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Sec61 channel subunit Sbh1/Sec61β promotes ER translocation of proteins with suboptimal targeting sequences and is fine-tuned by phosphorylation. J Biol Chem 2023; 299:102895. [PMID: 36639027 PMCID: PMC9947333 DOI: 10.1016/j.jbc.2023.102895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
The highly conserved endoplasmic reticulum (ER) protein translocation channel contains one nonessential subunit, Sec61β/Sbh1, whose function is poorly understood so far. Its intrinsically unstructured cytosolic domain makes transient contact with ER-targeting sequences in the cytosolic channel vestibule and contains multiple phosphorylation sites suggesting a potential for regulating ER protein import. In a microscopic screen, we show that 12% of a GFP-tagged secretory protein library depends on Sbh1 for translocation into the ER. Sbh1-dependent proteins had targeting sequences with less pronounced hydrophobicity and often no charge bias or an inverse charge bias which reduces their insertion efficiency into the Sec61 channel. We determined that mutating two N-terminal, proline-flanked phosphorylation sites in the Sbh1 cytosolic domain to alanine phenocopied the temperature-sensitivity of a yeast strain lacking SBH1 and its ortholog SBH2. The phosphorylation site mutations reduced translocation into the ER of a subset of Sbh1-dependent proteins, including enzymes whose concentration in the ER lumen is critical for ER proteostasis. In addition, we found that ER import of these proteins depended on the activity of the phospho-S/T-specific proline isomerase Ess1 (PIN1 in mammals). We conclude that Sbh1 promotes ER translocation of substrates with suboptimal targeting sequences and that its activity can be regulated by a conformational change induced by N-terminal phosphorylation.
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Humphrey SJ, Needham EJ. Targets mapped for almost all human kinase enzymes. Nature 2023; 613:637-638. [PMID: 36631581 DOI: 10.1038/d41586-022-04583-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC. An atlas of substrate specificities for the human serine/threonine kinome. Nature 2023; 613:759-766. [PMID: 36631611 PMCID: PMC9876800 DOI: 10.1038/s41586-022-05575-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is one of the most widespread post-translational modifications in biology1,2. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of serine and threonine phosphorylation have so far been identified, and several thousand have been associated with human diseases and biological processes3,4. For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein serine/threonine (Ser/Thr) kinases encoded in the human genome are responsible3. Here we used synthetic peptide libraries to profile the substrate sequence specificity of 303 Ser/Thr kinases, comprising more than 84% of those predicted to be active in humans. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. We used our kinome-wide dataset to computationally annotate and identify the kinases capable of phosphorylating every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites for which the putative protein kinases involved have been previously reported, our predictions were in excellent agreement. When this approach was applied to examine the signalling response of tissues and cell lines to hormones, growth factors, targeted inhibitors and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the intrinsic substrate specificity of the human Ser/Thr kinome, illuminate cellular signalling responses and provide a resource to link phosphorylation events to biological pathways.
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Affiliation(s)
- Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology & Medicine, Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center and The Rockefeller University, New York, NY, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander Kerelsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Junho Song
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amit Regev
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Cell and Developmental Biology Program, New York, NY, USA
| | - Katarina Liberatore
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daniel M Cizin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin M Cohen
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yilun Ma
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jaylissa Torres Robles
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Bert van de Kooij
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anne E van Vlimmeren
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole Andrée-Busch
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Norbert F Käufer
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maxim V Dorovkov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Alexey G Ryazanov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edward R Kastenhuber
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marcus D Goncalves
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Division of Endocrinology, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin D Hopkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Akio Yamashita
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Alexei Degterev
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Mohamed Uduman
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Jingyi Lu
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Sean D Landry
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Bin Zhang
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Ian Cossentino
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Rune Linding
- Rewire Tx, Humboldt-Universität zu Berlin, Berlin, Germany
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Peter V Hornbeck
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care, and Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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Leo KT, Chou CL, Yang CR, Park E, Raghuram V, Knepper MA. Bayesian analysis of dynamic phosphoproteomic data identifies protein kinases mediating GPCR responses. Cell Commun Signal 2022; 20:80. [PMID: 35659261 PMCID: PMC9164474 DOI: 10.1186/s12964-022-00892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
Background A major goal in the discovery of cellular signaling networks is to identify regulated phosphorylation sites (“phosphosites”) and map them to the responsible protein kinases. The V2 vasopressin receptor is a G-protein coupled receptor (GPCR) that is responsible for regulation of renal water excretion through control of aquaporin-2-mediated osmotic water transport in kidney collecting duct cells. Genome editing experiments have demonstrated that virtually all vasopressin-triggered phosphorylation changes are dependent on protein kinase A (PKA), but events downstream from PKA are still obscure. Methods Here, we used: 1) Tandem mass tag-based quantitative phosphoproteomics to experimentally track phosphorylation changes over time in native collecting ducts isolated from rat kidneys; 2) a clustering algorithm to classify time course data based on abundance changes and the amino acid sequences surrounding the phosphosites; and 3) Bayes’ Theorem to integrate the dynamic phosphorylation data with multiple prior “omic” data sets covering expression, subcellular location, known kinase activity, and characteristic surrounding sequences to identify a set of protein kinases that are regulated secondary to PKA activation. Results Phosphoproteomic studies revealed 185 phosphosites regulated by vasopressin over 15 min. The resulting groups from the cluster algorithm were integrated with Bayes’ Theorem to produce corresponding ranked lists of kinases likely responsible for each group. The top kinases establish three PKA-dependent protein kinase modules whose regulation mediate the physiological effects of vasopressin at a cellular level. The three modules are 1) a pathway involving several Rho/Rac/Cdc42-dependent protein kinases that control actin cytoskeleton dynamics; 2) mitogen-activated protein kinase and cyclin-dependent kinase pathways that control cell proliferation; and 3) calcium/calmodulin-dependent signaling. Conclusions Our findings identify a novel set of downstream small GTPase effectors and calcium/calmodulin-dependent kinases with potential roles in the regulation of water permeability through actin cytoskeleton rearrangement and aquaporin-2 trafficking. The proposed signaling network provides a stronger hypothesis for the kinases mediating V2 vasopressin receptor responses, encouraging future targeted examination via reductionist approaches. Furthermore, the Bayesian analysis described here provides a template for investigating signaling via other biological systems and GPCRs. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00892-6.
