Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

Article Details

Citation

Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475.

PubMed ID
20068231 [ View in PubMed
]
Abstract

Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialP56181Details
7-dehydrocholesterol reductaseQ9UBM7Details
RAF proto-oncogene serine/threonine-protein kinaseP04049Details
TransketolaseP29401Details
L-lactate dehydrogenase B chainP07195Details
Creatine kinase B-typeP12277Details
Pyruvate kinase PKMP14618Details
L-lactate dehydrogenase C chainP07864Details
Glutamate--cysteine ligase catalytic subunitP48506Details
DNA ligase 3P49916Details
Carnitine O-palmitoyltransferase 2, mitochondrialP23786Details
Bifunctional glutamate/proline--tRNA ligaseP07814Details
DNA ligase 1P18858Details
Large neutral amino acids transporter small subunit 1Q01650Details
Pyrroline-5-carboxylate reductase 1, mitochondrialP32322Details
Tryptophan--tRNA ligase, cytoplasmicP23381Details
Neutral amino acid transporter B(0)Q15758Details
5'-AMP-activated protein kinase subunit beta-1Q9Y478Details
Beta-1,4-galactosyltransferase 1P15291Details
Alanine--tRNA ligase, cytoplasmicP49588Details
GMP synthase [glutamine-hydrolyzing]P49915Details
Acetyl-coenzyme A synthetase, cytoplasmicQ9NR19Details
Sodium- and chloride-dependent creatine transporter 1P48029Details
Ferritin heavy chainP02794Details
Retinoic acid receptor RXR-alphaP19793Details
Annexin A1P04083Details
Serine/threonine-protein kinase A-RafP10398Details
Abelson tyrosine-protein kinase 2P42684Details
Monocarboxylate transporter 4O15427Details
Neutral amino acid transporter AP43007Details
Isoleucine--tRNA ligase, cytoplasmicP41252Details
Receptor tyrosine-protein kinase erbB-2P04626Details
Aspartyl/asparaginyl beta-hydroxylaseQ12797Details
Chromodomain-helicase-DNA-binding protein 1O14646Details
Glyceraldehyde-3-phosphate dehydrogenaseP04406Details
Methionine--tRNA ligase, cytoplasmicP56192Details
DNA polymerase alpha catalytic subunitP09884Details
Cationic amino acid transporter 2P52569Details
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrialP08559Details
Malate dehydrogenase, cytoplasmicP40925Details
Solute carrier family 12 member 4Q9UP95Details
Asparagine--tRNA ligase, cytoplasmicO43776Details
Choline-phosphate cytidylyltransferase AP49585Details
Tyrosine-protein phosphatase non-receptor type 1P18031Details
Acetyl-CoA carboxylase 1Q13085Details
Serine/threonine-protein kinase B-rafP15056Details
UDP-glucose 6-dehydrogenaseO60701Details
Cytosolic phospholipase A2P47712Details
Monocarboxylate transporter 1P53985Details
Argininosuccinate synthaseP00966Details
5'-AMP-activated protein kinase catalytic subunit alpha-1Q13131Details
Retinoic acid-induced protein 3Q8NFJ5Details
Cysteine--tRNA ligase, cytoplasmicP49589Details
DNA polymerase alpha subunit BQ14181Details
Inosine-5'-monophosphate dehydrogenase 2P12268Details
Pyrroline-5-carboxylate reductase 2Q96C36Details
Heme oxygenase 1P09601Details
DNA topoisomerase 2-alphaP11388Details
Sodium/hydrogen exchanger 1P19634Details
Thromboxane A2 receptorP21731Details
Methionine synthase reductaseQ9UBK8Details
Epidermal growth factor receptorP00533Details
5'-AMP-activated protein kinase subunit beta-2O43741Details
Sphingosine-1-phosphate lyase 1O95470Details
Multidrug resistance-associated protein 1P33527Details
Glucocorticoid receptorP04150Details
Tyrosine-protein kinase FynP06241Details
Ephrin type-A receptor 2P29317Details
Perilipin-3O60664Details
Insulin-like growth factor 1 receptorP08069Details
CTP synthase 1P17812Details
Signal transducer and activator of transcription 5BP51692Details
DNA (cytosine-5)-methyltransferase 1P26358Details
CalpastatinP20810Details
C-X-C chemokine receptor type 4P61073Details
Mitogen-activated protein kinase 1P28482Details
Fatty acid synthaseP49327Details
DNA topoisomerase 1P11387Details
