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1.
Open Biol ; 13(2): 220220, 2023 02.
Article in English | MEDLINE | ID: mdl-36809799

ABSTRACT

CK2 is a Ser/Thr protein kinase composed of two catalytic (α/α') subunits and a non-catalytic ß-subunit dimer, whose activity is often abnormally high in cancer cells. The concept that CK2 may be dispensable for cell survival has been challenged by the finding that viable CK2α/α' knock-out myoblast clones still express small amounts of an N-terminally deleted α' subunit generated during the CRISPR/Cas9 procedure. Here we show that, although the overall CK2 activity of these CK2α(-/-)/Δα' (KO) cells is less than 10% compared to wild-type (WT) cells, the number of phosphosites with the CK2 consensus is comparable to that of WT cells. A more in-depth analysis, however, reveals that the two phosphoproteomes are not superimposable according to a number of criteria, notably a functional analysis of the phosphoproteome found in the two types of cells, and variable sensitivity of the phosphosites to two structurally unrelated CK2 inhibitors. These data support the idea that a minimal CK2 activity, as in KO cells, is sufficient to perform basic housekeeping functions essential for cell survival, but not to accomplish several specialized tasks required upon cell differentiation and transformation. From this standpoint, a controlled downregulation of CK2 would represent a safe and valuable anti-cancer strategy.


Subject(s)
Casein Kinase II , Myoblasts , Casein Kinase II/metabolism , Cell Line , Myoblasts/metabolism
2.
Crit Rev Biochem Mol Biol ; 56(4): 321-359, 2021 08.
Article in English | MEDLINE | ID: mdl-33843388

ABSTRACT

CK2 is a constitutively active protein kinase that assuring a constant level of phosphorylation to its numerous substrates supports many of the most important biological functions. Nevertheless, its activity has to be controlled and adjusted in order to cope with the varying needs of a cell, and several examples of a fine-tune regulation of its activity have been described. More importantly, aberrant regulation of this enzyme may have pathological consequences, e.g. in cancer, chronic inflammation, neurodegeneration, and viral infection. Our review aims at summarizing our current knowledge about CK2 regulation. In the first part, we have considered the most important stimuli shown to affect protein kinase CK2 activity/expression. In the second part, we focus on the molecular mechanisms by which CK2 can be regulated, discussing controversial aspects and future perspectives.


Subject(s)
Casein Kinase II/metabolism , Neoplasm Proteins/metabolism , Neoplasms/enzymology , Signal Transduction , Virus Diseases/enzymology , Animals , Humans , Inflammation/enzymology
3.
Eur J Med Chem ; 214: 113217, 2021 Mar 15.
Article in English | MEDLINE | ID: mdl-33548633

ABSTRACT

CK2 (an acronym derived from the misnomer "casein kinase 2") denotes a ubiquitous, highly pleiotropic protein kinase which has been implicated in global human pathologies, with special reference to cancer. A large spectrum of fairly selective, cell permeable CK2 inhibitors are available, one of which, CX4945 is already in clinical trials for the treatment of neoplasia. Another recently developed CK2 inhibitor, GO289, displays in vitro potency and selectivity comparable to CX4945. Here the cellular efficiency of these two inhibitors has been evaluated by treating C2C12 myoblasts for 5 h with each of them at 4 µM concentration and running a quantitative phosphoproteomics analysis of phosphosites affected by the two compounds. A small but significant proportion of the quantified phosphosites is decreased by treatment with CX4945 and, even more with GO289. This figure substantially increases if a subset of quantified phosphosites conforming to the CK2 consensus (pS/pT-x-x-D/E/pS/pT) is considered. Also in this case GO289 is more effective than CX4945. By adopting stringent criteria two shortlists of 70 and 35 sites whose phosphorylation is decreased >50% by GO289 and CX4945, respectively, have been generated. All these phosphosites conform to the consensus of CK2 with just sporadic exceptions. Their WebLogos are indistinguishable from that of bona fide CK2 phosphosites and their Two-Sample Logos rule out any significant contribution of Pro-directed and basophilic protein kinases to their generation. To sum up, we can conclude that by treating C2C12 cells for 5 h with either CX4945 or GO289 off-target effects are negligible since almost all the phosphosites undergoing a substantial reduction are attributable to CK2, with a higher inhibitory efficacy displayed by GO289. CX4945 and GO289 provide highly selective tools to control the CK2-dependent phosphoproteome compared with previously developed CK2 inhibitors.


