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3.
Biochem J ; 474(6): 983-1001, 2017 03 07.
Article in English | MEDLINE | ID: mdl-28008135

ABSTRACT

Activation of AMP-activated protein kinase (AMPK) in endothelial cells regulates energy homeostasis, stress protection and angiogenesis, but the underlying mechanisms are incompletely understood. Using a label-free phosphoproteomic analysis, we identified glutamine:fructose-6-phosphate amidotransferase 1 (GFAT1) as an AMPK substrate. GFAT1 is the rate-limiting enzyme in the hexosamine biosynthesis pathway (HBP) and as such controls the modification of proteins by O-linked ß-N-acetylglucosamine (O-GlcNAc). In the present study, we tested the hypothesis that AMPK controls O-GlcNAc levels and function of endothelial cells via GFAT1 phosphorylation using biochemical, pharmacological, genetic and in vitro angiogenesis approaches. Activation of AMPK in primary human endothelial cells by 5-aminoimidazole-4-carboxamide riboside (AICAR) or by vascular endothelial growth factor (VEGF) led to GFAT1 phosphorylation at serine 243. This effect was not seen when AMPK was down-regulated by siRNA. Upon AMPK activation, diminished GFAT activity and reduced O-GlcNAc levels were observed in endothelial cells containing wild-type (WT)-GFAT1 but not in cells expressing non-phosphorylatable S243A-GFAT1. Pharmacological inhibition or siRNA-mediated down-regulation of GFAT1 potentiated VEGF-induced sprouting, indicating that GFAT1 acts as a negative regulator of angiogenesis. In cells expressing S243A-GFAT1, VEGF-induced sprouting was reduced, suggesting that VEGF relieves the inhibitory action of GFAT1/HBP on angiogenesis via AMPK-mediated GFAT1 phosphorylation. Activation of GFAT1/HBP by high glucose led to impairment of vascular sprouting, whereas GFAT1 inhibition improved sprouting even if glucose level was high. Our findings provide novel mechanistic insights into the role of HBP in angiogenesis. They suggest that targeting AMPK in endothelium might help to ameliorate hyperglycaemia-induced vascular dysfunction associated with metabolic disorders.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Acetylglucosamine/metabolism , Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)/metabolism , Neovascularization, Physiologic/drug effects , Protein Processing, Post-Translational , Vascular Endothelial Growth Factor A/pharmacology , AMP-Activated Protein Kinases/antagonists & inhibitors , AMP-Activated Protein Kinases/genetics , Alanine/chemistry , Alanine/metabolism , Amino Acid Substitution , Aminoimidazole Carboxamide/analogs & derivatives , Aminoimidazole Carboxamide/pharmacology , Animals , Fibroblasts/cytology , Fibroblasts/drug effects , Fibroblasts/metabolism , Glucose/pharmacology , Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)/antagonists & inhibitors , Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)/genetics , Hexosamines/biosynthesis , Human Umbilical Vein Endothelial Cells/cytology , Human Umbilical Vein Endothelial Cells/drug effects , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Mice , Phosphoproteins/genetics , Phosphoproteins/metabolism , Phosphorylation/drug effects , Primary Cell Culture , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Ribonucleotides/pharmacology , Serine/chemistry , Serine/metabolism
4.
BMC Cancer ; 15: 885, 2015 Nov 10.
Article in English | MEDLINE | ID: mdl-26555036

ABSTRACT

BACKGROUND: Cyclin-dependent protein kinase-5 (CDK5) is an unusual member of the CDK family as it is not cell cycle regulated. However many of its substrates have roles in cell growth and oncogenesis, raising the possibility that CDK5 modulation could have therapeutic benefit. In order to establish whether changes in CDK5 activity are associated with oncogenesis one could quantify phosphorylation of CDK5 targets in disease tissue in comparison to appropriate controls. However the identity of physiological and pathophysiological CDK5 substrates remains the subject of debate, making the choice of CDK5 activity biomarkers difficult. METHODS: Here we use in vitro and in cell phosphorylation assays to identify novel features of CDK5 target sequence determinants that confer enhanced CDK5 selectivity, providing means to select substrate biomarkers of CDK5 activity with more confidence. We then characterize tools for the best CDK5 substrate we identified to monitor its phosphorylation in human tissue and use these to interrogate human tumour arrays. RESULTS: The close proximity of Arg/Lys amino acids and a proline two residues N-terminal to the phosphorylated residue both improve recognition of the substrate by CDK5. In contrast the presence of a proline two residues C-terminal to the target residue dramatically reduces phosphorylation rate. Serine-522 of Collapsin Response Mediator-2 (CRMP2) is a validated CDK5 substrate with many of these structural criteria. We generate and characterise phosphospecific antibodies to Ser522 and show that phosphorylation appears in human tumours (lung, breast, and lymphoma) in stark contrast to surrounding non-neoplastic tissue. In lung cancer the anti-phospho-Ser522 signal is positive in squamous cell carcinoma more frequently than adenocarcinoma. Finally we demonstrate that it is a specific and unusual splice variant of CRMP2 (CRMP2A) that is phosphorylated in tumour cells. CONCLUSIONS: For the first time this data associates altered CDK5 substrate phosphorylation with oncogenesis in some but not all tumour types, implicating altered CDK5 activity in aspects of pathogenesis. These data identify a novel oncogenic mechanism where CDK5 activation induces CRMP2A phosphorylation in the nuclei of tumour cells.


