Modeling and analysis of the macronutrient signaling network in budding yeast

dc.contributor.authorJalihal, Amogh P.en
dc.contributor.authorKraikivski, Pavelen
dc.contributor.authorMurali, T. M.en
dc.contributor.authorTyson, John J.en
dc.contributor.editorEdelstein-Keshet, Leahen
dc.date.accessioned2022-12-21T14:33:09Zen
dc.date.available2022-12-21T14:33:09Zen
dc.date.issued2021-11-01en
dc.date.updated2022-12-21T02:19:53Zen
dc.description.abstractAdaptive modulation of the global cellular growth state of unicellular organisms is crucial for their survival in fluctuating nutrient environments. Because these organisms must be able to respond reliably to ever varying and unpredictable nutritional conditions, their nutrient signaling networks must have a certain inbuilt robustness. In eukaryotes, such as the budding yeast Saccharomyces cerevisiae, distinct nutrient signals are relayed by specific plasma membrane receptors to signal transduction pathways that are interconnected in complex information-processing networks, which have been well characterized. However, the complexity of the signaling network confounds the interpretation of the overall regulatory "logic"of the control system. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling network in budding yeast, focusing on early temporal responses to carbon and nitrogen signaling. We build a computational model of this network to reconcile literature-curated quantitative experimental data with our proposed molecular mechanism. We evaluate the robustness of our estimates of the model's kinetic parameter values. We test the model by comparing predictions made in mutant strains with qualitative experimental observations made in the same strains. Finally, we use the model to predict nutrient-responsive transcription factor activities in a number of mutant strains undergoing complex nutrient shifts.en
dc.description.versionPublished versionen
dc.format.extent14 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifierARTN ar20 (Article number)en
dc.identifier.doihttps://doi.org/10.1091/mbc.E20-02-0117en
dc.identifier.eissn1939-4586en
dc.identifier.issn1059-1524en
dc.identifier.issue21en
dc.identifier.orcidMurali, T [0000-0003-3688-4672]en
dc.identifier.orcidKraikivski, Pavel [0000-0001-7742-0140]en
dc.identifier.pmid34495680en
dc.identifier.urihttp://hdl.handle.net/10919/112966en
dc.identifier.volume32en
dc.language.isoenen
dc.publisherAmerican Society for Cell Biologyen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000743148500001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution-NonCommercial-ShareAlike 3.0en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/3.0/en
dc.subjectCell Biologyen
dc.subjectSNF1 PROTEIN-KINASEen
dc.subjectTRANSCRIPTION FACTOR MSN2en
dc.subjectAMINO-ACID POOLSen
dc.subjectSACCHAROMYCES-CEREVISIAEen
dc.subjectADENYLATE-CYCLASEen
dc.subjectNUCLEOCYTOPLASMIC OSCILLATIONSen
dc.subjectINTRACELLULAR ACIDIFICATIONen
dc.subjectDEPENDENT TRANSCRIPTIONen
dc.subjectRAS/CAMP/PKA PATHWAYen
dc.subjectRIBOSOME BIOGENESISen
dc.subjectNutritionen
dc.subjectGeneticsen
dc.subject1.1 Normal biological development and functioningen
dc.subject1 Underpinning researchen
dc.subjectGeneric health relevanceen
dc.subject.meshSaccharomyces cerevisiaeen
dc.subject.meshNitrogenen
dc.subject.meshCarrier Proteinsen
dc.subject.meshSaccharomyces cerevisiae Proteinsen
dc.subject.meshTranscription Factorsen
dc.subject.meshComputational Biologyen
dc.subject.meshSignal Transductionen
dc.subject.meshCell Cycleen
dc.subject.meshGene Expressionen
dc.subject.meshGene Expression Regulation, Fungalen
dc.subject.meshEatingen
dc.subject.meshModels, Theoreticalen
dc.subject.meshTranscriptomeen
dc.subject.meshNutrientsen
dc.titleModeling and analysis of the macronutrient signaling network in budding yeasten
dc.title.serialMolecular Biology of the Cellen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Tech/Science/Dean of Scienceen
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