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PlankMass SpectrometryShotgun proteomicsYeastGlucosehttps://www.ebi.ac.uk/pride/archive/projects/PXD036029-For each of the 10 conditions, 100 mg S. cerevisiae total protein was reduced alkylated (TCEP + Iodoacetamide) and digested with LysC and trypsin. C18 clean-up on Nest Group 96-well plate (HNS S18V-M), phospho-peptide enrichment with Ti(IV)-IMAC SN from ppep-enrichment used for TMT10plex labelling according to protocol based on Ogata, Tsai, and Ishihama 2021 [34292731]; elution in 80% CAN, 0.1% TFA Samples from 10 different labels combined and dried in SpeedVacPrideMaxQuant: TMT on N-terminus and lysine; fixed: carbamidomethyl; variable; phosphorylation and oxidationProteomicsAndrew CapaldiDept. of Molecular and Cellular Biology; University of ArizonaCOMPLETESaccharomyces Cerevisiae (baker's Yeast)michael.plank@unige.ch38446618 Plank M, Carmiol N, Mitri B, Lipinski AA, Langlais PR, Capaldi AP. Systems level analysis of time and stimuli specific signaling through PKA. Mol Biol Cell. 2024 35(4):ar60 10.1091/mbc.e23-02-0066University of ArizonaUnited States10.6019/PXD036029It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in <i>Saccharomyces cerevisiae</i> in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.Systems level analysis of time and stimuli specific signaling through PKA.Plank Michael M, Carmiol Nicole N, Mitri Bassam B, Lipinski Austin A AA, Langlais Paul R PR, Capaldi Andrew P APTPSG1, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Lysine Acetate, LYS, Lysine Hydrochloride, K, Acetate, Lysin, PRSS31, lysine, 2, Phosphorylations, epsilon-diaminocaproic acid, Lysine, phosphorylation., alpha, variable, 6-diaminohexanoic acid, TMT, L-Lysine, fixed, Enisyl, thiol methyltransferase activity, L Lysinestrain, gluco-hexose, glucose, D-Glucose, (beta-D)-Isomer, D Glucose, Glucose, Glukose, Dextrose, Sprain, Strain., Monohydrate, cultivar, Strains, (alpha-D)-Isomer, (DL)-Isomer, Glucose Monohydrate, Sprains, Strains and Sprains, Anhydrous, ecotype, DL-glucose, Anhydrous Dextrose, Glcglycogen synthase kinase activity, biochemical pathways, 6353, IPP2A2, Metabolic Process, Dmel_CG3263, protein kinase A activity, Activity, determination, FALL39, 5'-cyclic monophosphate, postnatal development, Addresses, Metabolic Concepts, growth and development, sci, CG18677, phosphorylation, Long Term, CG12452, Prp4 protein kinase activity, 5730420M11Rik, cAMP signaling, ATP-protein transphosphorylase activity, cAMP-dependent protein kinase, CAP-18, ATP:protein phosphotransferase (non-specific) activity, Concepts, HOW, How, 10.5, Protein Kinases, Dpck, mitogen-activated protein kinase activity, RI, Metabolism Concept, Phenomenon, Effect, C13orf8, Cyclic AMP Dependent Protein Kinases, l(3)j5D5, Protein Kinase A, 10.9, 24B, C, SET, me75, F, cAMP Dependent Protein Kinase, DmelCG2328, TAF-I, cAMP, catabolism, CG4379, stru, ZNF828, Pk72A, 3', Saccharomyes cerevisiae, 5' cAMP-dependent protein kinase complex, metabolic process resulting in cell growth, Baker, V, l(3)S053606, CG15862, Saccharomyces uvarum var. melibiosus, CG10293, D17Mit170, T1, cAMP-Dependent, Raf kinase activity, DmelCG4299, Cyclic AMP Dependent Protein Kinase, l(3)j5B5, IGAAD, set, serine kinase activity, DmelCG6117, 5' cAMP-dependent protein kinase activity, atypical protein kinase C activity, DmelCG10574, Saccharomyces capensis, mitogen-activated S6 kinase activity, Baker's, protein-aspartyl kinase activity, biotransformation, Mycoderma cerevisiae, cAMP-Dependent Protein Kinases, brewer's yeast, Catabolism, Long-Term Effects, HSD26, p82 kinase activity, phapii, 0904/17, Process, metabolism resulting