Subject(s)
Carcinogenesis/genetics , Cyclin-Dependent Kinase 5/metabolism , Intercellular Signaling Peptides and Proteins/metabolism , Neoplasms/genetics , Nerve Tissue Proteins/metabolism , Amino Acid Sequence , Biomarkers, Tumor , Cyclin-Dependent Kinase 5/genetics , Humans , Intercellular Signaling Peptides and Proteins/genetics , Neoplasms/metabolism , Neoplasms/pathology , Nerve Tissue Proteins/genetics , Phosphorylation , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA Splicing/genetics , Serine/metabolism
5.
Biochem J ; 469(3): 409-20, 2015 Aug 01.
Article in English | MEDLINE | ID: mdl-26205494

ABSTRACT

PCTAIRE-1 [also known as cyclin-dependent kinase 16 (CDK16)] is implicated in various physiological processes such as neurite outgrowth and vesicle trafficking; however, its molecular regulation and downstream targets are largely unknown. Cyclin Y has recently been identified as a key interacting/activating cyclin for PCTAIRE-1; however, the molecular mechanism by which it activates PCTAIRE-1 is undefined. In the present study, we initially performed protein sequence analysis and identified two candidate phosphorylation sites (Ser(12) and Ser(336)) on cyclin Y that might be catalysed by PCTAIRE-1. Although in vitro peptide analysis favoured Ser(12) as the candidate phosphorylation site, immunoblot analysis of cell lysates that had been transfected with wild-type (WT) or kinase-inactive (KI) PCTAIRE-1 together with WT or phospho-deficient mutants of cyclin Y suggested Ser(336), but not Ser(12), as a PCTAIRE-1-dependent phosphorylation site. Monitoring phosphorylation of Ser(336) may provide a useful read-out to assess cellular activity of PCTAIRE-1 in vivo; however, a phospho-deficient S336A mutant displayed normal interaction with PCTAIRE-1. Unbiased mass spectrometry and targeted mutagenesis analysis of cyclin Y identified key phosphorylation sites (Ser(100) and Ser(326)) required for 14-3-3 binding. Recombinant WT cyclin Y, but not a S100A/S326A mutant, prepared in COS-1 cells co-purified with 14-3-3 and was able to activate bacterially expressed recombinant PCTAIRE-1 in cell-free assays. Finally, we observed that recently identified PCTAIRE-1 variants found in patients with intellectual disability were unable to interact with cyclin Y, and were inactive enzymes. Collectively, the present work has revealed a new mechanistic insight into activation of PCTAIRE-1, which is mediated through interaction with the phosphorylated form of cyclin Y in complex with 14-3-3.


Subject(s)
14-3-3 Proteins/metabolism , Cyclin-Dependent Kinases/metabolism , Cyclins/metabolism , 14-3-3 Proteins/genetics , Amino Acid Motifs , Amino Acid Sequence , Cyclin-Dependent Kinases/genetics , Cyclins/chemistry , Cyclins/genetics , Enzyme Activation , Humans , Molecular Sequence Data , Phosphorylation , Protein Binding , Sequence Alignment
6.
Mol Cell Biol ; 35(15): 2699-713, 2015 Aug.
Article in English | MEDLINE | ID: mdl-25986610

