Global Screening of CK2 Kinase Substrates byan Integrated Phosphoproteomics Workflow
Yangyang Bian1, 2, Mingliang Ye1*, Chunli Wang1, 2,Kai Cheng1, 2,Chunxia Song1,2,Mingming Dong1, 2, Yanbo Pan1, 2, Hongqiang Qin1, 2,Hanfa Zou1*
1Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
2University of Chinese Academy of Sciences, Beijing 100049, China.
*To whom correspondence should be addressed:
Prof. Dr. Mingliang Ye,Prof. Dr. Hanfa Zou
Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, Fax: (+) 86-411-84379620
E-mail: ;
SupplementaryMethods
Materials and Chemicals
Dithiothreitol (DTT), iodoacetamide (IAA), Triethylammonium bicarbonate buffer (TEAB), trifluoroacetic acid (TFA), adenosine triphosphate (ATP), protease cocktail and trypsin were all obtained from Sigma Aldrich (St. Louis, MO, USA). EDTA, EGTA and PMSF were purchased from Amresco (Solon, Ohio, USA). Formic acid (FA) was bought from Fluka (Buches, Germany) and acetonitrile (ACN, HPLC grade) was purchased from Merck (Darmstadt, Germany). The CNBr-activated sepharose was obtained from GE Health. All the water used in the experiments was purified using a Mili-Q system from Millipore Company (Bedford, MA).Casein kinase 2 was also obtained from Millipore. Magic C18AQ (5 μm, 20 nm pore) was purchased from Michrom BioResources (Auburn, CA). Fused silica capillaries with 75 μm i.d. were purchased from Yongnian Optical Fiber Factory (Hebei, China).
Cell Culture and Protein Extraction
The HeLa cells and Jurkat cells were grown separately in RPMI-1640, supplemented with 10% bovine serum, 100 U/mL of streptomycin and penicillin in humidified atmosphere of 5% CO2 at 37℃. The cells were sonicated in buffer containing 50 mM HEPES (pH=7.5), 65 mM DTT, 2% protease cocktail (v/v), 1% Triton X-100 (v/v), 1 mM PMSF. The solution was thencentrifuged at 25000 g under 4℃ and the concentration of protein in the supernatant was measured by Bradford’s method.
Protein Immobilization and Dephosphorylation
The CNBr-activated sepharose (GE Health) were activated and washed with 1mM HCl solution.For immobilization of protein, 2mg Hela or jurkat cell proteins weremixed with 80mg CNBr-activated sepharose at 4 ℃ overnight in a cool-heat-shake (Multi-Therm). Then, thesepharose were blocked with 1M glycine solution for 3 h at 25℃, andwashedwith 50 mM HEPES buffer (pH=7.5). To reduce the interference of the endogenous phosphorylation, the sepharose were added into the dephosphorylation buffer containing 1mM MgCl2, 1mM ZnCl2, 50mM HEPES (pH=7.5).75Ualkaline phosphatase (Sigma) was added and the reaction was proceededfor 5 h at 37 ℃. After that, another 25 U alkaline phosphatase was added and left to react for another 12 h at 37℃.Finally, the solution was heated at 95 ℃ for 15 min to inactivate the alkaline phosphatase and endogenous kinases.