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Diakov A, Nesterov V, Dahlmann A, Korbmacher C. Two adjacent phosphorylation sites in the C-terminus of the channel's α-subunit have opposing effects on epithelial sodium channel (ENaC) activity. Pflugers Arch 2022; 474:681-697. [PMID: 35525869 PMCID: PMC9192390 DOI: 10.1007/s00424-022-02693-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/25/2022] [Indexed: 02/07/2023]
Abstract
How phosphorylation of the epithelial sodium channel (ENaC) contributes to its regulation is incompletely understood. Previously, we demonstrated that in outside-out patches ENaC activation by serum- and glucocorticoid-inducible kinase isoform 1 (SGK1) was abolished by mutating a serine residue in a putative SGK1 consensus motif RXRXX(S/T) in the channel’s α-subunit (S621 in rat). Interestingly, this serine residue is followed by a highly conserved proline residue rather than by a hydrophobic amino acid thought to be required for a functional SGK1 consensus motif according to invitro data. This suggests that this serine residue is a potential phosphorylation site for the dual-specificity tyrosine phosphorylated and regulated kinase 2 (DYRK2), a prototypical proline-directed kinase. Its phosphorylation may prime a highly conserved preceding serine residue (S617 in rat) to be phosphorylated by glycogen synthase kinase 3 β (GSK3β). Therefore, we investigated the effect of DYRK2 on ENaC activity in outside-out patches of Xenopus laevis oocytes heterologously expressing rat ENaC. DYRK2 included in the pipette solution significantly increased ENaC activity. In contrast, GSK3β had an inhibitory effect. Replacing S621 in αENaC with alanine (S621A) abolished the effects of both kinases. A S617A mutation reduced the inhibitory effect of GKS3β but did not prevent ENaC activation by DYRK2. Our findings suggest that phosphorylation of S621 activates ENaC and primes S617 for subsequent phosphorylation by GSK3β resulting in channel inhibition. In proof-of-concept experiments, we demonstrated that DYRK2 can also stimulate ENaC currents in microdissected mouse distal nephron, whereas GSK3β inhibits the currents.
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Affiliation(s)
- Alexei Diakov
- Institut für Zelluläre und Molekulare Physiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Waldstr, 6, 91054, Erlangen, Germany
| | - Viatcheslav Nesterov
- Institut für Zelluläre und Molekulare Physiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Waldstr, 6, 91054, Erlangen, Germany
| | - Anke Dahlmann
- Medizinische Klinik 4 - Nephrologie und Hypertensiologie, Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany
| | - Christoph Korbmacher
- Institut für Zelluläre und Molekulare Physiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Waldstr, 6, 91054, Erlangen, Germany.
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Bradley D, Viéitez C, Rajeeve V, Selkrig J, Cutillas PR, Beltrao P. Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases. Cell Rep 2021; 34:108602. [PMID: 33440154 PMCID: PMC7809594 DOI: 10.1016/j.celrep.2020.108602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023] Open
Abstract
Protein kinases lie at the heart of cell-signaling processes and are often mutated in disease. Kinase target recognition at the active site is in part determined by a few amino acids around the phosphoacceptor residue. However, relatively little is known about how most preferences are encoded in the kinase sequence or how these preferences evolved. Here, we used alignment-based approaches to predict 30 specificity-determining residues (SDRs) for 16 preferences. These were studied with structural models and were validated by activity assays of mutant kinases. Cancer mutation data revealed that kinase SDRs are mutated more frequently than catalytic residues. We have observed that, throughout evolution, kinase specificity has been strongly conserved across orthologs but can diverge after gene duplication, as illustrated by the G protein-coupled receptor kinase family. The identified SDRs can be used to predict kinase specificity from sequence and aid in the interpretation of evolutionary or disease-related genomic variants.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Cristina Viéitez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Vinothini Rajeeve
- Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Joel Selkrig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Pedro R Cutillas
- Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK.
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Phosphoproteomics reveals that the hVPS34 regulated SGK3 kinase specifically phosphorylates endosomal proteins including Syntaxin-7, Syntaxin-12, RFIP4 and WDR44. Biochem J 2020; 476:3081-3107. [PMID: 31665227 PMCID: PMC6824681 DOI: 10.1042/bcj20190608] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 01/04/2023]
Abstract
The serum- and glucocorticoid-regulated kinase (SGK) isoforms contribute resistance to cancer therapies targeting the PI3K pathway. SGKs are homologous to Akt and these kinases display overlapping specificity and phosphorylate several substrates at the same residues, such as TSC2 to promote tumor growth by switching on the mTORC1 pathway. The SGK3 isoform is up-regulated in breast cancer cells treated with PI3K or Akt inhibitors and recruited and activated at endosomes, through its phox homology domain binding to PtdIns(3)P. We undertook genetic and pharmacological phosphoproteomic screens to uncover novel SGK3 substrates. We identified 40 potential novel SGK3 substrates, including four endosomal proteins STX7 (Ser126) and STX12 (Ser139), RFIP4 (Ser527) and WDR44 (Ser346) that were efficiently phosphorylated in vitro by SGK3 at the sites identified in vivo, but poorly by Akt. We demonstrate that these substrates are inefficiently phosphorylated by Akt as they possess an n + 1 residue from the phosphorylation site that is unfavorable for Akt phosphorylation. Phos-tag analysis revealed that stimulation of HEK293 cells with IGF1 to activate SGK3, promoted phosphorylation of a significant fraction of endogenous STX7 and STX12, in a manner that was blocked by knock-out of SGK3 or treatment with a pan SGK inhibitor (14H). SGK3 phosphorylation of STX12 enhanced interaction with the VAMP4/VTI1A/STX6 containing the SNARE complex and promoted plasma membrane localization. Our data reveal novel substrates for SGK3 and suggest a mechanism by which STX7 and STX12 SNARE complexes are regulated by SGK3. They reveal new biomarkers for monitoring SGK3 pathway activity.
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Cho DH. Telmisartan Inhibits Nitric Oxide Production and Vessel Relaxation via Protein Phosphatase 2A-mediated Endothelial NO Synthase-Ser 1179 Dephosphorylation. J Korean Med Sci 2019; 34:e266. [PMID: 31674157 PMCID: PMC6823522 DOI: 10.3346/jkms.2019.34.e266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Apart from its blood pressure-lowering effect by blocking the renin-angiotensin-aldosterone system, telmisartan, an angiotensin II type 1 receptor blocker (ARB), exhibits various ancillary effects including cardiovascular protective effects in vitro. Nonetheless, the protective effects of telmisartan in cerebrocardiovascular diseases are somewhat variable in large-scale clinical trials. Dysregulation of endothelial nitric oxide (NO) synthase (eNOS)-derived NO contributes to the developments of various vascular diseases. Nevertheless, the direct effects of telmisartan on endothelial functions including NO production and vessel relaxation, and its action mechanism have not been fully elucidated. Here, we investigated the mechanism by which telmisartan regulates NO production and vessel relaxation in vitro and in vivo. METHODS We measured nitrite levels in culture medium and mouse serum, and performed inhibitor studies and western blot analyses using bovine aortic endothelial cells (BAECs) and a hyperglycemic mouse model. To assess vessel reactivity, we performed acetylcholine (ACh)-induced vessel relaxation assay on isolated rat aortas. RESULTS Telmisartan decreased NO production in normoglycemic and hyperglycemic BAECs, which was accompanied by reduced phosphorylation of eNOS at Ser1179 (p-eNOS-Ser1179). Telmisartan increased the expression of protein phosphatase 2A catalytic subunit (PP2Ac) and co-treatment with okadaic acid completely restored telmisartan-inhibited NO production and p-eNOS-Ser1179 levels. Of the ARBs tested (including losartan and fimasartan), only telmisartan decreased NO production and p-eNOS-Ser1179 levels, and enhanced PP2Ac expression. Co-treatment with GW9662 had no effect on telmisartan-induced changes. In line with in vitro observations, telmisartan reduced serum nitrite and p-eNOS-Ser1179 levels, and increased PP2Ac expression in high fat diet-fed mice. Furthermore, telmisartan attenuated ACh-induced rat aorta relaxation. CONCLUSION We demonstrated that telmisartan inhibited NO production and vessel relaxation at least in part by PP2A-mediated eNOS-Ser1179 dephosphorylation in a peroxisome proliferator-activated receptor γ-independent manner. These results may provide a mechanism that explains the inconsistent cerebrocardiovascular protective effects of telmisartan.