ABSTRACT

Scaffold attachment factor A (SAF-A), also called heterogenous nuclear ribonuclear protein U (hnRNP-U), is phosphorylated on serine 59 by the DNA-dependent protein kinase (DNA-PK) in response to DNA damage. Since SAF-A, DNA-PK catalytic subunit (DNA-PKcs), and protein phosphatase 6 (PP6), which interacts with DNA-PKcs, have all been shown to have roles in mitosis, we asked whether DNA-PKcs phosphorylates SAF-A in mitosis. We show that SAF-A is phosphorylated on serine 59 in mitosis, that phosphorylation requires polo-like kinase 1 (PLK1) rather than DNA-PKcs, that SAF-A interacts with PLK1 in nocodazole-treated cells, and that serine 59 is dephosphorylated by protein phosphatase 2A (PP2A) in mitosis. Moreover, cells expressing SAF-A in which serine 59 is mutated to alanine have multiple characteristics of aberrant mitoses, including misaligned chromosomes, lagging chromosomes, polylobed nuclei, and delayed passage through mitosis. Our findings identify serine 59 of SAF-A as a new target of both PLK1 and PP2A in mitosis and reveal that both phosphorylation and dephosphorylation of SAF-A serine 59 by PLK1 and PP2A, respectively, are required for accurate and timely exit from mitosis.


Subject(s)
Cell Cycle Proteins/metabolism , Cyclin-Dependent Kinases/metabolism , Heterogeneous-Nuclear Ribonucleoprotein U/metabolism , Mitosis/genetics , Protein Phosphatase 2/metabolism , Protein Serine-Threonine Kinases/metabolism , Proto-Oncogene Proteins/metabolism , CDC2 Protein Kinase , Cell Line, Tumor , Cyclin B1/metabolism , DNA Damage/genetics , HeLa Cells , Humans , Nocodazole/pharmacology , Paclitaxel/pharmacology , Phosphoprotein Phosphatases/genetics , Phosphoprotein Phosphatases/metabolism , Phosphorylation , RNA Interference , RNA, Small Interfering , Securin/metabolism , Tubulin Modulators/pharmacology , Polo-Like Kinase 1
7.
J Immunol ; 195(1): 265-76, 2015 Jul 01.
Article in English | MEDLINE | ID: mdl-26002976

ABSTRACT

In myeloid cells, the mRNA-destabilizing protein tristetraprolin (TTP) is induced and extensively phosphorylated in response to LPS. To investigate the role of two specific phosphorylations, at serines 52 and 178, we created a mouse strain in which those residues were replaced by nonphosphorylatable alanine residues. The mutant form of TTP was constitutively degraded by the proteasome and therefore expressed at low levels, yet it functioned as a potent mRNA destabilizing factor and inhibitor of the expression of many inflammatory mediators. Mice expressing only the mutant form of TTP were healthy and fertile, and their systemic inflammatory responses to LPS were strongly attenuated. Adaptive immune responses and protection against infection by Salmonella typhimurium were spared. A single allele encoding the mutant form of TTP was sufficient for enhanced mRNA degradation and underexpression of inflammatory mediators. Therefore, the equilibrium between unphosphorylated and phosphorylated TTP is a critical determinant of the inflammatory response, and manipulation of this equilibrium may be a means of treating inflammatory pathologies.


Subject(s)
Macrophages/immunology , Mutation , RNA, Messenger/immunology , Salmonella Infections, Animal/immunology , Tristetraprolin/immunology , Alanine/genetics , Alanine/metabolism , Amino Acid Substitution , Animals , Cell Line , Cytokines/antagonists & inhibitors , Cytokines/genetics , Cytokines/immunology , Female , Gene Expression , Inflammation/genetics , Inflammation/immunology , Inflammation/pathology , Lipopolysaccharides/pharmacology , Macrophages/drug effects , Macrophages/pathology , Male , Mice , Mice, Inbred C57BL , Phosphoproteins/genetics , Phosphoproteins/immunology , Phosphorylation , Primary Cell Culture , RNA Stability , RNA, Messenger/genetics , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/immunology , Salmonella Infections, Animal/genetics , Salmonella Infections, Animal/pathology , Salmonella typhimurium/immunology , Serine/genetics , Serine/metabolism , Tristetraprolin/genetics
8.
Mol Cell ; 58(1): 83-94, 2015 Apr 02.
Article in English | MEDLINE | ID: mdl-25752573

ABSTRACT

Polyubiquitin chains regulate diverse cellular processes through the ability of ubiquitin to form chains of eight different linkage types. Although detected in yeast and mammals, little is known about K29-linked polyubiquitin. Here we report the generation of K29 chains in vitro using a ubiquitin chain-editing complex consisting of the HECT E3 ligase UBE3C and the deubiquitinase vOTU. We determined the crystal structure of K29-linked diubiquitin, which adopts an extended conformation with the hydrophobic patches on both ubiquitin moieties exposed and available for binding. Indeed, the crystal structure of the NZF1 domain of TRABID in complex with K29 chains reveals a binding mode that involves the hydrophobic patch on only one of the ubiquitin moieties and exploits the flexibility of K29 chains to achieve linkage selective binding. Further, we establish methods to study K29-linked polyubiquitin and find that K29 linkages exist in cells within mixed or branched chains containing other linkages.


