{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":29,"searchCount":5},"additional":{"omics_type":["Other"],"submitter":["Iesmantavicius V, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Yeast"],"submitter_mail":["chuna.choudhary@cpr.ku.dk"],"publication":["24961812"],"submitter_affiliation":["Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003865","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003866","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003863","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003864","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003869","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003889","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003867","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003868","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003861","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003862","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003860","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003882","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003854","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003855","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003874","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003852","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003896","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003875","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003853","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003858","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003859","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003857","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003872","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003873","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003851","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003870","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003871"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["The target of rapamycin (TOR) kinase senses the availability of nutrients and coordinates cellular growth and proliferation with nutrient abundance. Inhibition of TOR mimics nutrient starvation and leads to the reorganization of many cellular processes, including autophagy, protein translation, and vesicle trafficking. TOR regulates cellular physiology by modulating phosphorylation and ubiquitylation signaling networks; however, the global scope of such regulation is not fully known. Here, we used a mass-spectrometry-based proteomics approach for the parallel quantification of ubiquitylation, phosphorylation, and proteome changes in rapamycin-treated yeast cells. Our data constitute a detailed proteomic analysis of rapamycin-treated yeast with 3590 proteins, 8961 phosphorylation sites, and 2299 di-Gly modified lysines (putative ubiquitylation sites) quantified. The phosphoproteome was extensively modulated by rapamycin treatment, with more than 900 up-regulated sites one hour after rapamycin treatment. Dynamically regulated phosphoproteins were involved in diverse cellular processes, prominently including transcription, membrane organization, vesicle-mediated transport, and autophagy. Several hundred ubiquitylation sites were increased after rapamycin treatment, and about half as many decreased in abundance. We found that proteome, phosphorylation, and ubiquitylation changes converged on the Rsp5-ubiquitin ligase, Rsp5 adaptor proteins, and Rsp5 targets. Putative Rsp5 targets were biased for increased ubiquitylation, suggesting activation of Rsp5 by rapamycin. Rsp5 adaptor proteins, which recruit target proteins for Rsp5-dependent ubiquitylation, were biased for increased phosphorylation. Furthermore, we found that permeases and transporters, which are often ubiquitylated by Rsp5, were biased for reduced ubiquitylation and reduced protein abundance. The convergence of multiple proteome-level changes on the Rsp5 system indicates a key role of this pathway in the response