Subject(s)
Casein Kinase II/antagonists & inhibitors , Naphthyridines/pharmacology , Phenazines/pharmacology , Protein Kinase Inhibitors/pharmacology , Proteomics , Animals , Casein Kinase II/metabolism , Cells, Cultured , Dose-Response Relationship, Drug , Mice , Molecular Structure , Naphthyridines/chemistry , Phenazines/chemistry , Protein Kinase Inhibitors/chemistry , Structure-Activity Relationship
4.
Redox Biol ; 36: 101639, 2020 09.
Article in English | MEDLINE | ID: mdl-32863204

ABSTRACT

Fyn is a tyrosine kinase belonging to the Src family (Src-Family-Kinase, SFK), ubiquitously expressed. Previously, we report that Fyn is important in stress erythropoiesis. Here, we show that in red cells Fyn specifically stimulates G6PD activity, resulting in a 3-fold increase enzyme catalytic activity (kcat) by phosphorylating tyrosine (Tyr)-401. We found Tyr-401 on G6PD as functional target of Fyn in normal human red blood cells (RBC), being undetectable in G6PD deficient RBCs (G6PD-Mediterranean and G6PD-Genova). Indeed, Tyr-401 is located to a region of the G6PD molecule critical for the formation of the enzymatically active dimer. Amino acid replacements in this region are mostly associated with a chronic hemolysis phenotype. Using mutagenesis approach, we demonstrated that the phosphorylation status of Tyr401 modulates the interaction of G6PD with G6P and stabilizes G6PD in a catalytically more efficient conformation. RBCs from Fyn-/-mice are defective in G6PD activity, resulting in increased susceptibility to primaquine-induced intravascular hemolysis. This negatively affected the recycling of reduced Prx2 in response to oxidative stress, indicating that defective G6PD phosphorylation impairs defense against oxidation. In human RBCs, we confirm the involvement of the thioredoxin/Prx2 system in the increase vulnerability of G6PD deficient RBCs to oxidation. In conclusion, our data suggest that Fyn is an oxidative radical sensor, and that Fyn-mediated Tyr-401 phosphorylation, by increasing G6PD activity, plays an important role in the physiology of RBCs. Failure of G6PD activation by this mechanism may be a major limiting factor in the ability of G6PD deficient RBCs to withstand oxidative stress.


Subject(s)
Glucosephosphate Dehydrogenase Deficiency , Glucosephosphate Dehydrogenase , Animals , Erythrocytes , Glucose-6-Phosphate , Glucosephosphate Dehydrogenase Deficiency/genetics , Hemolysis , Mice , Proto-Oncogene Proteins c-fyn
5.
Biochem Biophys Res Commun ; 531(3): 409-415, 2020 10 20.
Article in English | MEDLINE | ID: mdl-32800562

ABSTRACT

Viable clones of C2C12 myoblasts where both catalytic subunits of protein kinase CK2 had been knocked out by the CRISPR/Cas9 methodology have recently been generated, thus challenging the concept that CK2 is essential for cell viability. Here we present evidence that these cells are still endowed with a residual "CK2-like" activity that is able to phosphorylate Ser-13 of endogenous CDC37. Searching for a molecular entity accounting for such an activity we have identified a band running slightly ahead of CK2α' on SDS-PAGE. This band is not detectable by in-gel casein kinase assay but it co-immuno-precipitates with the ß-subunit being downregulated by specific CK2α' targeting siRNA treatment. Its size and biochemical properties are consistent with those of CK2α' mutants deleted upstream of Glu-15 generated during the knockout process. This mutant sheds light on the role of the CK2 N-terminal segment as a regulator of activity and stability. Comparable cytotoxic efficacy of two selective and structurally unrelated CK2 inhibitors support the view that survival of CK2α/α'-/- cells relies on this deleted form of CK2α', whose discovery provides novel perspectives about the biological role of CK2.