Online 2D-LC-MS/MS Analysis
A 14 cm RP-SCX biphasic column (200 μm i.d.) was prepared as previously described1.The column was used as the trapping column and the first dimensional separation column in the 2D-RPLC-MS/MS. Phosphopeptides were redissolved in 0.1% FA in water and automatically loaded onto the biphasic trapping column.The phosphopeptides retained on the RP segment were eluted by aRP gradient nanoflow LC-MS/MS (0 mM) onto the SCX monolithic column. Then a series of stepwise elution with salt concentrations of25, 50, 100, 1000 mM NH4AC were applied to elute phosphopeptides from the SCX monolithic column to the second dimensional analytical column. Each elution lasted10 min and followed by equilibrium by 0.1% FAin water for additional 10 min. Each elution step was followed by a subsequent RP-LC-MS/MS analysis with a 97 min gradient from 5-25% ACN.For the RPLCseparation, 0.1% FA in water and in acetonitrile were used asmobile phases A and B, and the separationcapillary column with a 75 μm i.d. was in-house packed with C18particles (3 μm, 120 Å) to 14 cm length.The MS analysis was performed on LTQ-Orbitrap Velos (Thermo, San Jose,CA) at a resolution of 60 000. The temperature of the ion transfercapillary was set at 250 ℃. The parameters were set as: ion spray voltage, 2.0 kV; MS range, 400-2000 m/z at a resolution of 60 000; normalized collision energy, 35%; the 20 most intense precursors were selected for subsequent fragmentation (CID) using a data-dependent acquisition mode, andthe multistage activation was enabled. The dynamic exclusion settings: repeat count 1, repeat duration 30 s, exclusion duration 60 s.
Database Search and Data Analysis
The raw data files generated by the LTQ-Orbitrap Velos were analyzed with softwareMaxQuant version 1.1.1.362,which were developed by Matthias Mann’s lab. The MS/MS spectras were searched against the human International Protein Index sequence database version 3.80 (63,012 sequences) supplemented by frequently observed contaminants, concatenated with reversed versions of all sequences.Enzyme specificity was set as trypsin (KR/P), up to two missed cleavage sites were allowed.Phospho (STY),loss of ammonia and water was chosen for variable modifications; carbamidomethyl was chosen for fixed modifications.Dimethyl (heavy or light) atN-terminal and lysine werealso set as variable modifications, and a maximum of three labeled amino acids were allowed.The required FDR was set to 0.01 at the peptide, proteinand site level respectively, andthe minimum required peptide length was six amino acids. The least modified peptides were chosen for the quantification of the phosphorylation sites.Sequence logos were automatically generated by theWebLogo program (
In VitroPhosphorylationof SyntheticPeptides by CK2
Syntheticpeptides were dissolved with a final concentration of 4 mg/mL. The reaction was performed in the kinase buffer described above, 4 μg peptides were added into 20 μL kinase buffer containing 500 μM ATP. For kinase reaction, 20 ng CK2 was added for each sample, and the control experiment was performed without addition of CK2. The reaction was incubated at 30℃ for 30 min and stopped by putting the sample on ice. The resultant solution was diluted and analyzed by ABI 5800 MALDI TOF/TOF with a reflectionmode.
SupplementaryFigure S1. Distribution of the H/L ratioof p-sites quantified by the quantitativephosphoproteomics approach for experiments 1 and 2.
SupplementaryFigure S2. Distribution of the RSD of the p-sites quantified by the quantitativephosphoproteomics approach for Hela cell and jurkat cell, respectively.
SupplementaryFigure S3. MALDI-TOF mass spectra of the peptide AALACCSEDEEDD incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S4.MALDI-TOF mass spectra of the peptide EDKLQNSDDDEKM incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S5.MALDI-TOF mass spectra of the peptide YEDDGISDDEIEG incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S6.MALDI-TOF mass spectra of the peptide AEDEGDSEPEAVG incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S7.MALDI-TOF mass spectra of the peptide NRPDYVSEEEEDD incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S8.MALDI-TOF mass spectra of the peptide EESLEDSDVDADF incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S9.MALDI-TOF mass spectra of the peptide EDICEDSDIDGDY incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S10.MALDI-TOF mass spectra of the peptide GGAGFGTDGDDQE incubated with A) ATP, B) ATP and CK2.
SupplementaryFigure S11.The extracted ion chromatograms for the peptides labeled with light (CH3, black line) and heavy (CHD2, red line) dimethyl labels. No significant retention time shifts between the peptide pairs were observed, indicating the deuterated and non-deuterated peptides do not compromise the quantification performance.