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Affiliation(s)
- Du Hyong Cho
- Department of Pharmacology, Yeungnam University College of Medicine, Daegu, Korea.
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Liu K, Jones S, Minis A, Rodriguez J, Molina H, Steller H. PI31 Is an Adaptor Protein for Proteasome Transport in Axons and Required for Synaptic Development. Dev Cell 2019; 50:509-524.e10. [PMID: 31327739 DOI: 10.1016/j.devcel.2019.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/18/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022]
Abstract
Protein degradation by the ubiquitin-proteasome system is critical for neuronal function. Neurons utilize microtubule-dependent molecular motors to allocate proteasomes to synapses, but how proteasomes are coupled to motors and how this is regulated to meet changing demand for protein breakdown remain largely unknown. We show that the conserved proteasome-binding protein PI31 serves as an adaptor to couple proteasomes with dynein light chain proteins (DYNLL1/2). The inactivation of PI31 inhibited proteasome motility in axons and disrupted synaptic proteostasis, structure, and function. Moreover, phosphorylation of PI31 by p38 MAPK enhanced binding to DYNLL1/2 and promoted the directional movement of proteasomes in axons, suggesting a mechanism to regulate loading of proteasomes onto motors. Inactivation of PI31 in mouse neurons attenuated proteasome movement in axons, indicating this process is conserved. Because mutations affecting PI31 activity are associated with human neurodegenerative diseases, impairment of PI31-mediated axonal transport of proteasomes may contribute to these disorders.
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Affiliation(s)
- Kai Liu
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sandra Jones
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Adi Minis
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jose Rodriguez
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Hermann Steller
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Bradley D, Beltrao P. Evolution of protein kinase substrate recognition at the active site. PLoS Biol 2019; 17:e3000341. [PMID: 31233486 PMCID: PMC6611643 DOI: 10.1371/journal.pbio.3000341] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023] Open
Abstract
Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase-substrate motif. Kinases have been extensively duplicated throughout evolution, but little is known about when in time new target motifs have arisen. Here, we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity-determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but are not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired around the time of the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
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Zaballa ME, van der Goot FG. The molecular era of protein S-acylation: spotlight on structure, mechanisms, and dynamics. Crit Rev Biochem Mol Biol 2018; 53:420-451. [DOI: 10.1080/10409238.2018.1488804] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- María-Eugenia Zaballa
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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12
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15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins. Proc Natl Acad Sci U S A 2018; 115:E1710-E1719. [PMID: 29432148 DOI: 10.1073/pnas.1717560115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Studies over the past decade have highlighted the functional significance of intrinsically disordered proteins (IDPs). Due to conformational heterogeneity and inherent dynamics, structural studies of IDPs have relied mostly on NMR spectroscopy, despite IDPs having characteristics that make them challenging to study using traditional 1H-detected biomolecular NMR techniques. Here, we develop a suite of 3D 15N-detected experiments that take advantage of the slower transverse relaxation property of 15N nuclei, the associated narrower linewidth, and the greater chemical shift dispersion compared with those of 1H and 13C resonances. The six 3D experiments described here start with aliphatic 1H magnetization to take advantage of its higher initial polarization, and are broadly applicable for backbone assignment of proteins that are disordered, dynamic, or have unfavorable amide proton exchange rates. Using these experiments, backbone resonance assignments were completed for the unstructured regulatory domain (residues 131-294) of the human transcription factor nuclear factor of activated T cells (NFATC2), which includes 28 proline residues located in functionally important serine-proline (SP) repeats. The complete assignment of the NFATC2 regulatory domain enabled us to study phosphorylation of NFAT by kinase PKA and phosphorylation-dependent binding of chaperone protein 14-3-3 to NFAT, providing mechanistic insight on how 14-3-3 regulates NFAT nuclear translocation.
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13
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Evolution, dynamics and dysregulation of kinase signalling. Curr Opin Struct Biol 2018; 48:133-140. [DOI: 10.1016/j.sbi.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022]
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14
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Chang JK, Ni Y, Han L, Sinnett-Smith J, Jacamo R, Rey O, Young SH, Rozengurt E. Protein kinase D1 (PKD1) phosphorylation on Ser 203 by type I p21-activated kinase (PAK) regulates PKD1 localization. J Biol Chem 2017; 292:9523-9539. [PMID: 28408623 DOI: 10.1074/jbc.m116.771394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/11/2017] [Indexed: 01/07/2023] Open
Abstract
Although PKC-mediated phosphorylation of protein kinase D1 (PKD1) has been extensively characterized, little is known about PKD1 regulation by other upstream kinases. Here we report that stimulation of epithelial or fibroblastic cells with G protein-coupled receptor agonists, including angiotensin II or bombesin, induced rapid and persistent PKD1 phosphorylation at Ser203, a highly conserved residue located within the PKD1 N-terminal domain. Exposure to PKD or PKC family inhibitors did not prevent PKD1 phosphorylation at Ser203, indicating that it is not mediated by autophosphorylation. In contrast, several lines of evidence indicated that the phosphorylation of PKD1 at Ser203 is mediated by kinases of the class I PAK subfamily, specifically 1) exposing cells to four structurally unrelated PAK inhibitors (PF-3758309, FRAX486, FRAX597, and IPA-3) that act via different mechanisms abrogated PKD1 phosphorylation at Ser203, 2) siRNA-mediated knockdown of PAK1 and PAK2 in IEC-18 and Swiss 3T3 cells blunted PKD1 phosphorylation at Ser203, 3) phosphorylation of Ser203 markedly increased in vitro when recombinant PKD1 was incubated with either PAK1 or PAK2 in the presence of ATP. PAK inhibitors did not interfere with G protein-coupled receptor activation-induced rapid translocation of PKD1 to the plasma membrane but strikingly prevented the dissociation of PKD1 from the plasma membrane and blunted the phosphorylation of nuclear targets, including class IIa histone deacetylases. We conclude that PAK-mediated phosphorylation of PKD1 at Ser203 triggers its membrane dissociation and subsequent entry into the nucleus, thereby regulating the phosphorylation of PKD1 nuclear targets, including class IIa histone deacetylases.