Subject(s)
Casein Kinase II/chemistry , Casein Kinase II/metabolism , Catalytic Domain , Sequence Deletion , Amino Acid Sequence , Animals , Casein Kinase II/deficiency , Cell Line , Cell Survival , Mice, Knockout , Peptides/metabolism , Phosphorylation , Phosphoserine/metabolism , Protein Stability , Substrate Specificity
6.
Cell Mol Life Sci ; 77(24): 5281-5298, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32052090

ABSTRACT

Protein phosphorylation is the most frequent post-translational modification by which the properties of eukaryotic proteins can be reversibly modified. In humans, over 500 protein kinases generate a huge phosphoproteome including more than 200,000 individual phosphosites, a figure which is still continuously increasing. The in vivo selectivity of protein kinases is the outcome of a multifaceted and finely tuned process where numerous factors play an integrated role. To gain information about the actual contribution to this process of local features that reflect the interaction of the protein targets with the catalytic site of the kinases, the prevalence of the commonest motifs determining the consensus sequence of Ser/Thr-specific kinases has been examined in the whole human phosphoproteome and in the phosphoproteomes generated by a panel of the 47 most pleiotropic protein kinases. Our analysis shows that: (1) most phosphosites do conform to at least one of the motifs considered, with a substantial proportion conforming to two or more of them; (2) some motifs, with special reference to the one recognized by protein kinase CK2 (pS/pT-x-x-E/D) are very promiscuous, being abundantly represented also at the phosphosites of all the other protein kinases considered; (3) by contrast, other phosphorylated motifs, notably pS/pT-P, pS/pT-Q and pS-x-E, are more discriminatory and selective, being nearly absent in the phosphosites that are not attributable to certain categories of kinases. The information provided will prove helpful to make reliable inferences based on the manual inspection of individual phosphosites.


Subject(s)
Amino Acid Motifs/genetics , Phosphorylation/genetics , Protein Processing, Post-Translational/genetics , Proteome/genetics , Casein Kinase II/genetics , Catalytic Domain/genetics , Humans , Phosphotransferases/genetics
7.
FEBS J ; 286(8): 1561-1575, 2019 04.
Article in English | MEDLINE | ID: mdl-30834696

ABSTRACT

The acronym CK2 (derived from the misnomer 'casein kinase-2') denotes a pleiotropic acidophilic protein kinase implicated in a plethora of cellular functions, whose abnormally high expression correlates with malignancy. CK2 holoenzyme is composed of two catalytic (α and/or α') and two noncatalytic ß-subunits. The ß-subunits are not responsible for either activation or inactivation of the catalytic ones. Hence, to gain additional information about the roles of the individual CK2 subunits, we have generated C2C12 myoblasts entirely devoid either of both catalytic subunits, or of the ß-subunit. Here, we show that while CK2α/α'(-/-) cells grow similarly to wild-type cells, the growth of CK2ß(-/-) cells is severely impaired, consistent with the hypothesis that not all cellular functions of the ß-subunit are mediated by CK2 holoenzyme. To get a deeper insight into the functional implications of the ß-subunit, a quantitative proteomics study of CK2ß(-/-) cells was performed, leading to the identification and quantification of more than 1200 proteins. Of these, 187 showed a significantly altered expression (fold change ≥ 1.5 or ≤ -1.5) as compared to wild-type cells. A functional analysis of these proteins discloses the implication of CK2ß in many processes, for example, cell cycle, proliferation, transport, metabolic processes, etc., and in some of which the catalytic subunits of CK2 do not seem to play a relevant role. On the other hand, the pool of ecto-CK2 is not apparently affected by the lack of the ß-subunit. Collectively, our data corroborate the concept that the cellular functions of the ß-subunit of CK2 are partially independent of CK2 holoenzyme.


Subject(s)
Casein Kinase II/metabolism , Myoblasts/metabolism , Proteomics/methods , Animals , Casein Kinase II/genetics , Catalytic Domain , Cell Line , Cell Proliferation , Gene Knockout Techniques , Mice , Protein Subunits , Tandem Mass Spectrometry
8.
Curr Protein Pept Sci ; 20(6): 547-562, 2019.
Article in English | MEDLINE | ID: mdl-30659536

ABSTRACT

Substrate pleiotropicity, a very acidic phosphorylation consensus sequence, and an apparent uncontrolled activity, are the main features of CK2, a Ser/Thr protein kinase that is required for a plethora of cell functions. Not surprisingly, CK2 appears to affect cytoskeletal structures and correlated functions such as cell shape, mechanical integrity, cell movement and division. This review outlines our current knowledge of how CK2 regulates cytoskeletal structures, and discusses involved pathways and molecular mechanisms.