in cell growth, betaIIPKC, cyclic AMP-dependent protein kinase complex, Longterm Effect, protein kinase A signaling, CG42341, StF-IT-1, CAP18, pka-C1, Tl3, Tl2, 5'-phosphate, CAMP, M phase-specific cdc2 kinase activity, Wee-kinase activity, Baker's Yeasts, Cyclic AMP, pka-R1, Saccharomyces diastaticus, SZ1, MAPK, 5'-cAMP-dependent protein kinase complex, Cos-1, RII[[DR]], secretion, VI, pka-c1, serine protein kinase activity, 5-23, PKA C, phosphorylase B kinase kinase activity, Yeast, 20.35, Drives, HLA-DR-associated protein II, protein glutamyl kinase activity, growth pattern, DI-2, non-developmental growth, CHAMP, I-2Dm, CG6117, non-specific serine/threonine protein kinase activity, Adenosine Cyclic Monophosphate-Dependent Protein Kinases, Dmel_CG12452, pka-RII, CG4299, cAMP Dependent Protein Kinases, I-2PP1, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, hydroxyalkyl-protein kinase activity, WEE1Hu, DmelCG4379, ATP:protein phosphotransferase (cAMP-dependent) activity, TAF-IBETA, PKA RII, serine-specific protein kinase activity, dPKA, epsilon PKC, PkaC1, Cells, Adenosine 3', PKAcA, HIPK2, cytidine 3', eve2, RII, anon-EST:Liang-2.39, TAF-Ibeta, Epa, Wee 1-like kinase activity, Protein Kinase, Dcpk, i2pp2a, adenosine 3', Brewer's Yeast, Eukaryotic, PKAC1, CG2328, 14.10, CRAMP, ribosomal S6 protein kinase activity, calcium/phospholipid-dependent protein kinase activity, region., Cyclic AMP-Dependent Protein Kinase, glycogen synthase A kinase activity, Effects, Processes, P62, glycogen synthase kinase 3 activity, Brewer's, Pk?5, baker's yeast, Gene, PKA-C3, PKA-C-3, PKA-C1, Metabolic Processes, BcDNA:GM01761, phosphorylase b kinase kinase activity, Saccharomyces italicus, PHAPII, 5'-Cyclic AMP, Cyclic adenylic acid, Pka-RI, Metabolism, yeast, l(2)cos[[1]], Gene Products, serine(threonine) protein kinase activity, even, Low, BG02142, AMPK, ribosomal protein S6 kinase II activity, Metabolism Phenomena, 18304, lager beer yeast, T-antigen kinase activity, galactosyltransferase-associated kinase activity, protein-serine kinase activity, Pka-C, l(3)s2612, PKAR, PkaR, Longterm, ipp2a2, STK32, inhibiteur, Metabolic Concept, 2pp2a, PKa-R2, PKa-R1, Long-Term, PKAc, cAMP Protein Kinase, CG10574, S. cerevisiae, protein kinase (phosphorylating) activity, PKA-R1, DmelCG15862, 5'-cyclophosphate-dependent protein kinase activity, Adenosine Cyclic Monophosphate Dependent Protein Kinases, PKA-R2, S cerevisiae, Cos, Candida robusta, inhibidor, 2PP2A, CdkA, protein-cysteine kinase activity, Raf-1, taf-ibeta, Hpr kinase activity, DmelCG10293, Dc0, dSET, dSet, STK22, site, Long-Term Effect, 1883, PKA signaling, casein kinase (phosphorylating) activity, DRI, PKA-RI, PKA Cl, inhibitors, lumen, cou, Cos1, degradation, 5'-cyclophosphate-dependent protein kinase complex, l(2)s4402, Saccharomyces cerevisiae 'var. diastaticus', clone 2.39, space, DC0, Proteins, igaad, DC2, Phosphorylations, dPKA-RI, inhibitor, CG3263, CdkR, protein serine kinase activity, qkr, l(3)S090417, Cell, Saccaromyces cerevisiae, protein phosphokinase activity, group, Concept, Metabolic Phenomena, development, Sccharomyces cerevisiae, Metabolism Concepts, cos1, twitchin kinase activity, PKAi, cyclic AMP-dependent protein kinase activity, Lr, pkA, PKA, Pka, PKAr, PKC, 5'-cyclic phosphate, I-2PP2A, KH93F, Long Term Effects, AP50 kinase activity, Protein, chemical analysis, Dm I-2, Phenomena, I2PP2A, dcO, DCO, Dco, Eve, EVE, anatomical spaces, intrinsic catalyst activity, metabolism, protein kinase p58 activity, Pka-RII, Metabolic Phenomenon, who, serine/threonine protein kinase activity, Saccharomyces oviformis, threonine-specific protein kinase activity, lumen