Supplementary Table S4. List of the known CK2 substrates with sites identified in this study. Class H dataset: CK2 substrate sites that had been identified in vivo by large scale phosphoproteomics. Class L dataset: CK2 substrate sites that had not been identified in vivo by large scale phosphoproteomics.
Number / Protein Names / Class H/L* / Accession / Identified CK2p-sites / Organisms / Reference1 / HMGA1 / Class H / P17096 / EGISQESpSpEEEQ_ / Human / 4
2 / ANP32B / Class H / Q92688 / EKRKRETpDDEGED / Human / 5
3 / HDGF / Class H / P51858 / GNAEGSSpDEEGKL / Human / 6, 7
4 / MYH9 / Class H / P35579 / KGAGDGSpDEEVDG / Human / 8
5 / DEK / Class H / P35659 / SKKESpESpEDSpSDD
PGPREESpEEEEDE
KNKEESpSpDDEDKESpEEE / Human / 9
6 / TOP2A / Class H / P11388 / PQKSVVSpDLEADD
EEENEESpDNEKET
NENTEGSpPQEDGV / Human / 10, 11
7 / eEF1D / Class H / P29692 / DIDLFGSpDNEEED / Human / 12
8 / MCM2 / Class H / P49736 / RGLLYDSpDEEDEE / Human / 13
9 / CANX / Class H / P27824 / EDGGTVSpQEEEDR / Human / 14
10 / HSP90B / Class H / P08238 / KIEDVGSpDEEDDS
EREKEISpDDEAEE / Human / 15
11 / HSP90A / Class H / P07900 / ERDKEVSpDDEAEE
EIEDVGSpDEEEEK / Human / 15
12 / SSB / Class H / P05455 / KKTKFASpDDEHDE / Human / 16
13 / HDAC1 / Class H / Q13547 / EEEFSpDSpEEEGEG / Human / 17
14 / HDAC2 / Class H / Q92769 / DAVHEDSpGDEDGE / Human / 18, 19
15 / SMC3 / Class H / Q9UQE7 / DVEGSQSpQDEGEG / Human / 20
16 / RAD9A / Class H / Q99638 / PVLAEDSpEGEG__ / Human / 21
17 / CTNNA1 / Class H / P35221 / PEELDDSpDFETED / Human / 22
18 / LIG1 / Class H / P18858 / AARVLGSpEGEEED / Human / 23
19 / HNRNPC / Class H / P07910 / EGGADDSpAEEGDL / Human / 24
20 / YY1 / Class H / P25490 / VVGGDDSpDGLRAE / Human / 25
21 / SPTAN1 / Class L / Q13813 / AERLIQSpHPESAE / Human / 26
22 / USP7 / Class H / Q93009 / AGEQQLSpEPEDME / Human / 27
23 / HDAC3 / Class H / O15379 / HDNDKESpDVEI / Human / 28
24 / MDC1 / Class H / Q14676 / PGEDSpDTpDVDDDS
TERDSpDTpDVEEEE / Human / 29
25 / MRE11A / Class H / P49959 / VIEVDESpDVEEDI / Human / 30
26 / LEF1 / Class H / Q9UJU2 / KIFAEISpHPEEEG / Human / 31
27 / HMGN1 / Class H / P05114 / TEESPASpDEAGEK / Human / 32
28 / IPP2 / Class H / P41236 / RIQEQESpSGEEDS / Human / 33
29 / MYH10 / Class H / P35580 / GASLELSpDDDTES / Human / 34
30 / PDIA6 / Class H / Q15084 / EDDIDLSpDVELDD / Cow / 35
31 / PSMA3 / Class H / P25788 / LKEEDESpDDDNM_ / Rat / 36
32 / eEF1B / Class H / P24534 / DIDLFGSpDDEEES
SDDEEESpEEAKRL / Rabbit / 37
33 / HP1A / Class L / P45973 / KSNFSNSpADDIKS / Mouse / 38
34 / MPR46 / Class H / P20645 / DQLGEESpEERDDH / Mouse / 39, 40
35 / PKR2 / Class H / P13861 / ADAKGDSpESpEEDE / Mouse / 41
36 / IGF2R / Class H / P11717 / VSFHDDSpDEDLLH
HGDDQDSpEDEVLT / Mouse / 42
37 / PML / Class H / P29590 / VVVISSSpEDSpDAE / Yeast/Human / 43, 44
38 / MRLC2 / Class L / O14950 / TMGDRFTpDEEVDE / Chicken / 45
39 / PDAP1 / Class H / Q62785 / KSLDSpDESpEDEE / Rat / 46
Supplementary Table S5.List of known CK2 substrates identified in this study, while the phosphorylation sites have not been identified as CK2 substrate sites in the literatures. Class H dataset: CK2 substrate sites that had been identified in vivo by large scale phosphoproteomics. Class L dataset: CK2 substrate sites that had not been identified in vivo by large scale phosphoproteomics.