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Affiliation(s)
- Jen-Kuan Chang
- From the Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine
| | - Yang Ni
- From the Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine
| | - Liang Han
- From the Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine
| | - James Sinnett-Smith
- From the Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine.,CURE: Digestive Diseases Research Center, and.,Veterans Affairs Greater Los Angeles Health Care System and
| | - Rodrigo Jacamo
- the Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030-4017, and
| | - Osvaldo Rey
- the Institute of Immunology, Genetics, and Metabolism, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Universidad de Buenos Aires, Buenos Aires C1120AAR, Argentina
| | - Steven H Young
- From the Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine.,CURE: Digestive Diseases Research Center, and.,Veterans Affairs Greater Los Angeles Health Care System and
| | - Enrique Rozengurt
- From the Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, .,CURE: Digestive Diseases Research Center, and.,Veterans Affairs Greater Los Angeles Health Care System and.,the Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095-1786
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15
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Kwon KJ, Park JH, Jo I, Song KH, Han JS, Park SH, Han SH, Cho DH. Disruption of neuronal nitric oxide synthase dimerization contributes to the development of Alzheimer's disease: Involvement of cyclin-dependent kinase 5-mediated phosphorylation of neuronal nitric oxide synthase at Ser(293). Neurochem Int 2016; 99:52-61. [PMID: 27296112 DOI: 10.1016/j.neuint.2016.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/27/2016] [Accepted: 06/09/2016] [Indexed: 01/09/2023]
Abstract
Although previous studies have suggested that neuronal nitric oxide synthase (nNOS)-derived NO has neuroprotective effects on the development of Alzheimer's disease (AD), the underlying molecular mechanisms are not fully elucidated. Here, we investigated whether and how disruption of nNOS dimerization contributes to the development of AD. No differences in synaptic number or expression of synaptic markers, including synaptophysin and postsynaptic density 95, were found in the cortex of 5 × FAD mice, which possess 5 familial AD mutations, at 6 months of age compared with control littermates. nNOS dimerization was disrupted in the 5 × FAD cortex, accompanied by an increase in reactive oxygen species (ROS) production. The subcellular distribution of cyclin-dependent kinase 5 (CDK5) shifted more diffusely toward a cytosolic compartment, but there was no change in total expression. Furthermore, the levels of p25, a CDK5 activator, increased significantly and it colocalized with nNOS in the 5 × FAD cortex. In silico analysis revealed that a new nNOS-specific GSP (glycine-serine-proline) motif was well-conserved across species at nNOS-Ser(293), which is located ahead of the N-terminal hook. This motif was not present in the closely related isoform, endothelial NOS. Motif scan analysis also predicted that CDK5 can phosphorylate nNOS-Ser(293) with a high likelihood. An in vitro phosphorylation assay clearly showed that CDK5/p25 does indeed phosphorylate nNOS-Ser(293). Finally, nNOS-S293D mutant, a phosphomimetic form of nNOS-Ser(293), and nNOS-S293A mutant, a neutral form of nNOS-Ser(293), significantly decreased nNOS dimerization and NO production. Taken together, our results demonstrate that nNOS dimers are disrupted in the 5 × FAD cortex, and nNOS-Ser(293), a potential site of CDK5 phosphorylation, may be involved in the decrease in nNOS dimerization and NO production, and the development of AD.
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Affiliation(s)
- Kyoung Ja Kwon
- Department of Neurology, Konkuk University Medical Center and Department of Neuroscience, Center for Geriatric Neuroscience Research, Institute of Biomedical Science and Technology, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701, South Korea
| | - Jung-Hyun Park
- Department of Molecular Medicine, Ewha Womans University Medical School, 911-1, Mok-6-dong, Yangchun-gu, Seoul 158-710, South Korea
| | - Inho Jo
- Department of Molecular Medicine, Ewha Womans University Medical School, 911-1, Mok-6-dong, Yangchun-gu, Seoul 158-710, South Korea
| | - Kee-Ho Song
- Department of Internal Medicine, Konkuk University School of Medicine, 120-1 Neungdong-ro, Gwangjin-gu, Seoul 143-729, South Korea
| | - Jung-Soo Han
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701, South Korea
| | - Seung Hwa Park
- Department of Neurology, Konkuk University Medical Center and Department of Neuroscience, Center for Geriatric Neuroscience Research, Institute of Biomedical Science and Technology, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701, South Korea
| | - Seol-Heui Han
- Department of Neurology, Konkuk University Medical Center and Department of Neuroscience, Center for Geriatric Neuroscience Research, Institute of Biomedical Science and Technology, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701, South Korea.
| | - Du-Hyong Cho
- Department of Pharmacology, School of Medicine, Eulji University, 77 Gyeryong-ro 771 Beon-gil, Jung-gu, Daejeon 301-746, South Korea.
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16
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Miller CJ, Turk BE. Rapid Identification of Protein Kinase Phosphorylation Site Motifs Using Combinatorial Peptide Libraries. Methods Mol Biol 2016; 1360:203-16. [PMID: 26501912 DOI: 10.1007/978-1-4939-3073-9_15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eukaryotic protein kinases phosphorylate substrates at serine, threonine, and tyrosine residues that fall within the context of short sequence motifs. Knowing the phosphorylation site motif for a protein kinase facilitates designing substrates for kinase assays and mapping phosphorylation sites in protein substrates. Here, we describe an arrayed peptide library protocol for rapidly determining kinase phosphorylation consensus sequences. This method uses a set of peptide mixtures in which each of the 20 amino acid residues is systematically substituted at nine positions surrounding a central site of phosphorylation. Peptide mixtures are arrayed in multiwell plates and analyzed by radiolabel assay with the kinase of interest. The preferred sequence is determined from the relative rate of phosphorylation of each peptide in the array. Consensus peptides based on these sequences typically serve as efficient and specific kinase substrates for high-throughput screening or incorporation into biosensors.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA.
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17
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Davey NE, Cyert MS, Moses AM. Short linear motifs - ex nihilo evolution of protein regulation. Cell Commun Signal 2015; 13:43. [PMID: 26589632 PMCID: PMC4654906 DOI: 10.1186/s12964-015-0120-z] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/13/2015] [Indexed: 12/12/2022] Open
Abstract
Short sequence motifs are ubiquitous across the three major types of biomolecules: hundreds of classes and thousands of instances of DNA regulatory elements, RNA motifs and protein short linear motifs (SLiMs) have been characterised. The increase in complexity of transcriptional, post-transcriptional and post-translational regulation in higher Eukaryotes has coincided with a significant expansion of motif use. But how did the eukaryotic cell acquire such a vast repertoire of motifs? In this review, we curate the available literature on protein motif evolution and discuss the evidence that suggests SLiMs can be acquired by mutations, insertions and deletions in disordered regions. We propose a mechanism of ex nihilo SLiM evolution – the evolution of a novel SLiM from “nothing” – adding a functional module to a previously non-functional region of protein sequence. In our model, hundreds of motif-binding domains in higher eukaryotic proteins connect simple motif specificities with useful functions to create a large functional motif space. Accessible peptides that match the specificity of these motif-binding domains are continuously created and destroyed by mutations in rapidly evolving disordered regions, creating a dynamic supply of new interactions that may have advantageous phenotypic novelty. This provides a reservoir of diversity to modify existing interaction networks. Evolutionary pressures will act on these motifs to retain beneficial instances. However, most will be lost on an evolutionary timescale as negative selection and genetic drift act on deleterious and neutral motifs respectively. In light of the parallels between the presented model and the evolution of motifs in the regulatory segments of genes and (pre-)mRNAs, we suggest our understanding of regulatory networks would benefit from the creation of a shared model describing the evolution of transcriptional, post-transcriptional and post-translational regulation.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada. .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.
