593CHEBI:27470CHEBI:16467CHEBI:15378CHEBI:18405CHEBI:15377CHEBI:17797CHEBI:15379CHEBI:17677CHEBI:17672CHEBI:17310CHEBI:17794CHEBI:17552CHEBI:18191CHEBI:29888CHEBI:15918CHEBI:17659CHEBI:16335CHEBI:15366CHEBI:16337CHEBI:17666CHEBI:16332CHEBI:16695CHEBI:18077CHEBI:16450CHEBI:18075CHEBI:48153CHEBI:18105CHEBI:15996CHEBI:15633CHEBI:17256CHEBI:17378CHEBI:17015CHEBI:16047CHEBI:17013CHEBI:16284CHEBI:32816CHEBI:30751CHEBI:16708CHEBI:28494CHEBI:16828CHEBI:17119CHEBI:16704CHEBI:15978CHEBI:17369CHEBI:4170CHEBI:17363CHEBI:17361CHEBI:37393CHEBI:15729CHEBI:15846CHEBI:15967CHEBI:15603CHEBI:16027CHEBI:15971CHEBI:17239CHEBI:17115CHEBI:17234CHEBI:17111CHEBI:16024CHEBI:16807CHEBI:35425CHEBI:18307CHEBI:15713CHEBI:16016CHEBI:16015CHEBI:17588CHEBI:16139CHEBI:15721CHEBI:16018CHEBI:17345CHEBI:16132CHEBI:16134CHEBI:16497CHEBI:58774CHEBI:17460<3dmet>B04619<3dmet>B01347<3dmet>B00015<3dmet>B01226<3dmet>B00137<3dmet>B00013<3dmet>B04618<3dmet>B00019<3dmet>B01229<3dmet>B00017<3dmet>B01228<3dmet>B01227<3dmet>B01185<3dmet>B00096<3dmet>B01182<3dmet>B01343<3dmet>B00011<3dmet>B01189<3dmet>B01188<3dmet>B01187<3dmet>B01180<3dmet>B00026<3dmet>B04626<3dmet>B01236<3dmet>B04628<3dmet>B04622<3dmet>B04743<3dmet>B04625<3dmet>B00029<3dmet>B01195<3dmet>B04620<3dmet>B04621<3dmet>B01233<3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