Subject(s)
Casein Kinase II/metabolism , Cytoskeleton/metabolism , Actin Cytoskeleton/metabolism , Actins/metabolism , Animals , Casein Kinase II/chemistry , Cell Division , Cell Movement , Cell Shape , Humans , Phosphorylation , Protein Conformation , Protein Processing, Post-Translational , Septins/metabolism , Signal Transduction , Tubulin/metabolism
9.
Cell Mol Life Sci ; 75(11): 2011-2026, 2018 06.
Article in English | MEDLINE | ID: mdl-29119230

ABSTRACT

CK2 denotes a ubiquitous and pleiotropic protein kinase whose holoenzyme is composed of two catalytic (α and/or α') and two regulatory ß subunits. The CK2 consensus sequence, S/T-x-x-D/E/pS/pT is present in numerous phosphosites, but it is not clear how many of these are really generated by CK2. To gain information about this issue, advantage has been taken of C2C12 cells entirely deprived of both CK2 catalytic subunits by the CRISPR/Cas9 methodology. A comparative SILAC phosphoproteomics analysis reveals that, although about 30% of the quantified phosphosites do conform to the CK2 consensus, only one-third of these are substantially reduced in the CK2α/α'(-/-) cells, consistent with their generation by CK2. A parallel study with C2C12 cells deprived of the regulatory ß subunit discloses a role of this subunit in determining CK2 targeting. We also find that phosphosites notoriously generated by CK2 are not fully abrogated in CK2α/α'(-/-) cells, while some phosphosites unrelated to CK2 are significantly altered. Collectively taken our data allow to conclude that the phosphoproteome generated by CK2 is not as ample and rigidly pre-determined as it was believed before. They also show that the lack of CK2 promotes phosphoproteomics perturbations attributable to kinases other than CK2.


Subject(s)
Casein Kinase II/metabolism , Phosphopeptides/metabolism , Animals , Casein Kinase II/genetics , Cell Line , Gene Deletion , Gene Knockout Techniques , Mice , Phosphopeptides/analysis , Phosphorylation , Proteomics/methods
10.
Sci Rep ; 7(1): 17569, 2017 12 14.
Article in English | MEDLINE | ID: mdl-29242563

ABSTRACT

Insulin plays a major role in glucose metabolism and insulin-signaling defects are present in obesity and diabetes. CK2 is a pleiotropic protein kinase implicated in fundamental cellular pathways and abnormally elevated in tumors. Here we report that in human and murine adipocytes CK2-inhibition decreases the insulin-induced glucose-uptake by counteracting Akt-signaling and GLUT4-translocation to the plasma membrane. In mice CK2 acts on insulin-signaling in adipose tissue, liver and skeletal muscle and its acute inhibition impairs glucose tolerance. Notably, CK2 protein-level and activity are greatly up-regulated in white adipose tissue from ob/ob and db/db mice as well as from obese patients, regardless the severity of their insulin-resistance and the presence of pre-diabetes or overt type 2 diabetes. Weight loss obtained by both bariatric surgery or hypocaloric diet reverts CK2 hyper-activation to normal level. Our data suggest a central role of CK2 in insulin-sensitivity, glucose homeostasis and adipose tissue remodeling. CK2 up-regulation is identified as a hallmark of adipose tissue pathological expansion, suggesting a new potential therapeutic target for human obesity.


Subject(s)
Adipocytes/pathology , Casein Kinase II/metabolism , Insulin/metabolism , Obesity/metabolism , Obesity/pathology , Signal Transduction , Up-Regulation , 3T3-L1 Cells , Adipose Tissue, White/pathology , Animals , Biological Transport , Glucose/metabolism , Humans , Liver/metabolism , Mice , Muscle, Skeletal/metabolism
11.
FEBS J ; 284(13): 1936-1951, 2017 07.
Article in English | MEDLINE | ID: mdl-28079298

ABSTRACT

The first phosphoprotein (casein) was discovered in 1883, yet the enzyme responsible for its phosphorylation was identified only 130 years later, in 2012. In the intervening time, especially in the last decades of the 1900s, it became evident that, far from being an oddity, phosphorylation affects the majority of eukaryotic proteins during their lifespan, and that this reaction is catalysed by the members of a large family of protein kinases, susceptible to a variety of stimuli controlling nearly every aspect of life and death. The aim of this review is to present a historical account of the main steps of this spectacular revolution, which transformed our conception of a biochemical reaction originally held as a sporadic curiosity into the master mechanism governing cell regulation, and, if it is perturbed, causing cell dysregulation.