Number / Protein name / Class H/L* / Accession / Identified site / Organisms / Reference1 / NPM / Class L / P06748 / KTPKGPSpSVEDIK / Human / 47, 48
2 / eIF2B / Class H / P20042 / KIESpDVQEPTpEPE / Human / 49
3 / HIRIP3 / Class H / Q9BW71 / SKAVEESpSpDEERQ
AQRGEESpSpEEEEK
QAREESpEESpEAEPV
GNKGTKSpLKESEQ
KESEQESpEEEILA
KRLLGDSpDSpEEEQ
GGKRLSpGSpSpEDEE
STSGEESpDLEREV / Human / 50
4 / SIRT1 / Class H / Q96EB6 / GGAGFGTpDGDDQE / Human / 51, 52
5 / SSRP1 / Class H/L / Q08945 / GMNPSpYDEYpADSDE / Human / 53
6 / ABC50 / Class H / Q8NE71 / KKAEQGSpEEEGEG
KKLSVPTpSDEEDE / Human / 54
7 / PRPF3 / Class H / O43395 / GDDDEESpDEEAVK / Human / 55
8 / WASP / Class L / P42768 / ISEAQLTpDAETSK / Human / 56
9 / CBX1 / Class H / P83916 / GKRKADSpDSEDKG / Human / 57
10 / hnRNPA1 / Class H / P09651 / ___MSKSpESPKEP / Human / 58
11 / KIF1C / Class H / O43896 / LYADSpDSpGDDSDK / Human / 59
12 / PC4 / Class H/L / P53999 / SSSGSDSpDSEVDK
QLKEQISpDIDDAV / Human / 60
13 / MAP1B / Class H / P46821 / KGEAEQSpEEEADE / Human / 61
14 / BTF3 / Class L / P20290 / GKAPLATpGEDDDD / Human / 62
15 / APEX / Class L / P27695 / DGDELRTpEPEAKK / Human / 63
16 / C1QBP / Class L / Q07021 / REVSFQSpTGESEW
AFVDFLSpDEIKEE / Human / 64
17 / LEDGF / Class H/L / O75475 / VKQPCPSpESDIIT
KQSNASSpDVEVEE
GVTSTSpDSpEEEGD
SVSKEDTpDHEEKA / Human / 65
18 / NAP2 / Class H / A8CGI3 / TDAESpEWHSpENEE / Human / 66
19 / DHPS / Class H / P49366 / KKLEPLSpDEDQH / Human / 67
20 / SRPK1 / Class L / A8K8B2 / SAPHSESpDLPEQE / Human / 68
21 / DDX54 / Class H/L / Q8TDD1 / PTSECTSpDVEPDT
KRFVGQSpGQEDKK / Human / 69
22 / PDCD4 / Class H / Q53EL6 / GRGDSVSpDSpGSDA / Human / 69
23 / RDBP / Class H/L / B4DYX9 / PFQRSISpADDDLQ
VIPPGLSpEEEEAL / Human / 69
24 / NUCKS / Class H / Q9H1E3 / DSHSpAEDSpEDEKE
KNSQEDSpEDSEDK
YSQFQESpDDADED
LMEDVGSpEEEQEE / Rat / 70
25 / NCL / Class H/L / P19338 / KGLSEDTpTEETLK
GFVDFNSpEEDAK
RARIVTpDRETGS
GYVDFESpAEDLE / Mouse / 71
26 / RIOK1 / Class H / Q9BRS2 / FDDADSSpDSENRD / Yeast / 72
27 / EXOSC9 / Class H / Q06265 / KAPIDTSpDVEEKA / Yeast / 73
28 / SEC63 / Class L / Q9UGP8 / EVSDKGSpDSEEEE / Yeast / 74
29 / SURF6 / Class H / O75683 / FNKVEVSpEDEPAS / Drosophila / 75
Reference
1.Wang, F.J. et al. A fully automated system with online sample loading, isotope dimethyl labeling and multidimensional separation for high-throughput quantitative proteome analysis. Anal Chem82, 3007-3015 (2010).