Catenin beta-1P35222Details
CalnexinP27824Details
Peptidyl-prolyl cis-trans isomerase AP62937Details
Mitogen-activated protein kinase 14Q16539Details
Transcription factor AP-1P05412Details
Proton-coupled folate transporterQ96NT5Details
Solute carrier family 2, facilitated glucose transporter member 1P11166Details
Mitogen-activated protein kinase 3P27361Details
Glycogen synthase kinase-3 betaP49841Details
Canalicular multispecific organic anion transporter 1Q92887Details
Tyrosine-protein phosphatase non-receptor type 11Q06124Details
Cyclin-dependent kinase 1P06493Details
Intercellular adhesion molecule 1P05362Details
78 kDa glucose-regulated proteinP11021Details
Phosphatidylserine synthase 1P48651Details
CD44 antigenP16070Details
Heat shock protein HSP 90-alphaP07900Details
Protein kinase C alpha typeP17252Details
Deoxyhypusine synthaseP49366Details
Inhibitor of nuclear factor kappa-B kinase subunit betaO14920Details
EndoplasminP14625Details
Microtubule-associated protein 1AP78559Details
14-3-3 protein zeta/deltaP63104Details
Phosphatidylethanolamine-binding protein 1P30086Details
Multidrug resistance-associated protein 4O15439Details
Cystic fibrosis transmembrane conductance regulatorP13569Details
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrialP33316Details
Casein kinase II subunit alphaP68400Details
Thymidine kinase, cytosolicP04183Details
cAMP-specific 3',5'-cyclic phosphodiesterase 4DQ08499Details
Tubulin alpha-1C chainQ9BQE3Details
Methionine aminopeptidase 2P50579Details
DNA repair protein XRCC4Q13426Details
Fructose-bisphosphate aldolase AP04075Details
Ras-related protein Rab-9AP51151Details
Poly [ADP-ribose] polymerase 1P09874Details
Early endosome antigen 1Q15075Details
Kinesin-like protein KIF11P52732Details
Heat shock protein HSP 90-betaP08238Details
Cyclin-dependent kinase 7P50613Details
ADP-ribose pyrophosphatase, mitochondrialQ9BW91Details
Keratin, type II cytoskeletal 8P05787Details
Retinoblastoma-associated proteinP06400Details
Pyridoxal-dependent decarboxylase domain-containing protein 1Q6P996Details
Molybdenum cofactor sulfuraseQ96EN8Details
Methylmalonic aciduria and homocystinuria type C proteinQ9Y4U1Details
Choline/ethanolaminephosphotransferase 1Q9Y6K0Details
Egl nine homolog 1Q9GZT9Details
Multifunctional protein ADE2P22234Details
CAD proteinP27708Details
Phosphoribosylformylglycinamidine synthaseO15067Details
Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrialP55809Details
N-acetyl-D-glucosamine kinaseQ9UJ70Details
Phosphatidylserine synthase 2Q9BVG9Details
Retinol dehydrogenase 14Q9HBH5Details
Peptidyl-prolyl cis-trans isomerase GQ13427Details
Proteasome subunit beta type-2P49721Details
Histone deacetylase 1Q13547Details
Histone deacetylase 2Q92769Details
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alphaP49354Details
Phosphatidylinositol 3-kinase regulatory subunit betaO00459Details
DNA-dependent protein kinase catalytic subunitP78527Details
Serine/threonine-protein kinase mTORP42345Details
Nuclear factor NF-kappa-B p100 subunitQ00653Details
Superoxide dismutase [Cu-Zn]P00441Details
NF-kappa-B essential modulatorQ9Y6K9Details
Protein kinase C delta typeQ05655Details
DNA topoisomerase 2-betaQ02880Details
Ribonucleoside-diphosphate reductase subunit M2P31350Details
E3 ubiquitin-protein ligase UBR4Q5T4S7Details
NAD-dependent protein deacetylase sirtuin-1Q96EB6Details
Voltage-dependent anion-selective channel protein 1P21796Details
Voltage-dependent anion-selective channel protein 2P45880Details
N-terminal kinase-like proteinQ96KG9Details
Prostaglandin E synthase 3Q15185Details
GephyrinQ9NQX3Details
U1 small nuclear ribonucleoprotein AP09012Details
Protein S100-A11P31949Details
Deoxycytidine kinaseP27707Details
Mismatch repair endonuclease PMS2P54278Details
Focal adhesion kinase 1Q05397Details
Wee1-like protein kinaseP30291Details