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18
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Mitra SK, Chen R, Dhandaydham M, Wang X, Blackburn RK, Kota U, Goshe MB, Schwartz D, Huber SC, Clouse SD. An autophosphorylation site database for leucine-rich repeat receptor-like kinases in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:1042-1060. [PMID: 25912465 DOI: 10.1111/tpj.12863] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
Leucine-rich repeat receptor-like kinases (LRR RLKs) form a large family of plant signaling proteins consisting of an extracellular domain connected by a single-pass transmembrane sequence to a cytoplasmic kinase domain. Autophosphorylation on specific Ser and/or Thr residues in the cytoplasmic domain is often critical for the activation of several LRR RLK family members with proven functional roles in plant growth regulation, morphogenesis, disease resistance, and stress responses. While identification and functional characterization of in vivo phosphorylation sites is ultimately required for a full understanding of LRR RLK biology and function, bacterial expression of recombinant LRR RLK cytoplasmic catalytic domains for identification of in vitro autophosphorylation sites provides a useful resource for further targeted identification and functional analysis of in vivo sites. In this study we employed high-throughput cloning and a variety of mass spectrometry approaches to generate an autophosphorylation site database representative of more than 30% of the approximately 223 LRR RLKs in Arabidopsis thaliana. We used His-tagged constructs of complete cytoplasmic domains to identify a total of 592 phosphorylation events across 73 LRR RLKs, with 497 sites uniquely assigned to specific Ser (268 sites) or Thr (229 sites) residues in 68 LRR RLKs. Multiple autophosphorylation sites per LRR RLK were the norm, with an average of seven sites per cytoplasmic domain, while some proteins showed more than 20 unique autophosphorylation sites. The database was used to analyze trends in the localization of phosphorylation sites across cytoplasmic kinase subdomains and to derive a statistically significant sequence motif for phospho-Ser autophosphorylation.
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Affiliation(s)
- Srijeet K Mitra
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ruiqiang Chen
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Murali Dhandaydham
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xiaofeng Wang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Robert Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Uma Kota
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael B Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Daniel Schwartz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269, USA
| | - Steven C Huber
- USDA/ARS, University of Illinois, Urbana, IL, 61801, USA
| | - Steven D Clouse
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
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19
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Abstract
Although members of the L1 (LINE-1) clade of non-LTR retrotransposons can be deleterious, the L1 clade has remained active in most mammals for ∼100 million years and generated almost 40% of the human genome. The details of L1-host interaction are largely unknown, however. Here we report that L1 activity requires phosphorylation of the protein encoded by the L1 ORF1 (ORF1p). Critical phospho-acceptor residues (two serines and two threonines) reside in four conserved proline-directed protein kinase (PDPK) target sites. The PDPK family includes mitogen-activated protein kinases and cyclin-dependent kinases. Mutation of any PDPK phospho-acceptor inhibits L1 retrotransposition. The phosphomimetic aspartic acid can restore activity at the two serine sites, but not at either threonine site, where it is strongly inhibitory. ORF1p also contains conserved PDPK docking sites, which promote specific interaction of PDPKs with their targets. As expected, mutations in these sites also inhibit L1 activity. PDPK mutations in ORF1p that inactivate L1 have no significant effect on the ability of ORF1p to anneal RNA in vitro, an important biochemical property of the protein. We show that phosphorylated PDPK sites in ORF1p are required for an interaction with the peptidyl prolyl isomerase 1 (Pin1), a critical component of PDPK-mediated regulation. Pin1 acts via isomerization of proline side chains at phosphorylated PDPK motifs, thereby affecting substrate conformation and activity. Our demonstration that L1 activity is dependent on and integrated with cellular phosphorylation regulatory cascades significantly increases our understanding of interactions between L1 and its host.
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20
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Madeira F, Tinti M, Murugesan G, Berrett E, Stafford M, Toth R, Cole C, MacKintosh C, Barton GJ. 14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides. Bioinformatics 2015; 31:2276-83. [PMID: 25735772 PMCID: PMC4495292 DOI: 10.1093/bioinformatics/btv133] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/25/2015] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION The 14-3-3 family of phosphoprotein-binding proteins regulates many cellular processes by docking onto pairs of phosphorylated Ser and Thr residues in a constellation of intracellular targets. Therefore, there is a pressing need to develop new prediction methods that use an updated set of 14-3-3-binding motifs for the identification of new 14-3-3 targets and to prioritize the downstream analysis of >2000 potential interactors identified in high-throughput experiments. RESULTS Here, a comprehensive set of 14-3-3-binding targets from the literature was used to develop 14-3-3-binding phosphosite predictors. Position-specific scoring matrix, support vector machines (SVM) and artificial neural network (ANN) classification methods were trained to discriminate experimentally determined 14-3-3-binding motifs from non-binding phosphopeptides. ANN, position-specific scoring matrix and SVM methods showed best performance for a motif window spanning from -6 to +4 around the binding phosphosite, achieving Matthews correlation coefficient of up to 0.60. Blind prediction showed that all three methods outperform two popular 14-3-3-binding site predictors, Scansite and ELM. The new methods were used for prediction of 14-3-3-binding phosphosites in the human proteome. Experimental analysis of high-scoring predictions in the FAM122A and FAM122B proteins confirms the predictions and suggests the new 14-3-3-predictors will be generally useful. AVAILABILITY AND IMPLEMENTATION A standalone prediction web server is available at http://www.compbio.dundee.ac.uk/1433pred. Human candidate 14-3-3-binding phosphosites were integrated in ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome database.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Geoffrey J Barton
- Division of Computational Biology, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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21
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Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. eLife 2014; 3:e04126. [PMID: 25310241 PMCID: PMC4228266 DOI: 10.7554/elife.04126] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/09/2014] [Indexed: 01/02/2023] Open
Abstract
Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.
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Affiliation(s)
- Conor J Howard
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Victor Hanson-Smith
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Kristopher J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Liam J Holt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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22
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Iqbal Z, Hoessli DC, Qazi WM, Ahmad M, Shakoori AR, Nasir-ud-Din. Exploring the sequence context of phosphorylatable amino acids: the contribution of the upgraded MAPRes tool. J Cell Biochem 2014; 116:370-9. [PMID: 25258092 DOI: 10.1002/jcb.24983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/19/2014] [Indexed: 11/10/2022]
Abstract
Several models that predict where post-translational modifications are likely to occur and formulate the corresponding association rules are available to analyze the functional potential of a protein sequence, but an algorithm incorporating the functional groups of the involved amino acids in the sequence analyses process is not yet available. In its previous version, MAPRes was utilized to investigate the influence of the surrounding amino acids of post- translationally and co-translationally modifiable sites. The MAPRes has been upgraded to take into account the different biophysical and biochemical properties of the amino acids that have the potential to influence different post- translational modifications (PTMs). In the present study, the upgraded version of MAPRes was implemented on phosphorylated Ser/Thr/Tyr data by considering the polarity and charge of the surrounding amino acids. The patterns mined by MAPRes incorporating structural information on polarity and charge of amino acids suggest distinct structure-function relationships for phosphorylated serines in a multifunctional protein such as the insulin-receptor substrate-1 (IRS-1) protein. The new version of MAPRes is freely available at http://www.imsb.edu.pk/Database.htm.