2.Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol26, 1367-1372 (2008).
3.Crooks, G.E., Hon, G., Chandonia, J.M. & Brenner, S.E. WebLogo: a sequence logo generator. Genome Res14, 1188-1190 (2004).
4.Zou, Y. & Wang, Y. Tandem mass spectrometry for the examination of the posttranslational modifications of high-mobility group A1 proteins: symmetric and asymmetric dimethylation of Arg25 in HMGA1a protein. Biochemistry44, 6293-6301 (2005).
5.Chemnitz, J., Pieper, D., Gruettner, C. & Hauber, J. Phosphorylation of the HuR ligand APRIL by casein kinase 2 regulates CD83 expression. Eur J Immunol39, 267-279 (2009).
6.Salvi, M., Sarno, S., Cesaro, L., Nakamura, H. & Pinna, L.A. Extraordinary pleiotropy of protein kinase CK2 revealed by weblogo phosphoproteome analysis. BBA-Mol Cell Res1793, 847-859 (2009).
7.Li, X. et al. The reverse in-gel kinase assay to profile physiological kinase substrates. Nat Methods4, 957-962 (2007).
8.Dulyaninova, N.G., House, R.P., Betapudi, V. & Bresnick, A.R. Myosin-IIA heavy-chain phosphorylation regulates the motility of MDA-MB-231 carcinoma cells. Mol Biol Cell18, 3144-3155 (2007).
9.Kappes, F. et al. Phosphorylation by protein kinase CK2 changes the DNA binding properties of the human chromatin protein DEK. Mol Cell Biol24, 6011 (2004).
10.Chen, M.-C. et al. Novel Mechanism by Which Histone Deacetylase Inhibitors Facilitate Topoisomerase II alpha Degradation in Hepatocellular Carcinoma Cells. Hepatology53, 148-159 (2011).
11.Wells, N.J., Addison, C.M., Fry, A.M., Ganapathi, R. & Hickson, I.D. Serine 1524 is a major site of phosphorylation on human topoisomerase II alpha protein in vivo and is a substrate for casein kinase II in vitro. J Biol Chem269, 29746-29751 (1994).
12.Gyenis, L., Duncan, J.S., Turowec, J.P., Bretner, M. & Litchfield, D.W. Unbiased Functional Proteomics Strategy for Protein Kinase Inhibitor Validation and Identification ofbona fideProtein Kinase Substrates: Application to Identification of as a Substrate for CK2. J Proteome Res10, 4887-4901 (2011).
13.Montagnoli, A. et al. Identification of Mcm2 phosphorylation sites by S-phase-regulating kinases. J Biol Chem281, 10281-10290 (2006).
14.Wong, H.N. et al. Conserved in vivo phosphorylation of calnexin at casein kinase II sites as well as a protein kinase C/proline-directed kinase site. J Biol Chem273, 17227-17235 (1998).