Serine/threonine-protein kinase Chk1O14757Details
Aurora kinase BQ96GD4Details
Bcl-2-like protein 2Q92843Details
Far upstream element-binding protein 1Q96AE4Details
cAMP-dependent protein kinase type II-alpha regulatory subunitP13861Details
cAMP-dependent protein kinase type I-alpha regulatory subunitP10644Details
High mobility group protein B1P09429Details
Heat shock protein beta-1P04792Details
Signal transducer and activator of transcription 3P40763Details
Ribosome-binding protein 1Q9P2E9Details
Microtubule-associated protein 4P27816Details
Heat shock factor protein 1Q00613Details
Histone deacetylase 4P56524Details
Histone deacetylase 7Q8WUI4Details
DNA polymerase epsilon catalytic subunit AQ07864Details
DNA polymerase epsilon subunit 4Q9NR33Details
DNA polymerase epsilon subunit 3Q9NRF9Details
Cation-independent mannose-6-phosphate receptorP11717Details
Multidrug resistance-associated protein 5O15440Details
Solute carrier organic anion transporter family member 4A1Q96BD0Details
Copper-transporting ATPase 1Q04656Details
High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8AO60658Details
High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8BO95263Details
Nuclear receptor coactivator 1Q15788Details
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortP63092Details
Nuclear receptor coactivator 2Q15596Details
Serine/threonine-protein kinase PLK1P53350Details
Disintegrin and metalloproteinase domain-containing protein 17P78536Details
S-phase kinase-associated protein 1P63208Details
Uracil-DNA glycosylaseP13051Details
BAG family molecular chaperone regulator 1Q99933Details
Heat shock cognate 71 kDa proteinP11142Details
Dual specificity protein kinase TTKP33981Details
Inner centromere proteinQ9NQS7Details
Serine/threonine-protein phosphatase PP1-alpha catalytic subunitP62136Details
60S ribosomal protein L23aP62750Details
60S ribosomal protein L37P61927Details
60S ribosomal protein L3P39023Details
Triosephosphate isomeraseP60174Details
Cytosol aminopeptidaseP28838Details
Protein kinase C iota typeP41743Details
Proteasome subunit alpha type-3P25788Details
Proteasome subunit alpha type-4P25789Details
Proteasome subunit alpha type-5P28066Details
Proteasome subunit beta type-7Q99436Details
Casein kinase I isoform gamma-3Q9Y6M4Details
STE20-like serine/threonine-protein kinaseQ9H2G2Details
Dual specificity protein kinase CLK3P49761Details
Nuclear receptor coactivator 5Q9HCD5Details
Hydroxymethylglutaryl-CoA synthase, cytoplasmicQ01581Details
Geranylgeranyl transferase type-2 subunit betaP53611Details
Cyclin-dependent kinase 16Q00536Details
Serine/threonine-protein kinase Sgk1O00141Details
Serine/threonine-protein kinase 26Q9P289Details
MKL/myocardin-like protein 1Q969V6Details
DestrinP60981Details
Cofilin-1P23528Details
Rho-associated protein kinase 2O75116Details
Actin-related protein 2/3 complex subunit 1BO15143Details
Ribosomal protein S6 kinase alpha-1Q15418Details
Elongation factor 2P13639Details
Tyrosine-protein kinase LynP07948Details
SRSF protein kinase 2P78362Details
Glycylpeptide N-tetradecanoyltransferase 1P30419Details
AfadinP55196Details
Interleukin-1 receptor-associated kinase 4Q9NWZ3Details
CREB-binding proteinQ92793Details
Mediator of RNA polymerase II transcription subunit 1Q15648Details
Calcium/calmodulin-dependent protein kinase type II subunit gammaQ13555Details
Mothers against decapentaplegic homolog 2Q15796Details
Protein arginine N-methyltransferase 3O60678Details
Epsin-1Q9Y6I3Details
Phosphoglycerate kinase 1P00558Details
Phosphoglucomutase-1P36871Details
VimentinP08670Details
Uridine 5'-monophosphate synthaseP11172Details
Acyl-CoA-binding proteinP07108Details
Ras-related protein Rab-7aP51149Details
Aconitate hydratase, mitochondrialQ99798Details
Poly(A) polymerase alphaP51003Details
6-pyruvoyl tetrahydrobiopterin synthaseQ03393Details