Subject(s)
Phosphoproteins/metabolism , Proteome/metabolism , Proteomics/methods , Caseins/metabolism , Humans , Phosphates/metabolism , Phosphorus/metabolism , Phosphorylation , Phosvitin/metabolism , Protein Kinases/metabolism , Proteomics/trends
12.
Pharmaceuticals (Basel) ; 10(1)2017 Jan 20.
Article in English | MEDLINE | ID: mdl-28117670

ABSTRACT

The history of protein kinase CK2 is crowded with paradoxes and unanticipated findings. Named after a protein (casein) that is not among its physiological substrates, CK2 remained in search of its targets for more than two decades after its discovery in 1954, but it later came to be one of the most pleiotropic protein kinases. Being active in the absence of phosphorylation and/or specific stimuli, it looks unsuitable to participate in signaling cascades, but its "lateral" implication in a variety of signaling pathways is now soundly documented. At variance with many "onco-kinases", CK2 is constitutively active, and no oncogenic CK2 mutant is known; still high CK2 activity correlates to neoplasia. Its pleiotropy and essential role may cast doubts on the actual "druggability" of CK2; however, a CK2 inhibitor is now in Phase II clinical trials for the treatment of cancer, and cell clones viable in the absence of CK2 are providing information about the mechanism by which cancer becomes addicted to high CK2 levels. A phosphoproteomics analysis of these CK2 null cells suggests that CK2 pleiotropy may be less pronounced than expected and supports the idea that the phosphoproteome generated by this kinase is flexible and not rigidly pre-determined.

13.
Protein Pept Lett ; 23(6): 518-24, 2016.
Article in English | MEDLINE | ID: mdl-27030551

ABSTRACT

ESCRTs (Endosomal Sorting Complexes Required for Transport) are required for the formation of the intraluminal vesicles in the multivesicular bodies and are involved in other topologically similar processes such as cytokinesis, nuclear envelope sealing and viral egress. The final complex ESCRT-III is disassembled by the recruitment and activation of the AAA-ATPase VPS4 to the endosomal membranes. This recruitment is due to the binding of VPS4 N-terminal MIT with MIM1 and MIM2 domains present in the CHMPs proteins. By analyzing different cellular membrane remodeling events in which VPS4 is involved, here we provide evidence that the K61 residue, mapping within the MIT domain of VPS4B (K59 in VPS4A), is involved in VPS4 functioning. Posttranslational modifications of this residue might modulate MIT-MIM2 binding affinity and, as a consequence, VPS4 functions.


Subject(s)
Cell Membrane/metabolism , Endosomal Sorting Complexes Required for Transport/metabolism , Endosomes/metabolism , Vacuolar Proton-Translocating ATPases/metabolism , ATPases Associated with Diverse Cellular Activities , Amino Acid Sequence , Cell Line, Tumor , HEK293 Cells , HeLa Cells , Humans , Protein Binding , Protein Structure, Tertiary , Protein Transport
14.
Oncotarget ; 7(14): 18204-18, 2016 Apr 05.
Article in English | MEDLINE | ID: mdl-26919095