Subject(s)
Endopeptidases/chemistry , Lysine/chemistry , Protein Processing, Post-Translational , Ubiquitin-Protein Ligases/chemistry , Ubiquitin/chemistry , Amino Acid Sequence , Crystallography, X-Ray , Endopeptidases/genetics , Endopeptidases/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , HEK293 Cells , Humans , Hydrophobic and Hydrophilic Interactions , Lysine/metabolism , Models, Molecular , Molecular Sequence Data , Proteasome Endopeptidase Complex/metabolism , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Proteolysis , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Signal Transduction , Ubiquitin/genetics , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination
9.
Biochem J ; 467(2): 345-52, 2015 Apr 15.
Article in English | MEDLINE | ID: mdl-25723849

ABSTRACT

Ubiquitylation regulates a multitude of biological processes and this versatility stems from the ability of ubiquitin (Ub) to form topologically different polymers of eight different linkage types. Whereas some linkages have been studied in detail, other linkage types including Lys33-linked polyUb are poorly understood. In the present study, we identify an enzymatic system for the large-scale assembly of Lys33 chains by combining the HECT (homologous to the E6-AP C-terminus) E3 ligase AREL1 (apoptosis-resistant E3 Ub protein ligase 1) with linkage selective deubiquitinases (DUBs). Moreover, this first characterization of the chain selectivity of AREL1 indicates its preference for assembling Lys33- and Lys11-linked Ub chains. Intriguingly, the crystal structure of Lys33-linked diUb reveals that it adopts a compact conformation very similar to that observed for Lys11-linked diUb. In contrast, crystallographic analysis of Lys33-linked triUb reveals a more extended conformation. These two distinct conformational states of Lys33-linked polyUb may be selectively recognized by Ub-binding domains (UBD) and enzymes of the Ub system. Importantly, our work provides a method to assemble Lys33-linked polyUb that will allow further characterization of this atypical chain type.


Subject(s)
Lysine/chemistry , Polyubiquitin/chemistry , Protein Folding , Ubiquitin-Protein Ligases/chemistry , Animals , Humans , Lysine/genetics , Lysine/metabolism , Polyubiquitin/genetics , Polyubiquitin/metabolism , Protein Structure, Quaternary , Protein Structure, Tertiary , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism
10.
Cell Signal ; 27(5): 978-88, 2015 May.
Article in English | MEDLINE | ID: mdl-25683918

ABSTRACT

AMP-activated protein kinase (AMPK) is a key cellular energy sensor and regulator of metabolic homeostasis. Although it is best known for its effects on carbohydrate and lipid metabolism, AMPK is implicated in diverse cellular processes, including mitochondrial biogenesis, autophagy, and cell growth and proliferation. To further our understanding of energy homeostasis through AMPK-dependent processes, the design and application of approaches to identify and characterise novel AMPK substrates are invaluable. Here, we report an affinity proteomicstrategy for the discovery and validation of AMPK targets using an antibody to isolate proteins containing the phospho-AMPK substrate recognition motif from hepatocytes that had been treated with pharmacological AMPK activators. We identified 57 proteins that were uniquely enriched in the activator-treated hepatocytes, but were absent in hepatocytes lacking AMPK. We focused on two candidates, cingulin and mitochondrial fission factor (MFF), and further characterised/validated them as AMPK-dependent targets by immunoblotting with phosphorylation site-specific antibodies. A small-molecule AMPK activator caused transient phosphorylation of endogenous cingulin at S137 in intestinal Caco2 cells. Multiple splice-variants of MFF appear to express in hepatocytes and we identified a common AMPK-dependent phospho-site (S129) in all the 3 predominant variants spanning the mass range and a short variant-specific site (S146). Collectively, our proteomic-based approach using a phospho-AMPK substrate antibody in combination with genetic models and selective AMPK activators will provide a powerful and reliable platform for identifying novel AMPK-dependent cellular targets.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Hepatocytes/metabolism , Membrane Proteins/metabolism , Mitochondrial Proteins/metabolism , AMP-Activated Protein Kinases/analysis , Amino Acid Sequence , Animals , Caco-2 Cells , Cells, Cultured , Humans , Male , Mass Spectrometry , Membrane Proteins/analysis , Mice , Mice, Inbred C57BL , Mitochondrial Proteins/analysis , Molecular Sequence Data , Phosphorylation , Proteomics
11.
Nat Commun ; 6: 6001, 2015 Jan 23.
Article in English | MEDLINE | ID: mdl-25613188