Inositol 1,4,5-trisphosphate receptor type 1Q14643Details
Unconventional myosin-IeQ12965Details
Gamma-enolaseP09104Details
14-3-3 protein epsilonP62258Details
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrialO14874Details
Transitional endoplasmic reticulum ATPaseP55072Details
Ubiquitin-like modifier-activating enzyme 1P22314Details
Sorting nexin-3O60493Details
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5O60264Details
Uridine-cytidine kinase-like 1Q9NWZ5Details
Spectrin beta chain, non-erythrocytic 1Q01082Details
Spliceosome RNA helicase DDX39BQ13838Details
Selenocysteine lyaseQ96I15Details
Ribosomal protein S6 kinase alpha-4O75676Details
Kinesin-like protein KIF2CQ99661Details
Transient receptor potential cation channel subfamily M member 7Q96QT4Details
Hepatocyte growth factor-regulated tyrosine kinase substrateO14964Details
Serine/threonine-protein kinase TAO2Q9UL54Details
ADP-ribosylation factor-like protein 3P36405Details
Peroxiredoxin-6P30041Details
Sodium bicarbonate cotransporter 3Q9Y6M7Details
Myc proto-oncogene proteinP01106Details
Equilibrative nucleoside transporter 2Q14542Details
Folate transporter 1P41440Details
Dual specificity mitogen-activated protein kinase kinase 2P36507Details
Mitogen-activated protein kinase kinase kinase 2Q9Y2U5Details
Transferrin receptor protein 1P02786Details
Ribosomal protein S6 kinase alpha-3P51812Details
Membrane-associated progesterone receptor component 1O00264Details
Inositol 1,4,5-trisphosphate receptor type 3Q14573Details
Cyclic AMP-dependent transcription factor ATF-1P18846Details
Cyclic AMP-dependent transcription factor ATF-2P15336Details
Cyclic AMP-dependent transcription factor ATF-4P18848Details
Intracellular hyaluronan-binding protein 4Q5JVS0Details
Histone H1.4P10412Details
Casein kinase II subunit betaP67870Details
Mitogen-activated protein kinase kinase kinase MLTQ9NYL2Details
Dihydropyrimidinase-related protein 2Q16555Details
Alpha-enolaseP06733Details
Protein PMLP29590Details
Nucleolar and coiled-body phosphoprotein 1Q14978Details
TGF-beta-activated kinase 1 and MAP3K7-binding protein 1Q15750Details
Protein O-GlcNAcaseO60502Details
UtrophinP46939Details
Proprotein convertase subtilisin/kexin type 9Q8NBP7Details
Sodium-dependent phosphate transporter 2Q08357Details
Translationally-controlled tumor proteinP13693Details
Nucleobindin-2P80303Details
Protein S100-A16Q96FQ6Details
60 kDa heat shock protein, mitochondrialP10809Details
40S ribosomal protein S2P15880Details
Heterogeneous nuclear ribonucleoproteins A2/B1P22626Details
Heterogeneous nuclear ribonucleoprotein HP31943Details
Heterogeneous nuclear ribonucleoprotein H3P31942Details
Heterogeneous nuclear ribonucleoprotein LP14866Details
Splicing factor, proline- and glutamine-richP23246Details
Stress-induced-phosphoprotein 1P31948Details
Eukaryotic translation initiation factor 6P56537Details
Hepatoma-derived growth factorP51858Details
Phosphoglycerate mutase 1P18669Details
Ran-specific GTPase-activating proteinP43487Details
Protein S100-A9P06702Details
HuntingtinP42858Details
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1Q8N1G2Details
Neural cell adhesion molecule L1P32004Details
Flap endonuclease 1P39748Details
Eukaryotic translation initiation factor 3 subunit FO00303Details
Heterogeneous nuclear ribonucleoprotein FP52597Details
Heterogeneous nuclear ribonucleoprotein KP61978Details
10 kDa heat shock protein, mitochondrialP61604Details
Heat shock protein 105 kDaQ92598Details
Nuclear migration protein nudCQ9Y266Details
26S protease regulatory subunit 6AP17980Details
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1Q969G3Details
Tumor protein D54O43399Details
Ubiquitin carboxyl-terminal hydrolase 14P54578Details
14-3-3 protein thetaP27348Details
Chromobox protein homolog 5P45973Details
Keratin, type II cytoskeletal 1P04264Details
DesmoplakinP15924Details