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Affiliation(s)
- Zeeshan Iqbal
- Institute of Molecular Sciences and Bioinformatics, Lahore, Pakistan
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23
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Hausmann R, Bahrenberg G, Kuhlmann D, Schumacher M, Braam U, Bieler D, Schlusche I, Schmalzing G. A hydrophobic residue in position 15 of the rP2X3 receptor slows desensitization and reveals properties beneficial for pharmacological analysis and high-throughput screening. Neuropharmacology 2014; 79:603-15. [PMID: 24452010 DOI: 10.1016/j.neuropharm.2014.01.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 12/24/2013] [Accepted: 01/09/2014] [Indexed: 11/19/2022]
Abstract
The homotrimeric P2X3 subtype, one of the seven members of the ATP-gated P2X receptor family, plays a role in sensory neurotransmission, including nociception. To overcome the bias resulting from fast desensitization of the P2X3 receptor in dose-response analyses, a non-desensitizing P2X2-X3 receptor chimera has been repeatedly used as a surrogate for the P2X3 receptor for functional analysis. Here, we show that only three of the P2X2-specific amino acid residues of the P2X2-X3 chimera, (19)P(21)V(22)I, are needed to confer a slowly desensitizing phenotype to the P2X3 receptor. The strongest delay in desensitization of the P2X3 receptor by a single residue was observed when (15)Ser was replaced by Val or another hydrophobic residue. Pharmacologically, the S(15)V-rP2X3 mutant behaved similarly to the wt-P2X3 receptor. Analysis of the S(15)V-rP2X3 receptor in 1321N1 astrocytoma cells by a common calcium-imaging-based assay showed 10-fold higher calcium transients relative to those of the wt-rP2X3 receptor. The S(15)V-rP2X3 cell line enabled reliable analysis of antagonistic potencies and correctly reported the mechanism of action of the P2X3 receptor antagonists A-317491 and TNP-ATP by a calcium-imaging assay. Together, these data suggest that the S(15)V-rP2X3 mutant may be suitable not only for automated fluorescence-based screening of molecule libraries for identification of lead compounds but also for facilitated pharmacological characterization of specific P2X3 receptor ligands. We suggest that the mechanism of desensitization of the P2X3 receptor may involve the movement of an N-terminal inactivation particle, in analogy to the "hinged-lid" or "ball and chain" mechanisms of voltage-gated NaV and Shaker KV channels, respectively.
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Affiliation(s)
- Ralf Hausmann
- Department of Molecular Pharmacology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany.
| | - Gregor Bahrenberg
- Grünenthal GmbH, Global Drug Discovery, Department of Molecular Pharmacology, Zieglerstrasse 6, 52078 Aachen, Germany
| | - Daniel Kuhlmann
- Department of Molecular Pharmacology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Michaela Schumacher
- Department of Molecular Pharmacology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Ursula Braam
- Department of Molecular Pharmacology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Dagmar Bieler
- Grünenthal GmbH, Global Drug Discovery, Department of Molecular Pharmacology, Zieglerstrasse 6, 52078 Aachen, Germany
| | - Ilka Schlusche
- Grünenthal GmbH, Global Drug Discovery, Department of Molecular Pharmacology, Zieglerstrasse 6, 52078 Aachen, Germany
| | - Günther Schmalzing
- Department of Molecular Pharmacology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
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24
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Trinh TB, Xiao Q, Pei D. Profiling the substrate specificity of protein kinases by on-bead screening of peptide libraries. Biochemistry 2013; 52:5645-55. [PMID: 23848432 DOI: 10.1021/bi4008947] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A robust, high-throughput method has been developed to screen one-bead-one-compound peptide libraries to systematically profile the sequence specificity of protein kinases. Its ability to provide individual sequences of the preferred substrates permits the identification of sequence contextual effects and nonpermissive residues. Application of the library method to kinases Pim1, MKK6, and Csk revealed that Pim1 and Csk are highly active toward peptide substrates and recognize specific sequence motifs, whereas MKK6 has little activity or sequence selectivity against peptide substrates. Pim1 recognizes peptide substrates of the consensus RXR(H/R)X(S/T); it accepts essentially any amino acid at the S/T-2 and S/T+1 positions, but strongly disfavors acidic residues (Asp or Glu) at the S/T-2 position and a proline residue at the S/T+1 position. The selected Csk substrates show strong sequence covariance and fall into two classes with the consensus sequences of (D/E)EPIYϕXϕ and (D/E)(E/D)S(E/D/I)YϕXϕ (where X is any amino acid and ϕ is a hydrophobic amino acid). Database searches and in vitro kinase assays identified phosphatase PTP-PEST as a Pim1 substrate and phosphatase SHP-1 as a potential Csk substrate. Our results demonstrate that the sequence specificity of protein kinases is defined not only by favorable interactions between permissive residue(s) on the substrate and their cognate binding site(s) on the kinase but also by repulsive interactions between the kinase and nonpermissive residue(s).
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Affiliation(s)
- Thi B Trinh
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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Tinti M, Johnson C, Toth R, Ferrier DEK, Mackintosh C. Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates. Open Biol 2013; 2:120103. [PMID: 22870394 PMCID: PMC3411107 DOI: 10.1098/rsob.120103] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 06/29/2012] [Indexed: 01/09/2023] Open
Abstract
14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.
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Affiliation(s)
- Michele Tinti
- MRC Protein Phosphorylation Unit, College of Life Sciences, James Black Centre, University of Dundee, Dow Street, Dundee DD1 5EH , UK
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26
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Cho DH, Lee EJ, Kwon KJ, Shin CY, Song KH, Park JH, Jo I, Han SH. Troglitazone, a thiazolidinedione, decreases tau phosphorylation through the inhibition of cyclin-dependent kinase 5 activity in SH-SY5Y neuroblastoma cells and primary neurons. J Neurochem 2013; 126:685-95. [DOI: 10.1111/jnc.12264] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 03/11/2013] [Accepted: 04/10/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Du-Hyong Cho
- Department of Neurology; Konkuk University Medical Center; Konkuk University; Seoul South Korea
- Department of Pharmacology; Center for Geriatric Neuroscience Research; SMART Institute of Advanced Biomedical Science School of Medicine; Konkuk University; Seoul South Korea
| | - Eun Joo Lee
- Department of Neurology; Konkuk University Medical Center; Konkuk University; Seoul South Korea
- Department of Pharmacology; Center for Geriatric Neuroscience Research; SMART Institute of Advanced Biomedical Science School of Medicine; Konkuk University; Seoul South Korea
| | - Kyoung Ja Kwon
- Department of Neurology; Konkuk University Medical Center; Konkuk University; Seoul South Korea
- Department of Pharmacology; Center for Geriatric Neuroscience Research; SMART Institute of Advanced Biomedical Science School of Medicine; Konkuk University; Seoul South Korea
| | - Chan Young Shin
- Department of Neurology; Konkuk University Medical Center; Konkuk University; Seoul South Korea
- Department of Pharmacology; Center for Geriatric Neuroscience Research; SMART Institute of Advanced Biomedical Science School of Medicine; Konkuk University; Seoul South Korea
| | - Kee-Ho Song
- Department of Internal Medicine; Konkuk University School of Medicine; Seoul South Korea
| | - Jung-Hyun Park
- Department of Molecular Medicine; Ewha Womans University Medical School; Seoul South Korea
| | - Inho Jo
- Department of Molecular Medicine; Ewha Womans University Medical School; Seoul South Korea
| | - Seol-Heui Han
- Department of Neurology; Konkuk University Medical Center; Konkuk University; Seoul South Korea
- Department of Pharmacology; Center for Geriatric Neuroscience Research; SMART Institute of Advanced Biomedical Science School of Medicine; Konkuk University; Seoul South Korea
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27
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Theillet FX, Kalmar L, Tompa P, Han KH, Selenko P, Dunker AK, Daughdrill GW, Uversky VN. The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24360. [PMID: 28516008 PMCID: PMC5424786 DOI: 10.4161/idp.24360] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 03/17/2013] [Indexed: 11/19/2022]
Abstract
A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.