ABSTRACT

Mutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) are associated with a highly malignant form of renal cancer. We combined analytical chemistry and metabolic computational modelling to investigate the metabolic implications of FH loss in immortalized and primary mouse kidney cells. Here, we show that the accumulation of fumarate caused by the inactivation of FH leads to oxidative stress that is mediated by the formation of succinicGSH, a covalent adduct between fumarate and glutathione. Chronic succination of GSH, caused by the loss of FH, or by exogenous fumarate, leads to persistent oxidative stress and cellular senescence in vitro and in vivo. Importantly, the ablation of p21, a key mediator of senescence, in Fh1-deficient mice resulted in the transformation of benign renal cysts into a hyperplastic lesion, suggesting that fumarate-induced senescence needs to be bypassed for the initiation of renal cancers.


Subject(s)
Fumarates/chemistry , Glutathione/metabolism , Animals , Cell Line , Cell Proliferation , Cell Transformation, Neoplastic , Cellular Senescence , Chromatography, Liquid , Computational Biology , Female , Fibroblasts/metabolism , Fumarate Hydratase/chemistry , Glutamine/chemistry , Immunohistochemistry , Kidney/metabolism , Magnetic Resonance Spectroscopy , Male , Mass Spectrometry , Metabolomics , Mice , Mice, Inbred C57BL , Mutation , Oxidation-Reduction , Oxidative Stress , Transcriptome
12.
J Cell Sci ; 128(3): 472-86, 2015 Feb 01.
Article in English | MEDLINE | ID: mdl-25472719

ABSTRACT

Salt-inducible kinase 2 (SIK2) is an AMP-activated protein kinase (AMPK) related kinase abundantly expressed in adipose tissue. Our aim was to identify molecular targets and functions of SIK2 in adipocytes, and to address the role of PKA-mediated phosphorylation of SIK2 on Ser358. Modulation of SIK2 in adipocytes resulted in altered phosphorylation of CREB-regulated transcription co-activator 2 (CRTC2), CRTC3 and class IIa histone deacetylase 4 (HDAC4). Furthermore, CRTC2, CRTC3, HDAC4 and protein phosphatase 2A (PP2A) interacted with SIK2, and the binding of CRTCs and PP2A to wild-type but not Ser358Ala SIK2, was reduced by cAMP elevation. Silencing of SIK2 resulted in reduced GLUT4 (also known as SLC2A4) protein levels, whereas cells treated with CRTC2 or HDAC4 siRNA displayed increased levels of GLUT4. Overexpression or pharmacological inhibition of SIK2 resulted in increased and decreased glucose uptake, respectively. We also describe a SIK2­CRTC2­HDAC4 pathway and its regulation in human adipocytes, strengthening the physiological relevance of our findings. Collectively, we demonstrate that SIK2 acts directly on CRTC2, CRTC3 and HDAC4, and that the cAMP­PKA pathway reduces the interaction of SIK2 with CRTCs and PP2A. Downstream, SIK2 increases GLUT4 levels and glucose uptake in adipocytes.


Subject(s)
Glucose/metabolism , Histone Deacetylases/metabolism , Protein Serine-Threonine Kinases/metabolism , Transcription Factors/metabolism , 3T3 Cells , Adipocytes/metabolism , Adipose Tissue/metabolism , Animals , Cell Line , Cyclic AMP/metabolism , Glucose Transporter Type 4/metabolism , HEK293 Cells , Histone Deacetylases/genetics , Humans , Mice , Mice, Knockout , Phosphorylation , Protein Binding , Protein Phosphatase 2/metabolism , Protein Serine-Threonine Kinases/antagonists & inhibitors , Protein Serine-Threonine Kinases/genetics , RNA Interference , RNA, Small Interfering , Rats , Signal Transduction , Transcription Factors/genetics
13.
Protein Expr Purif ; 108: 23-29, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25527037

ABSTRACT

We report the successful expression and purification of functional human muscle glycogen synthase (GYS1) in complex with human glycogenin-1 (GN1). Stoichiometric GYS1:GN1 complex was produced by co-expression of GYS1 and GN1 using a bicistronic pFastBac™-Dual expression vector, followed by affinity purification and subsequent size-exclusion chromatography. Mass spectrometry analysis identified that GYS1 is phosphorylated at several well-characterised and uncharacterised Ser/Thr residues. Biochemical analysis, including activity ratio (in the absence relative to that in the presence of glucose-6-phosphate) measurement, covalently attached phosphate estimation as well as phosphatase treatment, revealed that recombinant GYS1 is substantially more heavily phosphorylated than would be observed in intact human or rodent muscle tissues. A large quantity of highly-pure stoichiometric GYS1:GN1 complex will be useful to study its structural and biochemical properties in the future, which would reveal mechanistic insights into its functional role in glycogen biosynthesis.