space, multicellular organism metabolic process, LL37, pka, pka C1, pKA, dr[[1]], PKA C3, FALL-39, biodegradation, distinct, Metabolic, ensemble, dco, postnatal growth, l(2)46Ce, 5'-(hydrogen phosphate), Who/How, 5'-cAMP-dependent protein kinase activity, dsk1, 5'-CYCLIC-MONOPHOSPHATE, PKA-RII, 5'-cyclic monophosphate-responsive protein kinase activity, atypical PKC activity, l(2)46Cg, Longterm Effects, DmelCG42341, Protein Gene Products, l(2)46CFj, Eukaryotic Cell, PKA CI, Gene Proteins, l(2)46CFh, dSET/TAF-Ibeta, 2610030F17Rik, l(2)46CFp, l(2)01272, ADENOSINE-3', Bra, qkr[93F], assay, cAMP-Dependent Protein Kinase, Baker's Yeast, E(eve), AA407739, growth, protein serine-threonine kinase activity, General activity, Baker Yeast, l(2)46CFg, A-kinase activity, AnabolismDmelCG7535, DrosGluCl-alpha1, GluCl, D-Glucose, DmGluClalpha, Dm-GluCl, BcDNA:HL07853, (beta-D)-Isomer, PKA1., Glucose, Glukose, Monohydrate, SRA3, DrosGluCl, (DL)-Isomer, DL-glucose, Anhydrous Dextrose, glc, DrosGluCl-alpha, D Glucose, Dextrose, glu, CT23049, CG7535, GLUCL, DmGlu, (alpha-D)-Isomer, GluCla, Glucose Monohydrate, Anhydrous, dGluCl-alpha, DrosGlu-Cl-alpha, Glcsodium salt, DmelCG8566, Dunc104, Brewer's, baker's yeast, Gene, protein, DmKlp53D, protein-containing complex, Saccharomyces italicus, peptide, Polypeptides, protein polypeptide chains, method, 1H-imidazoleacetic acid, peptido, polypeptide chain, reduced, method used in an experiment, yeast, B1, Gene Products, tiny, protein aggregate, lager beer yeast, peptides, beta-Trypsin, hypoplasia, imidazolyl-4-acetic acid, Saccharomyes cerevisiae, Baker, proteins, labeling, Saccharomyces uvarum var. melibiosus, S. cerevisiae, set, IMAC, S cerevisiae, Candida robusta, MIP-4a, Saccharomyces capensis, grupos, D1, Baker's, TF, peptidos, Mycoderma cerevisiae, 1883, brewer's yeast, imac, 2-iodo-, TCEP, PTHB1, small, grupo, Saccharomyces cerevisiae 'var. diastaticus', protein complex, TSC-1, Proteins, imidazole-4-acetic acid, KIF1B, Saccaromyces cerevisiae, Peptide, group, CD142, Baker's Yeasts, Sccharomyces cerevisiae, polypeptide, native protein, natural protein, Saccharomyces diastaticus, C18, Unc104, Protein, CG8566, Saccharomyces oviformis, imidazole-4-acetic acid hydrochloride, Yeast, PRSS, underdeveloped, ensemble, Tripcellim, Rest, MIP-4alpha, Klp53D, TFA., study protocol, beta Trypsin, Unc-104, Protein Gene Products, plan specification, Gene Proteins, Trypure, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, DmCG8566, SCYA26, Acetamide, Peptid, Polypeptide, Baker's Yeast, Brewer's Yeast, groupe, Baker Yeast, Gruppeglycogen synthase kinase activity, 6353, ribosomal S6 protein kinase activity, calcium/phospholipid-dependent protein kinase activity, Dmel_CG3263, protein kinase A activity, glycogen synthase A kinase activity, determination, Effects, glycogen synthase kinase 3 activity, Pk?5, PKA-C3, PKA-C-3, PKA-C1, CG18677, BcDNA:GM01761, phosphorylase b kinase kinase activity, Long Term, CG12452, Prp4 protein kinase activity, Pka-RI, ATP-protein transphosphorylase activity, cAMP-dependent protein kinase, ATP:protein phosphotransferase (non-specific) activity, l(2)cos[[1]], serine(threonine) protein kinase activity, Dpck, mitogen-activated protein kinase activity, BG02142, RI, AMPK, ribosomal protein S6 kinase II activity, Effect, 18304, T-antigen kinase activity, galactosyltransferase-associated kinase activity, C, protein-serine kinase activity, Pka-C, PKAR, PkaR, Longterm, CG4379, STK32, Pk72A, 3', 5' cAMP-dependent protein kinase complex, PKa-R2, PKa-R1, Long-Term, PKAc, CG15862, Raf kinase activity, protein kinase (phosphorylating) activity, PKA-R1, DmelCG15862, serine kinase activity, 