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Affiliation(s)
- Francois-Xavier Theillet
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - Lajos Kalmar
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium.,Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics; University of Science and Technology; Daejeon, Yuseong-gu, Korea.,Biomedical Translational Research Center; Division of Convergent Biomedical Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Yuseong-gu, Korea
| | - Philipp Selenko
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Department of Biochemistry and Molecular Biology; Indiana University School of Medicine; Indianapolis, IN USA
| | - Gary W Daughdrill
- Center for Drug Discovery and Innovation; Department of Cell Biology, Microbiology and Molecular Biology; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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28
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Walkinshaw DR, Weist R, Xiao L, Yan K, Kim GW, Yang XJ. Dephosphorylation at a conserved SP motif governs cAMP sensitivity and nuclear localization of class IIa histone deacetylases. J Biol Chem 2013; 288:5591-605. [PMID: 23297420 DOI: 10.1074/jbc.m112.445668] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Histone deacetylase 4 (HDAC4) and its paralogs, HDAC5, -7, and -9 (all members of class IIa), possess multiple phosphorylation sites crucial for 14-3-3 binding and subsequent nuclear export. cAMP signaling stimulates nuclear import of HDAC4 and HDAC5, but the underlying mechanisms remain to be elucidated. Here we show that cAMP potentiates nuclear localization of HDAC9. Mutation of an SP motif conserved in HDAC4, -5, and -9 prevents cAMP-stimulated nuclear localization. Unexpectedly, this treatment inhibits phosphorylation at the SP motif, indicating an inverse relationship between the phosphorylation event and nuclear import. Consistent with this, leptomycin B-induced nuclear import and adrenocorticotropic hormone (ACTH) treatment result in the dephosphorylation at the motif. Moreover, the modification synergizes with phosphorylation at a nearby site, and similar kinetics was observed for both phosphorylation events during myoblast and adipocyte differentiation. These results thus unravel a previously unrecognized mechanism whereby cAMP promotes dephosphorylation and differentially regulates multisite phosphorylation and the nuclear localization of class IIa HDACs.
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Affiliation(s)
- Donald R Walkinshaw
- Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3A 1A3, Canada
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29
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Douglass J, Gunaratne R, Bradford D, Saeed F, Hoffert JD, Steinbach PJ, Knepper MA, Pisitkun T. Identifying protein kinase target preferences using mass spectrometry. Am J Physiol Cell Physiol 2012; 303:C715-27. [PMID: 22723110 DOI: 10.1152/ajpcell.00166.2012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A general question in molecular physiology is how to identify candidate protein kinases corresponding to a known or hypothetical phosphorylation site in a protein of interest. It is generally recognized that the amino acid sequence surrounding the phosphorylation site provides information that is relevant to identification of the cognate protein kinase. Here, we present a mass spectrometry-based method for profiling the target specificity of a given protein kinase as well as a computational tool for the calculation and visualization of the target preferences. The mass spectrometry-based method identifies sites phosphorylated in response to in vitro incubation of protein mixtures with active recombinant protein kinases followed by standard phosphoproteomic methodologies. The computational tool, called "PhosphoLogo," uses an information-theoretic algorithm to calculate position-specific amino acid preferences and anti-preferences from the mass-spectrometry data (http://helixweb.nih.gov/PhosphoLogo/). The method was tested using protein kinase A (catalytic subunit α), revealing the well-known preference for basic amino acids in positions -2 and -3 relative to the phosphorylated amino acid. It also provides evidence for a preference for amino acids with a branched aliphatic side chain in position +1, a finding compatible with known crystal structures of protein kinase A. The method was also employed to profile target preferences and anti-preferences for 15 additional protein kinases with potential roles in regulation of epithelial transport: CK2, p38, AKT1, SGK1, PKCδ, CaMK2δ, DAPK1, MAPKAPK2, PKD3, PIM1, OSR1, STK39/SPAK, GSK3β, Wnk1, and Wnk4.
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Ben-Shimon A, Niv MY. Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping. PLoS Comput Biol 2011; 7:e1002288. [PMID: 22125489 PMCID: PMC3219626 DOI: 10.1371/journal.pcbi.1002288] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phospho-accepting residue in the substrate. Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important for understanding kinase specificities toward their substrates and for designing substrate-like peptidic inhibitors. We applied ANCHORSmap, a new fragment-based computational approach for mapping amino acid side chains on protein surfaces, to predict and characterize the preference of kinases toward Arginine binding. We focus on positions P−2 and P−5, commonly occupied by Arginine (Arg) in substrates of basophilic Ser/Thr kinases. The method accurately identified all the P−2/P−5 Arg binding sites previously determined by X-ray crystallography and produced Arg preferences that corresponded to those experimentally found by peptide arrays. The predicted Arg-binding positions and their associated pockets were analyzed in terms of shape, physicochemical properties, amino acid composition, and in-silico mutagenesis, providing structural rationalization for previously unexplained trends in kinase preferences toward Arg moieties. This methodology sheds light on several kinases that were described in the literature as having non-trivial preferences for Arg, and provides some surprising departures from the prevailing views regarding residues that determine kinase specificity toward Arg. In particular, we found that the preference for a P−5 Arg is not necessarily governed by the 170/230 acidic pair, as was previously assumed, but by several different pairs of acidic residues, selected from positions 133, 169, and 230 (PKA numbering). The acidic residue at position 230 serves as a pivotal element in recognizing Arg from both the P−2 and P−5 positions. Protein kinases are key signaling enzymes and major drug targets that catalyze the transfer of phosphate group to a phospho-accepting residue in the substrate. Unraveling molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor (substrate consensus sequence, SCS) is important for understanding kinase-substrates specificities and for designing peptidic inhibitors. Current methods used to predict this set of essential residues usually rely on linking between experimentally determined SCSs to kinase sequences. As such, these methods are less sensitive when specificity is dictated by subtle or kinase-unique sequence/structural features. In this study, we took a different approach for studying kinases specificities, by applying a new fragment-based method for mapping amino acid side chains on protein surfaces. We predicted and characterized the preference of Ser/Thr kinases toward Arginine binding, using the unbound kinase structures. The method produced high quality predictions and was able to provide novel insights and interesting departures from the prevailing views regarding the specificity-determining elements governing specificity toward Arginine. This work paves the way for studying the kinase binding preferences for other amino acids, for predicting protein-peptide structures, for facilitating the design of novel inhibitors, and for re-engineering of kinase specificities.