Subject(s)
Gene Expression , Glucosyltransferases , Glycogen Synthase , Glycoproteins , Multienzyme Complexes , Animals , Glucosyltransferases/biosynthesis , Glucosyltransferases/genetics , Glucosyltransferases/isolation & purification , Glycogen Synthase/biosynthesis , Glycogen Synthase/genetics , Glycogen Synthase/isolation & purification , Glycoproteins/biosynthesis , Glycoproteins/genetics , Glycoproteins/isolation & purification , Humans , Multienzyme Complexes/biosynthesis , Multienzyme Complexes/genetics , Multienzyme Complexes/isolation & purification , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Sf9 Cells , Spodoptera
14.
Genes Dev ; 28(24): 2712-25, 2014 Dec 15.
Article in English | MEDLINE | ID: mdl-25512559

ABSTRACT

Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in nonproliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene-induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression.


Subject(s)
Cell Cycle Proteins/metabolism , Cellular Senescence/physiology , Histone Chaperones/metabolism , Transcription Factors/metabolism , Animals , Antineoplastic Agents, Hormonal/pharmacology , Carcinogenesis/drug effects , Carcinogenesis/genetics , Cell Cycle Proteins/genetics , Cell Line , Cell Proliferation , Cellular Senescence/genetics , Chromatin/metabolism , Female , Gene Expression Regulation/drug effects , Genetic Markers , Histone Chaperones/genetics , Histones/genetics , Histones/metabolism , Humans , Male , Mice , Papilloma/pathology , Skin Neoplasms/pathology , Tamoxifen/pharmacology , Transcription Factors/genetics
15.
Nat Commun ; 5: 4763, 2014 Aug 27.
Article in English | MEDLINE | ID: mdl-25159004

ABSTRACT

Deubiquitylases (DUBs) are key regulators of the ubiquitin system which cleave ubiquitin moieties from proteins and polyubiquitin chains. Several DUBs have been implicated in various diseases and are attractive drug targets. We have developed a sensitive and fast assay to quantify in vitro DUB enzyme activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Unlike other current assays, this method uses unmodified substrates, such as diubiquitin topoisomers. By analysing 42 human DUBs against all diubiquitin topoisomers we provide an extensive characterization of DUB activity and specificity. Our results confirm the high specificity of many members of the OTU and JAB/MPN/Mov34 metalloenzyme DUB families and highlight that all USPs tested display low linkage selectivity. We also demonstrate that this assay can be deployed to assess the potency and specificity of DUB inhibitors by profiling 11 compounds against a panel of 32 DUBs.


Subject(s)
Protease Inhibitors/pharmacology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Ubiquitin-Specific Proteases/metabolism , Humans , Inhibitory Concentration 50 , Nitriles/pharmacology , Nitrofurans/pharmacology , Reproducibility of Results , Substrate Specificity , Sulfones/pharmacology , Ubiquitin/metabolism , Ubiquitin Thiolesterase/antagonists & inhibitors , Ubiquitin Thiolesterase/metabolism , Ubiquitin-Specific Peptidase 7 , Ubiquitin-Specific Proteases/analysis , Ubiquitin-Specific Proteases/antagonists & inhibitors , Ubiquitin-Specific Proteases/genetics
16.
PLoS One ; 9(2): e89399, 2014.
Article in English | MEDLINE | ID: mdl-24558497