to rapamycin treatment. Collectively, these data reveal new insights into the global proteome dynamics in response to rapamycin treatment and provide a first detailed view of the co-regulation of phosphorylation- and ubiquitylation-dependent signaling networks by this compound."],"pubmed_title":["Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells."],"pubmed_authors":["Iesmantavicius Vytautas V,Weinert Brian T BT,Choudhary Chunaram C,","Iesmantavicius Vytautas V, Weinert Brian T BT, Choudhary Chunaram C"],"name_synonyms":["26E, biological signaling, Antibiotic AY 22989, 18R, 35-hexamethyl-11, Phosphorylations, baker's yeast, 30S, phosphorylation, Saccaromyces cerevisiae, Saccharomyces italicus, 10, (-)-Rapamycin, Sccharomyces cerevisiae, 14, 17, 19R, 15R, C51H79NO13, yeast, 18-dihydroxy-12-{(2S)-1-[(1S, 23S, 3, Cell., 9S, 30-dimethoxy-15, lager beer yeast, 28E, 21, 16E, Saccharomyces oviformis, 23, 24, 24E, Yeast, Sirolimus, 26, Ubiquitylation, 29, 35R)-1, 4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-19, 9)]hexatriaconta-16, 12S, 28-tetraene-2, 32S, Saccharomyes cerevisiae, Rapamune, Saccharomyces uvarum var. melibiosus, signalling, 20-pentone, Candida robusta, signalling process, (1R, Saccharomyces capensis, signaling process, 36-dioxa-4-azatricyclo[30.3.1.0(4, 21R, brewer's yeast, single organism signaling, 3R"],"description_synonyms":["26E, data, Antibiotic AY 22989, Bhlha41, mol, 18R, 35-hexamethyl-11, Proteins, Phosphorylations, bHLHa48, FBN, baker's yeast, Gene, 30S, SCXB, Cell, phosphorylation, Saccaromyces cerevisiae, Saccharomyces italicus, SCXA, 10, ACMICD, Spectroscopy, (-)-Rapamycin, Sccharomyces cerevisiae, polypeptide, 14, Experiment, 17, 19R, ECTOL1, BB114693, 15R, C51H79NO13, yeast, Protein, proteomic analysis, 18-dihydroxy-12-{(2S)-1-[(1S, Gene Products, 23S, MFS1, 3, Analysis, 9S, 30-dimethoxy-15, WMS, WMS2, lager beer yeast, 28E, 21, 16E, Saccharomyces oviformis, 23, 24, 24E, Yeast, Sirolimus, 26, Ubiquitylation, 29, 35R)-1, 4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-19, cell, 9)]hexatriaconta-16, Spectrum, Spectrometry, 12S, 28-tetraene-2, 32S, Saccharomyes cerevisiae, proteins, MASS, Rapamune, Saccharomyces uvarum var. melibiosus, OCTD, Protein Gene Products, Gene Proteins, 20-pentone, Candida robusta, (1R, Saccharomyces capensis, 36-dioxa-4-azatricyclo[30.3.1.0(4, SSKS, Ubiquitylation., 21R, brewer's yeast, GPHYSD2, Proteomes, Scl, SGS, 3R"],"pubmed_title_synonyms":["26E, biological signaling, Antibiotic AY 22989, 18R, 35-hexamethyl-11, Phosphorylations, baker's yeast, 30S, phosphorylation, Saccaromyces cerevisiae, Saccharomyces italicus, 10, (-)-Rapamycin, Sccharomyces cerevisiae, 14, 17, 19R, 15R, C51H79NO13, yeast, 18-dihydroxy-12-{(2S)-1-[(1S, 23S, 3, Cell., 9S, 30-dimethoxy-15, lager beer yeast, 28E, 21, 16E, Saccharomyces oviformis, 23, 24, 24E, Yeast, Sirolimus, 26, Ubiquitylation, 29, 35R)-1, 4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-19, 9)]hexatriaconta-16, 12S, 28-tetraene-2, 32S, Saccharomyes cerevisiae, Rapamune, Saccharomyces uvarum var. melibiosus, signalling, 20-pentone, Candida robusta, signalling process, (1R, Saccharomyces capensis, signaling process, 36-dioxa-4-azatricyclo[30.3.1.0(4, 21R, brewer's yeast, single organism signaling, 3R"],"pubmed_abstract_synonyms":["projections, protein translation, protein sorting along secretory pathway, Nuclear receptor RZR-gamma, phosphorylation, 10, 14, autophagy, 17, Autophagic Cell Deaths, vesicle transport, Roles, NR1F3, Famines, Cellular Autophagies, thymus orphan receptor, Concepts, 23S, 3, Kinase, Analysis, Nutrient, present in fewer numbers in organism, WMS, 21, 23, treatment, 24, 24E, increased, Sirolimus, 26, Ubiquitylation, 29, High Mobility Protein 20, Autophagies, availability, non-developmental growth of a unicellular organism, Macro autophagy, single-organism membrane organization, 12S, Macro-autophagies, hypoplasia, Saccharomyes cerevisiae, Ubiquitin-related 1, metabolic process resulting in cell growth, proteins, Saccharomyces