15.Lees-Miller, S.P. & Anderson, C.W. Two human 90-kDa heat shock proteins are phosphorylated in vivo at conserved serines that are phosphorylated in vitro by casein kinase II. J Biol Chem264, 2431 (1989).
16.Schwartz, E.I., Intine, R.V. & Maraia, R.J. CK2 is responsible for phosphorylation of human La protein serine-366 and can modulate rpL37 5'-terminal oligopyrimidine mRNA metabolism. Mol Cell Biol24, 9580 (2004).
17.Pflum, M.K.H., Tong, J.K., Lane, W.S. & Schreiber, S.L. Histone deacetylase 1 phosphorylation promotes enzymatic activity and complex formation. J Biol Chem276, 47733 (2001).
18.Eom, G.H. et al. Casein Kinase-2α1 Induces Hypertrophic Response by Phosphorylation of Histone Deacetylase 2 S394 and its Activation in the HeartClinical Perspective. Circulation123, 2392-2403 (2011).
19.Adenuga, D. & Rahman, I. Protein kinase CK2-mediated phosphorylation of HDAC2 regulates co-repressor formation, deacetylase activity and acetylation of HDAC2 by cigarette smoke and aldehydes. Arch Biochem Biophys498, 62-73 (2010).
20.Luo, H. et al. Regulation of intra-S phase checkpoint by ionizing radiation (IR)-dependent and IR-independent phosphorylation of SMC3. J Biol Chem283, 19176-19183 (2008).
21.Takeishi, Y. et al. Casein kinase 2-dependent phosphorylation of human Rad9 mediates the interaction between human Rad9-Hus1-Rad1 complex and TopBP1. Genes Cells15, 761-771 (2010).
22.Ji, H. et al. EGF-Induced ERK Activation Promotes CK2-Mediated Disassociation of alpha-Catenin from beta-Catenin and Transactivation of beta-Catenin. Mol Cell36, 547-559 (2009).
23.Rossi, R. et al. The replication factory targeting sequence/PCNA-binding site is required in G1 to control the phosphorylation status of DNA ligase I. EMBO J18, 5745-5754 (1999).
24.Stone, J.R., Maki, J.L. & Collins, T. Basal and hydrogen peroxide stimulated sites of phosphorylation in heterogeneous nuclear ribonucleoprotein C1/C2. Biochemistry42, 1301-1308 (2003).
25.Riman, S. et al. Phosphorylation of the Transcription Factor YY1 by CK2α Prevents Cleavage by Caspase 7 during Apoptosis. Mol Cell Biol32, 797-807 (2012).
26.Ramser, E.M., Buck, F., Schachner, M. & Tilling, T. Binding of [alpha] II spectrin to 14-3-3 [beta] is involved in NCAM-dependent neurite outgrowth. Mol Cell Neurosci45, 66-74 (2010).
27.Khoronenkova, S.V. et al. ATM-Dependent Downregulation of USP7/HAUSP by PPM1G Activates p53 Response to DNA Damage. Mol Cell45, 801-813 (2012).
28.Zhang, X. et al. Histone deacetylase 3 (HDAC3) activity is regulated by interaction with protein serine/threonine phosphatase 4. Genes Deve19, 827 (2005).
29.Wu, L., Luo, K., Lou, Z. & Chen, J. MDC1 regulates intra-S-phase checkpoint by targeting NBS1 to DNA double-strand breaks. Proc Natl Acad Sci U S A105, 11200-11205 (2008).
30.Kim, S.T. Protein kinase CK2 interacts with Chk2 and phosphorylates Mre11 on serine 649. Biochem Biophys Res Commun331, 247-252 (2005).
31.Wang, S. & Jones, K.A. CK2 controls the recruitment of Wnt regulators to target genes in vivo. Curr Biol16, 2239-2244 (2006).
32.Jiang, X.G. & Wang, Y. Phosphorylation of human high mobility group N1 protein by protein kinase CK2. Biochem Biophys Res Commun345, 1497-1503 (2006).