ABSTRACT

Chronic myeloid leukaemia (CML) is a myeloproliferative disorder promoted by the constitutive tyrosine kinase activity of Bcr-Abl oncoprotein. Although treatment with the Bcr-Abl-inhibitor imatinib represents the first-line therapy against CML, almost 20-30% of patients develop chemotherapeutic resistance and require alternative therapy. Here we show that a strong hyper-phosphorylation/activation of ERK1/2, Akt Ser473, and 40S ribosomal protein S6 (rpS6) is detectable in imatinib-resistant KCL22 and K562 CML cells as compared to the -sensitive cell variants. In imatinib-resistant CML cells, high concentration of imatinib is required to strongly inhibit Bcr-Abl, ERK1/2 and Akt Ser473 phosphorylation, but under these conditions the phosphorylation of rpS6, a common downstream effector of MEK/ERK1/2 and PI3K/Akt/mTOR pathways is only slightly reduced. By contrast, down-regulation of the protein kinase CK2 by the inhibitor CX-5011 or by silencing the CK2 subunits does not affect the activation state of MEK/ERK1/2 or PI3K/Akt/mTOR signalling, but causes a drop in rpS6 phosphorylation in parallel with reduced protein synthesis. CK2-inhibition by CX-5011 induces cell death by apoptosis and acts synergistically with imatinib or the MEK-inhibitor U0126 in reducing the viability of imatinib-resistant CML cells. The ternary mixture containing CX-5011, imatinib and U0126 represents the most effective synergistic combination to counteract CML cell viability. These results disclose a novel CK2-mediated mechanism of acquired imatinib-resistance resulting in hyper-phosphorylation of rpS6. We suggest that co-targeting CK2 and MEK protein kinases is a promising strategy to restore responsiveness of resistant CML cells to imatinib.


Subject(s)
Antineoplastic Agents/pharmacology , Antineoplastic Combined Chemotherapy Protocols/pharmacology , Drug Resistance, Neoplasm/drug effects , Imatinib Mesylate/pharmacology , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Protein Kinase Inhibitors/pharmacology , Pyrimidines/pharmacology , Quinolines/pharmacology , Apoptosis/drug effects , Butadienes/pharmacology , Casein Kinase II/antagonists & inhibitors , Casein Kinase II/genetics , Cell Survival/drug effects , Drug Synergism , Enzyme Activation , Extracellular Signal-Regulated MAP Kinases/metabolism , Fusion Proteins, bcr-abl/antagonists & inhibitors , Humans , K562 Cells , MAP Kinase Signaling System/drug effects , Nitriles/pharmacology , Phosphorylation/drug effects , Proto-Oncogene Proteins c-akt/metabolism , RNA Interference , RNA, Small Interfering/genetics , Ribosomal Protein S6/metabolism , Tumor Cells, Cultured
15.
Mol Biosyst ; 11(10): 2666-79, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26211804

ABSTRACT

In the infancy of studies on protein phosphorylation the occurrence of clusters of three or more consecutive phosphoseryl residues in secreted and in cellular phosphoproteins was reported. Later however, while the reversible phosphorylation of Ser, Thr and Tyr residues was recognized to be the most frequent and general mechanism of cell regulation and signal transduction, the phenomenon of multi-phosphorylation of adjacent residues was entirely neglected. Nowadays, in the post-genomic era, the availability of large phosphoproteomics database makes possible a comprehensive re-visitation of this intriguing aspect of protein phosphorylation, aimed at shedding light on both its mechanistic occurrence and its functional meaning. Here we describe an analysis of the human phosphoproteome disclosing the existence of more than 800 rows of 3 to >10 consecutive phosphoamino acids, composed almost exclusively of phosphoserine, while clustered phosphothreonines and phosphotyrosines are almost absent. A scrutiny of these phosphorylated rows supports the conclusion that they are generated through the major contribution of a few hierarchical protein kinases, with special reference to CK2. Also well documented is the combined intervention of CK1 and GSK3, the former acting as priming and primed, the latter as primed kinase. The by far largest proportion of proteins containing (pS)n clusters display a nuclear localization where they play a prominent role in the regulation of transcription. Consistently the molecular function of the by far largest majority of these proteins is the ability to bind other macromolecules and/or nucleotides and metal ions. A "String" analysis performed under stringent conditions reveals that >80% of them are connected to each other by physical and/or functional links, and that this network of interactions mostly take place at the nuclear level.