HornerinQ86YZ3Details
Junction plakoglobinP14923Details
Far upstream element-binding protein 2Q92945Details
Cysteine and glycine-rich protein 1P21291Details
Filamin-AP21333Details
Heterogeneous nuclear ribonucleoprotein D0Q14103Details
Heterochromatin protein 1-binding protein 3Q5SSJ5Details
Ras GTPase-activating-like protein IQGAP1P46940Details
NucleophosminP06748Details
60S ribosomal protein L14P50914Details
60S ribosomal protein L18Q07020Details
60S ribosomal protein L4P36578Details
40S ribosomal protein S17P08708Details
40S ribosomal protein S6P62753Details
Splicing factor 1Q15637Details
Small nuclear ribonucleoprotein Sm D2P62316Details
Serine/arginine-rich splicing factor 4Q08170Details
Transgelin-2P37802Details
ZyxinQ15942Details
Serine/arginine-rich splicing factor 1Q07955Details
Survival motor neuron proteinB4DP61Details
Myosin-9P35579Details
Probable ATP-dependent RNA helicase DDX5P17844Details
Splicing factor 3B subunit 1O75533Details
Elongation of very long chain fatty acids protein 5Q9NYP7Details
Serine/threonine-protein kinase 24Q9Y6E0Details
Serine/threonine-protein kinase 38Q15208Details
Serine/threonine-protein kinase 38-likeQ9Y2H1Details
STE20/SPS1-related proline-alanine-rich protein kinaseQ9UEW8Details
Serine/threonine-protein kinase TAO3Q9H2K8Details
Serine/threonine-protein kinase tousled-like 1Q9UKI8Details
Non-receptor tyrosine-protein kinase TNK1Q13470Details
Serine/threonine-protein kinase ULK1O75385Details
AP2-associated protein kinase 1Q2M2I8Details
BMP-2-inducible protein kinaseQ9NSY1Details
Calcium/calmodulin-dependent protein kinase kinase 1Q8N5S9Details
Citron Rho-interacting kinaseO14578Details
Casein kinase I isoform alphaP48729Details
Interferon-induced, double-stranded RNA-activated protein kinaseP19525Details
eIF-2-alpha kinase GCN2Q9P2K8Details
Dual specificity mitogen-activated protein kinase kinase 3P46734Details
Mitogen-activated protein kinase kinase kinase kinase 4O95819Details
Serine/threonine-protein kinase MARK2Q7KZI7Details
CLIP-associating protein 1Q7Z460Details
Misshapen-like kinase 1Q8N4C8Details
Serine/threonine-protein kinase Nek9Q8TD19Details
Serine/threonine-protein kinase OSR1O95747Details
Serine/threonine-protein kinase PAK 2Q13177Details
Serine/threonine-protein kinase PAK 4O96013Details
Phosphatidylinositol 4-kinase betaQ9UBF8Details
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinaseQ99640Details
Serine/threonine-protein kinase N1Q16512Details
Serine/threonine-protein kinase N2Q16513Details
Serine/threonine-protein kinase PRP4 homologQ13523Details
Serine/threonine-protein kinase RIO1Q9BRS2Details
Serine/threonine-protein kinase RIO2Q9BVS4Details
Receptor-interacting serine/threonine-protein kinase 2O43353Details
Serine/threonine-protein kinase 10O94804Details
Intestinal-type alkaline phosphataseP09923Details
Histone-lysine N-methyltransferase EZH2Q15910Details
Exportin-1O14980Details
POU domain, class 2, transcription factor 1P14859Details
DystrophinP11532Details
Solute carrier family 43 member 3Q8NBI5Details
Cytochrome b reductase 1Q53TN4Details
ATP-citrate synthaseP53396Details
Very long-chain acyl-CoA synthetaseO14975Details
Sodium-coupled neutral amino acid transporter 1Q9H2H9Details
Sodium-coupled neutral amino acid transporter 2Q96QD8Details
DNA (cytosine-5)-methyltransferase 3AQ9Y6K1Details
Zinc transporter SLC39A7Q92504Details
Zinc transporter 5Q8TAD4Details
Zinc transporter ZIP3Q9BRY0Details
Tyrosine-protein phosphatase non-receptor type 12Q05209Details
V-type proton ATPase 116 kDa subunit a isoform 4Q9HBG4Details
Caspase-4P49662Details
Plasma membrane calcium-transporting ATPase 1P20020Details
Caspase-9P55211Details
DNA (cytosine-5)-methyltransferase 3BQ9UBC3Details
Interleukin-6 receptor subunit betaP40189Details
Molybdopterin synthase catalytic subunitO96007Details
Receptor protein-tyrosine kinaseQ504U8Details