33.Kakinoki, Y., Somers, J. & Brautigan, D.L. Multisite phosphorylation and the nuclear localization of phosphatase inhibitor 2-green fluorescent protein fusion protein during S phase of the cell growth cycle. J Biol Chem272, 32308-32314 (1997).
34.Murakami, N., Chauhan, V.P.S. & Elzinga, M. Two nonmuscle myosin II heavy chain isoforms expressed in rabbit brains: filament forming properties, the effects of phosphorylation by protein kinase C and casein kinase II, and location of the phosphorylation sites. Biochemistry37, 1989-2003 (1998).
35.Janson, I.M., Ek, B. & Ek, P. Phosphorylation of CaBP1 and CaBP2 by Protein Kinase CK21. J Biochem121, 112 (1997).
36.Castaño, J.G., Mahillo, E., Arizti, P. & Arribas, J. Phosphorylation of C8 and C9 subunits of the multicatalytic proteinase by casein kinase II and identification of the C8 phosphorylation sites by direct mutagenesis. Biochemistry35, 3782-3789 (1996).
37.Sheu, G.T. & Traugh, J.A. A structural model for elongation factor 1 (EF-1) and phosphorylation by protein kinase CKII. Mol Cell Biochem191, 181-186 (1999).
38.Hiragami-Hamada, K. et al. N-terminal phosphorylation of HP1 {alpha} promotes its chromatin binding. Mol Cell Biol31, 1186 (2011).
39.Dittié, A.S., Klumperman, J. & Tooze, S.A. Differential distribution of mannose-6-phosphate receptors and furin in immature secretory granules. J Cell Sci112, 3955-3966 (1999).
40.Stöckli, J., Höning, S. & Rohrer, J. The acidic cluster of the CK2 site of the cation-dependent mannose 6-phosphate receptor (CD-MPR) but not its phosphorylation is required for GGA1 and AP-1 binding. J Biol Chem279, 23542-23549 (2004).
41.Carmichael, D., Geahlen, R., Allen, S. & Krebs, E. Type II regulatory subunit of cAMP-dependent protein kinase. Phosphorylation by casein kinase II at a site that is also phosphorylated in vivo. J Biol Chem257, 10440-10445 (1982).
42.Rosorius, O. et al. Characterization of phosphorylation sites in the cytoplasmic domain of the 300 kDa mannose-6-phosphate receptor. Biochem J292, 833 (1993).
43.Scaglioni, P.P. et al. A CK2-dependent mechanism for degradation of the PML tumor suppressor. Cell126, 269-283 (2006).
44.Stehmeier, P. & Muller, S. Phospho-Regulated SUMO Interaction Modules Connect the SUMO System to CK2 Signaling. Mol. Cell33, 400-409 (2009).
45.Tashiro, Y., Matsumura, S., Murakami, N. & Kumon, A. The phosphorylation site for casein kinase II on 20,000-Da light chain of gizzard myosin. Arch Biochem Biophys233, 540-546 (1984).
46.Shen, L., Huang, K.P., Chen, H.C. & Huang, F.L. Molecular cloning and characterization of a novel casein kinase II substrate, HASPP28, from rat brain. Arch Biochem Biophys327, 131-141 (1996).
47.Wang, G., Pan, Y., Ahmad, K.A. & Ahmed, K. Protein B23/nucleophosmin/numatrin nuclear dynamics in relation to protein kinase CK2 and apoptotic activity in prostate cells. Biochemistry49, 3842-3852 (2010).
48.Chan, P., Liu, Q. & Durban, E. The major phosphorylation site of nucleophosmin (B23) is phosphorylated by a nuclear kinase II. Biochem J270, 549 (1990).
49.Llorens, F. et al. The N-terminal domain of the human eIF2β subunit and the CK2 phosphorylation sites are required for its function. Biochem J394, 227 (2006).