Subject(s)
Phosphoproteins/chemistry , Phosphoproteins/metabolism , Phosphoserine/metabolism , Casein Kinase I/metabolism , Casein Kinase II/metabolism , Glycogen Synthase Kinase 3/metabolism , Humans , Threonine/metabolism , Tyrosine/metabolism
16.
Curr Genomics ; 16(2): 128-38, 2015 Apr.
Article in English | MEDLINE | ID: mdl-26085811

ABSTRACT

Post-translational modification is the most common mechanism of regulating protein function. If phosphorylation is considered a key event in many signal transduction pathways, other modifications must be considered as well. In particular the side chain of lysine residues is a target of different modifications; notably acetylation, methylation, ubiquitylation, sumoylation, neddylation, etc. Mass spectrometry approaches combining highly sensitive instruments and specific enrichment strategies have enabled the identification of modified sites on a large scale. Here we make a comparative analysis of the most representative lysine modifications (ubiquitylation, acetylation, sumoylation and methylation) identified in the human proteome. This review focuses on conserved amino acids, secondary structures preference, subcellular localization of modified proteins, and signaling pathways where these modifications are implicated. We discuss specific differences and similarities between these modifications, characteristics of the crosstalk among lysine post translational modifications, and single nucleotide polymorphisms that could influence lysine post-translational modifications in humans.

17.
Biochim Biophys Acta ; 1853(7): 1693-701, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25887626

ABSTRACT

In eukaryotic protein synthesis the translation initiation factor 3 (eIF3) is a key player in the recruitment and assembly of the translation initiation machinery. Mammalian eIF3 consists of 13 subunits, including the loosely associated eIF3j subunit that plays a stabilizing role in the eIF3 complex formation and interaction with the 40S ribosomal subunit. By means of both co-immunoprecipitation and mass spectrometry analyses we demonstrate that the protein kinase CK2 interacts with and phosphorylates eIF3j at Ser127. Inhibition of CK2 activity by CX-4945 or down-regulation of the expression of CK2 catalytic subunit by siRNA cause the dissociation of j-subunit from the eIF3 complex as judged from glycerol gradient sedimentation. This finding proves that CK2-phosphorylation of eIF3j is a prerequisite for its association with the eIF3 complex. Expression of Ser127Ala-eIF3j mutant impairs both the interaction of mutated j-subunit with the other eIF3 subunits and the overall protein synthesis. Taken together our data demonstrate that CK2-phosphorylation of eIF3j at Ser127 promotes the assembly of the eIF3 complex, a crucial step in the activation of the translation initiation machinery.


Subject(s)
Casein Kinase II/metabolism , Eukaryotic Initiation Factor-3/metabolism , Phosphoserine/metabolism , Protein Biosynthesis , Casein Kinase II/antagonists & inhibitors , Gene Silencing/drug effects , HEK293 Cells , HeLa Cells , Humans , Mutation/genetics , Naphthyridines/pharmacology , Phenazines , Phosphorylation/drug effects , Protein Binding/drug effects , Protein Biosynthesis/drug effects , Protein Subunits/metabolism , Substrate Specificity/drug effects
18.
Biochim Biophys Acta ; 1854(6): 609-23, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25278378

ABSTRACT

CK2 is an extremely pleiotropic Ser/Thr protein kinase, responsible for the generation of a large proportion of the human phosphoproteome and implicated in a wide variety of biological functions. CK2 plays a global role as an anti-apoptotic agent, a property which is believed to partially account for the addiction of many cancer cells to high CK2 levels. To gain information about the CK2 targets whose phosphorylation is primarily implicated in its pro-survival signaling advantage has been taken of quinalizarin (QZ) a cell permeable fairly specific CK2 inhibitor, previously shown to be able to block endogenous CK2 triggering an apoptotic response. HEK-293T cells either treated or not for 3h with 50µM QZ were exploited to perform a quantitative SILAC phosphoproteomic analysis of phosphosites readily responsive to QZ treatment. Our analysis led to the identification of 4883 phosphosites, belonging to 1693 phosphoproteins. 71 phosphosites (belonging to 47 proteins) underwent a 50% or more decreased occupancy upon QZ treatment. Almost 50% of these fulfilled the typical consensus sequence recognized by CK2 (S/T-x-x-E/D/pS) and in several cases were validated as bona fide substrates of CK2 either based on data in the literature or by performing in vitro phosphorylation experiments with purified proteins. The majority of the remaining phosphosites drastically decreased upon QZ treatment display the pS/T-P motif typical of proline directed protein kinases and a web logo extracted from them differentiates from the web logo extracted from all the proline directed phosphosites quantified during our analysis (1151 altogether). A paradoxical outcome of our study was the detection of 116 phosphosites (belonging to 92 proteins altogether) whose occupancy is substantially increased (50% or more), rather than decreased by QZ treatment: 40% of these display the typical motif recognized by proline directed kinases, while about 25% fulfill the CK2 consensus. Collectively taken our data on one side have led to the disclosure of a subset of CK2 targets which are likely to be implicated in the early steps of CK2 signaling counteracting apoptosis, on the other they provide evidence for the existence of side and off-target effects of the CK2 inhibitor quinalizarin, paving the road toward the detection of other kinases susceptible to this compound. This article is part of a Special Issue entitled: Medical Proteomics.