ABSTRACT

The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional proteins (Survivin/Bir1 and Borealin/Nbl1). Here we have identified multiple sites of CPC autophosphorylation on yeast Sli15 that are located within its central microtubule-binding domain and examined the functional significance of their phosphorylation by Ipl1 through mutation of these sites, either to non-phosphorylatable alanine (sli15-20A) or to acidic residues to mimic constitutive phosphorylation (sli15-20D). Both mutant sli15 alleles confer chromosome instability, but this is mediated neither by changes in the capacity of Sli15 to activate Ipl1 kinase nor by decreased efficiency of chromosome biorientation, a key process in cell division that requires CPC function. Instead, we find that mimicking constitutive phosphorylation of Sli15 on the Ipl1 phosphorylation sites causes delocalization of the CPC in metaphase, whereas blocking phosphorylation of Sli15 on the Ipl1 sites drives excessive localization of Sli15 to the mitotic spindle in pre-anaphase cells. Consistent with these results, direct interaction of Sli15 with microtubules in vitro is greatly reduced either following phosphorylation by Ipl1 or when constitutive phosphorylation at the Ipl1-dependent phosphorylation sites is mimicked by aspartate or glutamate substitutions. Furthermore, we find that mimicking Ipl1 phosphorylation of Sli15 interferes with the 'tension checkpoint'--the CPC-dependent mechanism through which cells activate the spindle assembly checkpoint to delay anaphase in the absence of tension on kinetochore-microtubule attachments. Ipl1-dependent phosphorylation of Sli15 therefore inhibits its association with microtubules both in vivo and in vitro and may negatively regulate the tension checkpoint mechanism.


Subject(s)
Cell Division/physiology , Chromosomal Instability/physiology , Multiprotein Complexes/metabolism , Saccharomyces cerevisiae/genetics , Aurora Kinases/metabolism , Carrier Proteins/metabolism , Microscopy, Fluorescence , Microtubule-Associated Proteins/metabolism , Microtubules/metabolism , Phosphorylation , Saccharomyces cerevisiae/physiology , Saccharomyces cerevisiae Proteins/metabolism , Time-Lapse Imaging
17.
Cell Commun Signal ; 11: 58, 2013 Aug 14.
Article in English | MEDLINE | ID: mdl-23945128

ABSTRACT

BACKGROUND: Cucurbitacins are a class of triterpenoid natural compounds with potent bioactivities that led to their use as traditional remedies, and which continue to attract considerable attention as chemical biology tools and potential therapeutics. One obvious target is the actin-cytoskeleton; treatment with cucurbitacins results in cytoskeletal rearrangements that impact upon motility and cell morphology. FINDINGS: Cucurbitacin reacted with protein cysteine thiols as well as dithiothreitol, and we propose that the cucurbitacin mechanism of action is through broad protein thiol modifications that could result in inhibition of numerous protein targets. An example of such a target protein is Cofilin1, whose filamentous actin severing activity is inhibited by cucurbitacin conjugation. CONCLUSIONS: The implications of these results are that cucurbitacins are unlikely to be improved for selectivity by medicinal chemistry and that their use as chemical biology probes to analyse the role of specific signalling pathways should be undertaken with caution.


Subject(s)
Cofilin 1/metabolism , Cucurbitacins/pharmacology , Actin Cytoskeleton/metabolism , Cysteine/metabolism , Humans , MCF-7 Cells , Protein Binding
18.
Biochem J ; 452(2): 359-65, 2013 Jun 01.
Article in English | MEDLINE | ID: mdl-23557442

ABSTRACT

Activation of PKR (double-stranded-RNA-dependent protein kinase) by DNA plasmids decreases translation, and limits the amount of recombinant protein produced by transiently transfected HEK (human embryonic kidney)-293 cells. Co-expression with Ebola virus VP35 (virus protein 35), which blocked plasmid activation of PKR, substantially increased production of recombinant TPL-2 (tumour progression locus 2)-ABIN-2 [A20-binding inhibitor of NF-κB (nuclear factor κB) 2]-NF-κB1 p105 complex. VP35 also increased expression of other co-transfected proteins, suggesting that VP35 could be employed generally to boost recombinant protein production by HEK-293 cells.


Subject(s)
Adaptor Proteins, Signal Transducing/biosynthesis , Ebolavirus/physiology , MAP Kinase Kinase Kinases/biosynthesis , NF-kappa B p50 Subunit/biosynthesis , Proto-Oncogene Proteins/biosynthesis , Up-Regulation/genetics , Viral Regulatory and Accessory Proteins/physiology , Adaptor Proteins, Signal Transducing/genetics , Ebolavirus/genetics , HEK293 Cells , Humans , MAP Kinase Kinase Kinases/genetics , Multiprotein Complexes/biosynthesis , Multiprotein Complexes/genetics , NF-kappa B p50 Subunit/genetics , Proto-Oncogene Proteins/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Transfection , Viral Regulatory and Accessory Proteins/genetics
19.
Mol Cell Biol ; 33(8): 1671-86, 2013 Apr.
Article in English | MEDLINE | ID: mdl-23428871