50.Assrir, N., Filhol, O., Galisson, F. & Lipinski, M. HIRIP3 is a nuclear phosphoprotein interacting with and phosphorylated by the serine-threonine kinase CK2. Biol Chem388, 391-398 (2007).
51.McFarland, T.P., Sleiman, N.H., Yaeger, D.B. & Cala, S.E. The cytosolic protein kinase CK2 phosphorylates cardiac calsequestrin in intact cells. Mol Cell Biochem353, 1-11 (2011).
52.Zschoernig, B. & Mahlknecht, U. Carboxy-terminal phosphorylation of SIRT1 by protein kinase CK2. Biochem Biophys Res Commun381, 372-377 (2009).
53.Li, Y., Keller, D.M., Scott, J.D. & Lu, H. CK2 phosphorylates SSRP1 and inhibits its DNA-binding activity. J Biol Chem280, 11869-11875 (2005).
54.Paytubi, S., Morrice, N., Boudeau, J. & Proud, C. The N-terminal region of ABC50 interacts with eukaryotic initiation factor eIF2 and is a target for regulatory phosphorylation by CK2. Biochem J409, 223-231 (2008).
55.Lehnert, S., Götz, C., Kartarius, S., Schäfer, B. & Montenarh, M. Protein kinase CK2 interacts with the splicing factor hPrp3p. Oncogene27, 2390-2400 (2007).
56.Cory, G.O.C., Cramer, R., Blanchoin, L. & Ridley, A.J. Phosphorylation of the WASP-VCA domain increases its affinity for the Arp2/3 complex and enhances actin polymerization by WASP. Mol Cell11, 1229-1239 (2003).
57.Ayoub, N., Jeyasekharan, A.D., Bernal, J.A. & Venkitaraman, A.R. HP1-β mobilization promotes chromatin changes that initiate the DNA damage response. Nature453, 682-686 (2008).
58.Cobianchi, F., Calvio, C., Stoppini, M., Buvoli, M. & Riva, S. Phosphorylation of human hnRNP protein A1 abrogates in vitro strand annealing activity. Nucleic Acids Res21, 949 (1993).
59.Dorner, C., Ullrich, A., Haring, H.U. & Lammers, R. The kinesin-like motor protein KIF1C occurs in intact cells as a dimer and associates with proteins of the 14-3-3 family. J Biol Chem274, 33654-33660 (1999).
60.Ge, H., Zhao, Y., Chait, B.T. & Roeder, R.G. Phosphorylation negatively regulates the function of coactivator PC4. Proc Natl Acad Sci U S A91, 12691 (1994).
61.Avila, J., Ulloa, L., Gonzalez, J., Moreno, F. & Diaz-Nido, J. Phosphorylation of microtubule-associated proteins by protein kinase CK2 in neuritogenesis. Cell Mol Biol Res40, 573-579 (1994).
62.Grein, S. & Pyerin, W. BTF3 is a potential new substrate of protein kinase CK2. A Molecular and Cellular View of Protein Kinase CK227, 121-128 (1999).
63.Fritz, G. & Kaina, B. Phosphorylation of the DNA repair protein APE/REF-1 by CKII affects redox regulation of AP-1. Oncogene18, 1033 (1999).
64.Bryant, H.E. et al. Interaction between herpes simplex virus type 1 IE63 protein and cellular protein p32. J Virol74, 11322-11328 (2000).
65.Garcia-Rivera, J.A. et al. Implication of serine residues 271, 273, and 275 in the human immunodeficiency virus type 1 cofactor activity of lens epithelium-derived growth factor/p75. J Virol84, 740 (2010).
66.Rodriguez, P., Pelletier, J., Price, G.B. & Zannis-Hadjopoulos, M. NAP-2: histone chaperone function and phosphorylation state through the cell cycle1. J Mol Biol298, 225-238 (2000).
67.Kang, K.R. & Chung, S.I. Protein kinase CK2 phosphorylates and interacts with deoxyhypusine synthase in HeLa cells. Exp Mol Med35, 556-564 (2003).