5'-cyclophosphate-dependent protein kinase activity, PKA-R2, Cos, DmelCG6117, 5' cAMP-dependent protein kinase activity, CdkA, protein-cysteine kinase activity, atypical protein kinase C activity, Raf-1, Hpr kinase activity, Dc0, mitogen-activated S6 kinase activity, STK22, protein-aspartyl kinase activity, Long-Term Effect, 5'-cAMP-dependent protein kinase activity., casein kinase (phosphorylating) activity, DRI, Long-Term Effects, PKA-RI, single organism signaling, p82 kinase activity, PKA Cl, Cos1, 5'-cyclophosphate-dependent protein kinase complex, l(2)s4402, DC0, betaIIPKC, cyclic AMP-dependent protein kinase complex, Longterm Effect, DC2, dPKA-RI, CG42341, CG3263, CdkR, protein serine kinase activity, pka-C1, protein phosphokinase activity, M phase-specific cdc2 kinase activity, Wee-kinase activity, cos1, twitchin kinase activity, PKAi, cyclic AMP-dependent protein kinase activity, pkA, PKA, Pka, PKAr, pka-R1, PKC, MAPK, chemical analysis, Long Term Effects, AP50 kinase activity, 5'-cAMP-dependent protein kinase complex, Cos-1, dcO, DCO, Dco, RII[[DR]], intrinsic catalyst activity, pka-c1, serine protein kinase activity, protein kinase p58 activity, Pka-RII, serine/threonine protein kinase activity, 5-23, threonine-specific protein kinase activity, PKA C, phosphorylase B kinase kinase activity, pka, pka C1, pKA, dr[[1]], PKA C3, protein glutamyl kinase activity, dco, CG6117, non-specific serine/threonine protein kinase activity, Dmel_CG12452, pka-RII, dsk1, PKA-RII, 5'-cyclic monophosphate-responsive protein kinase activity, atypical PKC activity, Longterm Effects, DmelCG42341, PKA CI, hydroxyalkyl-protein kinase activity, WEE1Hu, DmelCG4379, ATP:protein phosphotransferase (cAMP-dependent) activity, signalling process, PKA RII, serine-specific protein kinase activity, dPKA, epsilon PKC, PkaC1, l(2)01272, PKAcA, HIPK2, cytidine 3', RII, assay, Epa, Wee 1-like kinase activity, Dcpk, adenosine 3', protein serine-threonine kinase activity, PKAC1, A-kinase activityfalseglc and 1-NM-PP1 timecourses in tpk1/2/3as; TMT2 (4646)Samples taken at different timepoints after glucose addition. Strain ACY142. Different timepoints after 1-NM-PP1; for model building2024-06-162022-08-12PXD036029NEWT:1773NEWT:3555NEWT:1182590NEWT:10090NEWT:749200NEWT:35554NEWT:4120NEWT:5693NEWT:347515NEWT:1216979NEWT:307972NEWT:92867NEWT:990346NEWT:544496NEWT:5334NEWT:145953NEWT:257309NEWT:284812NEWT:115104NEWT:43330NEWT:67825NEWT:44544NEWT:13076NEWT:544404NEWT:3702NEWT:8839NEWT:4232NEWT:1736309NEWT:4113NEWT:7227NEWT:11298NEWT:885318NEWT:876138NEWT:4081NEWT:554NEWT:5691NEWT:260710NEWT:106592NEWT:237561NEWT:9913NEWT:10036NEWT:4100NEWT:7574NEWT:1351NEWT:1076NEWT:6763NEWT:7215NEWT:8030NEWT:380394NEWT:272563NEWT:507601NEWT:1639NEWT:188229NCBITaxon:79857NEWT:746360NEWT:6239NEWT:135588NEWT:135622NEWT:6915NEWT:9986NEWT:101510NEWT:95486NEWT:3880NEWT:58002NEWT:9103NEWT:4577NEWT:146479NEWT:1000589NEWT:145943NEWT:85962NEWT:160488NEWT:317447NEWT:3635NEWT:7955NCBITaxon:2NEWT:235443NEWT:985076NEWT:7959NEWT:2261NEWT:3197NEWT:9615NEWT:884019NEWT:4565NEWT:1264690NEWT:169963NCBITaxon:38727NEWT:36329NEWT:34305NEWT:59729NCBITaxon:183674NEWT:626528NEWT:139927NEWT:4558NEWT:9606NEWT:367830NEWT:243230NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NEWT:470NCBITaxon:79824NCBITaxon:4563NEWT:3218NEWT:5759NEWT:9838NCBITaxon:9615NEWT:1736231NEWT:1193501NEWT:6287NEWT:6326NEWT:9796NEWT:2762NEWT:5476NEWT:562NEWT:260707NEWT:287NEWT:10117NEWT:10116NEWT:1280NEWT:1836NEWT:29760NEWT:260705NEWT:1148NEWT:4932NEWT:70448NEWT:9825NEWT:3603NEWT:698936NEWT:39946NEWT:11676NEWT:9823NEWT:100226NCBITaxon:6073NEWT:4896NEWT:6279NEWT:7370NEWT:573NEWT:6282NEWT:7091384466180000-0002-4967-2591