ABSTRACT

The mitogen-activated protein (MAP) kinase extracellular signal-regulated kinase 5 (ERK5) plays a crucial role in cell proliferation, regulating gene transcription. ERK5 has a unique C-terminal tail which contains a transcriptional activation domain, and activates transcription by phosphorylating transcription factors and acting itself as a transcriptional coactivator. However, the molecular mechanisms that regulate its nucleocytoplasmatic traffic are unknown. We have used tandem affinity purification to identify proteins that interact with ERK5. We show that ERK5 interacts with the Hsp90-Cdc37 chaperone in resting cells, and that inhibition of Hsp90 or Cdc37 results in ERK5 ubiquitylation and proteasomal degradation. Interestingly, activation of cellular ERK5 induces Hsp90 dissociation from the ERK5-Cdc37 complex, leading to ERK5 nuclear translocation and activation of transcription, by a mechanism which requires the autophosphorylation at its C-terminal tail. Consequently, active ERK5 is no longer sensitive to Hsp90 or Cdc37 inhibitors. Cdc37 overexpression also induces Hsp90 dissociation and the nuclear translocation of a kinase-inactive form of ERK5 which retains transcriptional activity. This is the first example showing that ERK5 transcriptional activity does not require kinase activity. Since Cdc37 cooperates with ERK5 to promote cell proliferation, Cdc37 overexpression (as happens in some cancers) might represent a new, noncanonical mechanism by which ERK5 regulates tumor proliferation.


Subject(s)
Active Transport, Cell Nucleus , Cell Cycle Proteins/metabolism , Cell Nucleus/metabolism , Chaperonins/metabolism , HSP90 Heat-Shock Proteins/metabolism , Mitogen-Activated Protein Kinase 7/metabolism , Animals , Cell Cycle Proteins/biosynthesis , Cell Cycle Proteins/genetics , Cell Line , Cell Proliferation , Chaperonins/biosynthesis , Chaperonins/genetics , HEK293 Cells , HeLa Cells , Humans , Mice , Mitogen-Activated Protein Kinase 7/genetics , Phosphorylation , RNA Interference , RNA, Small Interfering , Signal Transduction , Transcription, Genetic , Transcriptional Activation , Ubiquitination
20.
Cell Signal ; 24(9): 1863-71, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22588126

ABSTRACT

Salt-inducible kinase (SIK) 3 is a virtually unstudied, ubiquitously expressed serine/threonine kinase, belonging to the AMP-activated protein kinase (AMPK)-related family of kinases, all of which are regulated by LKB1 phosphorylation of a threonine residue in their activation (T)-loops. Findings in adrenal cells have revealed a role for cAMP in the regulation of SIK1, and recent findings suggest that insulin can regulate an SIK isoform in Drosophila. As cAMP has important functions in adipocytes, mainly in the regulation of lipolysis, we have evaluated a potential role for cAMP, as well as for insulin, in the regulation of SIK3 in these cells. We establish that raised cAMP levels in response to forskolin and the ß-adrenergic receptor agonist CL 316,243 induce a phosphorylation of SIK3 in HEK293 cells and primary adipocytes. This phosphorylation coincides with increased 14-3-3 binding to SIK3 in these cell types. Our findings also show that cAMP-elevation results in reduced SIK3 activity in adipocytes. Phosphopeptide mapping and site-directed mutagenesis reveal that the cAMP-mediated regulation of SIK3 appears to depend on three residues, T469, S551 and S674, that all contribute to some extent to the cAMP-induced phosphorylation and 14-3-3-binding. As the cAMP-induced regulation can be reversed with the protein kinase A (PKA) inhibitor H89, and a role for other candidate kinases, including PKB and RSK, could be excluded, we believe that PKA is the kinase responsible for SIK3 regulation in response to elevated cAMP levels. Our findings of cAMP-mediated regulation of SIK3 suggest that SIK3 may mediate some of the effects of this important second messenger in adipocytes.


Subject(s)
Adipocytes/drug effects , Adipocytes/enzymology , Adrenergic beta-Agonists/pharmacology , Cyclic AMP/metabolism , Protein Kinases/metabolism , Receptors, Adrenergic, beta/metabolism , 14-3-3 Proteins/metabolism , Cells, Cultured , Cyclic AMP-Dependent Protein Kinases/antagonists & inhibitors , Cyclic AMP-Dependent Protein Kinases/metabolism , HEK293 Cells , Humans , Isoquinolines/pharmacology , Phosphorylation , Sulfonamides/pharmacology
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