uvarum var. melibiosus, RZRG, cellular membrane organisation, APF-1, DNA-dependent, 20-pentone, Nr1f3, decreased, h, (1R, Saccharomyces capensis, papilla, signaling process, Role Concepts, disease management, cellular growth, brewer's yeast, ATP Phosphotransferases, GPHYSD2, ATP, single organism signaling, SGS, 3R, 26E, protein anabolism, anatomical protrusion, protein biosynthetic process, Autophagic, DNA-dependent transcription, metabolism resulting in cell growth, lamina, flanges, CEP52, Autophagic Cell, ACMICD, (-)-Rapamycin, RZR-GAMMA, Spectroscopy, hNEDD4-2, Role Concept, non-developmental cell growth, 15R, Autophagic Programmed Cell Death, shelf, Autophagocytosis, protein formation, Role, Cellular, Autophagic Cell Death, Starvations, 30-dimethoxy-15, activation, 28E, 16E, NEDD4-2, Ubiquitin, Transphosphorylases, Yeast, Thymus orphan receptor, nonselective vesicle transport, membrane organization and biogenesis, 4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-19, Autophagy, shelves, Spectrometry, Human Ubiquitin, Cell Death, MASS, Nutrients, projection, ridge, organ system, NEDD4.2, protein synthesis, spine, 36-dioxa-4-azatricyclo[30.3.1.0(4, Proteomes, accessory, hyperphosphorylated, transcription, Antibiotic AY 22989, biological signaling, RORC, 18R, lamellae, 35-hexamethyl-11, Macroautophagy, FBN, RORG, baker's yeast, Gene, ATP Dependent Proteolysis Factor 1, Ubiquitin carboxyl extension protein 80, process of organ, supernumerary, body system, Saccharomyces italicus, Nuclear receptor subfamily 1 group F member 3, protrusion, Human, nuclear receptor subfamily 1 group F member 3, lamella, reduced, 19R, ECTOL1, subnumerary, yeast, 18-dihydroxy-12-{(2S)-1-[(1S, Gene Products, Cellular Autophagy, HMG-20, system, transcription regulator activity, TOR, tiny, ubiquitin-like protein modifier, 9S, Macro-autophagy, lager beer yeast, vesicle trafficking, anatomical systems, 35R)-1, growth of cell, retinoid-related orphan receptor-gamma, nuclear receptor RZR-gamma, 9)]hexatriaconta-16, nutrients, Spectrum, Thor, Famine, cellular membrane organization, ridges, Deaths, decreased number, OCTD, 40S ribosomal protein S27a, Candida robusta, ubiquitin, Retinoid-related orphan receptor-gamma, laminae, protein tagging activity, single organism signaling., small, nutrient, Macroautophagies, data, cellular transcription, anatomical process, Proteins, Phosphorylations, 30S, function, Phosphotransferases, Saccaromyces cerevisiae, Cell, vesicular transport, Concept, Sccharomyces cerevisiae, polypeptide, cell expansion, Ubiquitin A-52 residue ribosomal protein fusion product 1, Ubiquitin-related 2, Programmed Cell Death, C51H79NO13, Protein, proteomic analysis, protein biosynthesis, MFS1, ATP-Dependent Proteolysis Factor 1, connected anatomical system, Death, Foods, flange, organ process, Cell Deaths, WMS2, Saccharomyces oviformis, RSP5, covalent modifier, membrane organisation, underdeveloped, Kinases, increased number, 28-tetraene-2, 32S, Rapamune, signalling, Protein Gene Products, RAR-related orphan receptor C, RORgamma, process, processes, Gene Proteins, present in greater numbers in organism, signalling process, 60S ribosomal protein L40, ligase, SSKS, processus, 21R, Ubiquitin-related, regulation, Type 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Experiment: SILAC_SC_Rap048_2ndrep_SCX, file: folder summary. Published as part of Mol Cell Proteomics. 2014 Aug;13(8):1979-92  . From the Abstract: {{i}} ... Here, we used a mass-spectrometry-based proteomics approach for the parallel quantification of ubiquitylation, phosphorylation, and proteome changes in rapamycin-treated yeast cells. Our data constitute a detailed proteomic analysis of rapamycin-treated yeast with 3590 proteins, 8961 phosphorylation sites, and 2299 di-Gly modified lysines (putative ubiquitylation sites) quantified ... {{/i}}","dates":{"submission":"2014-10-05"},"accession":"GPM32320003896","cross_references":{"pubmed":["24961812"],"Pride":["PXD000554"],"pride":[],"Pride Archive":["PXD000554"]}}