Subject(s)
Anthraquinones/pharmacology , Casein Kinase II/antagonists & inhibitors , Phosphoproteins/metabolism , Protein Kinase Inhibitors/pharmacology , Proteome/metabolism , HEK293 Cells , Humans
19.
PLoS One ; 9(10): e111018, 2014.
Article in English | MEDLINE | ID: mdl-25338102

ABSTRACT

Polo-like kinase 2 (PLK2) has been recently recognized as the major enzyme responsible for phosphorylation of α-synuclein at S129 in vitro and in vivo, suggesting that this kinase may play a key role in the pathogenesis of Parkinson's disease and other synucleinopathies. Moreover PLK2 seems to be implicated in cell division, oncogenesis, and synaptic regulation of the brain. However little is known about the phosphoproteome generated by PLK2 and, consequently the overall impact of PLK2 on cellular signaling. To fill this gap we exploited an approach based on in vitro kinase assay and quantitative phosphoproteomics. A proteome-derived peptide library obtained by digestion of undifferentiated human neuroblastoma cell line was exhaustively dephosphorylated by lambda phosphatase followed by incubation with or without PLK2 recombinant kinase. Stable isotope labeling based quantitative phosphoproteomics was applied to identify the phosphosites generated by PLK2. A total of 98 unique PLK2-dependent phosphosites from 89 proteins were identified by LC-MS/MS. Analysis of the primary structure of the identified phosphosites allowed the detailed definition of the kinase specificity and the compilation of a list of potential PLK2 targets among those retrieved in PhosphositePlus, a curated database of in cell/vivo phosphorylation sites.


Subject(s)
Protein Serine-Threonine Kinases/physiology , Proteome/metabolism , Amino Acid Sequence , Catalytic Domain , Cell Line, Tumor , Consensus Sequence , Humans , Models, Molecular , Molecular Sequence Data , Phosphoproteins/chemistry , Phosphoproteins/metabolism , Phosphorylation , Protein Processing, Post-Translational , Protein Serine-Threonine Kinases/chemistry , Proteome/chemistry , Tandem Mass Spectrometry
20.
Amino Acids ; 45(6): 1423-9, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24178769

ABSTRACT

The cystic fibrosis transmembrane conductance regulator (CFTR) harbors, close to Phe-508, whose deletion is the commonest cause of cystic fibrosis, a conserved potential CK2 phospho-acceptor site (Ser511), which however is not susceptible to phosphorylation by CK2. To shed light on this apparent paradox, a series of systematically substituted peptides encompassing Ser511 were assayed for their ability to be phosphorylated. The main outcomes of our study are the following: (a) Tyr512 plays a prominent role as a negative determinant as its replacement by Ala restores Ser511 phosphorylation by CK2; (b) an even more pronounced phosphorylation of Ser511 is promoted if Tyr512 is replaced by phospho-tyrosine instead of alanine; (c) Tyr512 and, to a lesser extent, Tyr515 are readily phosphorylated by Lyn, a protein tyrosine kinase of the Src family, in a manner which is enhanced by the concomitant Phe508 deletion. Collectively taken, our data, in conjunction with the notion that Tyr515 is phosphorylated in vivo, disclose the possibility that CFTR Ser511 can be phosphorylated by the combined action of tyrosine kinases and CK2 and disclose a new mechanism of hierarchical phosphorylation where the role of the priming kinase is that of removing negative determinant(s).


Subject(s)
Casein Kinase II/metabolism , Cystic Fibrosis Transmembrane Conductance Regulator/chemistry , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Phenylalanine/metabolism , Protein-Tyrosine Kinases/metabolism , Serine/metabolism , Tyrosine/metabolism , Humans , Phosphorylation
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