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Affiliation(s)
- Avraham Ben-Shimon
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Israel
| | - Masha Y. Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Israel
- * E-mail:
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31
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Alexander J, Lim D, Joughin BA, Hegemann B, Hutchins JRA, Ehrenberger T, Ivins F, Sessa F, Hudecz O, Nigg EA, Fry AM, Musacchio A, Stukenberg PT, Mechtler K, Peters JM, Smerdon SJ, Yaffe MB. Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci Signal 2011; 4:ra42. [PMID: 21712545 DOI: 10.1126/scisignal.2001796] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The timing and localization of events during mitosis are controlled by the regulated phosphorylation of proteins by the mitotic kinases, which include Aurora A, Aurora B, Nek2 (never in mitosis kinase 2), Plk1 (Polo-like kinase 1), and the cyclin-dependent kinase complex Cdk1/cyclin B. Although mitotic kinases can have overlapping subcellular localizations, each kinase appears to phosphorylate its substrates on distinct sites. To gain insight into the relative importance of local sequence context in kinase selectivity, identify previously unknown substrates of these five mitotic kinases, and explore potential mechanisms for substrate discrimination, we determined the optimal substrate motifs of these major mitotic kinases by positional scanning oriented peptide library screening (PS-OPLS). We verified individual motifs with in vitro peptide kinetic studies and used structural modeling to rationalize the kinase-specific selection of key motif-determining residues at the molecular level. Cross comparisons among the phosphorylation site selectivity motifs of these kinases revealed an evolutionarily conserved mutual exclusion mechanism in which the positively and negatively selected portions of the phosphorylation motifs of mitotic kinases, together with their subcellular localizations, result in proper substrate targeting in a coordinated manner during mitosis.
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Affiliation(s)
- Jes Alexander
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Chiasson VL, Quinn MA, Young KJ, Mitchell BM. Protein kinase CbetaII-mediated phosphorylation of endothelial nitric oxide synthase threonine 495 mediates the endothelial dysfunction induced by FK506 (tacrolimus). J Pharmacol Exp Ther 2011; 337:718-23. [PMID: 21383022 DOI: 10.1124/jpet.110.178095] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
FK506 [tacrolimus; hexadecahydro-5,19-dihydroxy-3-[2-(4-hydroxy-3-methoxycyclohexyl)-1-methylethenyl]-14,16-dimethoxy-4,10,12,18-tetramethyl-8-(2-propenyl)-15,19-epoxy-3H-pyrido[2,1-c][1,4]oxa-azacyclotricosine-1,7,20,21(4H,23H)-tetrone] is used clinically to reduce the incidence of allograft rejection; however, chronic administration leads to endothelial dysfunction and hypertension. We have previously shown that FK506 activates Ca(2+)/diacylglycerol-dependent conventional protein kinase C (cPKC), which phosphorylates endothelial nitric oxide synthase (eNOS) at one of its inhibitory sites, Thr495. However, which cPKC isoform is responsible for phosphorylating eNOS Thr495 is unknown. The aim of the current study was to determine the cPKC isoform that is activated by FK506, leading to decreased endothelial function. FK506 reduced endothelium-dependent relaxation responses, yet had no effect on endothelium-independent relaxation responses in aortas from control mice. Of the various cPKC isoforms, only the administration of a PKCβ(II) isoform-specific peptide inhibitor restored aortic relaxation responses to that of controls. In aortic endothelial cells, FK506 significantly increased PKCβ(II) activation compared with vehicle-treated controls, and this was prevented by a PKCβ(II) isoform-specific peptide inhibitor. In addition, a PKCβ(II) isoform-specific peptide inhibitor prevented the increase in eNOS Thr495 phosphorylation induced by FK506. Taken together, our results indicate that β(II) is the cPKC isoform responsible for phosphorylating eNOS at the inhibitory site Thr495 in response to FK506. PKCβ(II) inhibition could prove beneficial in ameliorating the endothelial dysfunction and hypertension in patients treated with FK506.
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Affiliation(s)
- Valorie L Chiasson
- Department of Internal Medicine, Division of Nephrology and Hypertension, Texas A&M Health Science Center, Temple, TX 76504, USA
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O'Leary B, Rao S, Plaxton W. Phosphorylation of bacterial-type phosphoenolpyruvate carboxylase at Ser425 provides a further tier of enzyme control in developing castor oil seeds. Biochem J 2011; 433:65-74. [PMID: 20950272 PMCID: PMC3010082 DOI: 10.1042/bj20101361] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 10/12/2010] [Accepted: 10/15/2010] [Indexed: 11/17/2022]
Abstract
PEPC [PEP (phosphoenolpyruvate) carboxylase] is a tightly controlled anaplerotic enzyme situated at a pivotal branch point of plant carbohydrate metabolism. Two distinct oligomeric PEPC classes were discovered in developing COS (castor oil seeds). Class-1 PEPC is a typical homotetramer of 107 kDa PTPC (plant-type PEPC) subunits, whereas the novel 910-kDa Class-2 PEPC hetero-octamer arises from a tight interaction between Class-1 PEPC and 118 kDa BTPC (bacterial-type PEPC) subunits. Mass spectrometric analysis of immunopurified COS BTPC indicated that it is subject to in vivo proline-directed phosphorylation at Ser425. We show that immunoblots probed with phosphorylation site-specific antibodies demonstrated that Ser425 phosphorylation is promoted during COS development, becoming maximal at stage IX (maturation phase) or in response to depodding. Kinetic analyses of a recombinant, chimaeric Class-2 PEPC containing phosphomimetic BTPC mutant subunits (S425D) indicated that Ser425 phosphorylation results in significant BTPC inhibition by: (i) increasing its Km(PEP) 3-fold, (ii) reducing its I50 (L-malate and L-aspartate) values by 4.5- and 2.5-fold respectively, while (iii) decreasing its activity within the physiological pH range. The developmental pattern and kinetic influence of Ser425 BTPC phosphorylation is very distinct from the in vivo phosphorylation/activation of COS Class-1 PEPC's PTPC subunits at Ser11. Collectively, the results establish that BTPC's phospho-Ser425 content depends upon COS developmental and physiological status and that Ser425 phosphorylation attenuates the catalytic activity of BTPC subunits within a Class-2 PEPC complex. To the best of our knowledge, this study provides the first evidence for protein phosphorylation as a mechanism for the in vivo control of vascular plant BTPC activity.
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Key Words
- oil seed metabolism
- phosphoenolpyruvate carboxylase (pepc)
- phosphorylation site-specific antibodies
- protein phosphorylation
- ricinus communis (castor oil plant)
- site-directed mutagenesis
- atppc, plant-type phosphoenolpyruvate carboxylase isozyme from arabidopsis thaliana
- btpc, bacterial-type phosphoenolpyruvate carboxylase
- cos, castor (ricinus communis) oil seed(s)
- i50, inhibitor concentration producing 50% inhibition of enzyme activity
- pep, phosphoenolpyruvate
- pepc, pep carboxylase
- pp2a, protein phosphatase type-2a
- pp2ac, catalytic subunit of pp2a
- ptpc, plant-type pepc
- rcppc, btpc from ricinus communis
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Affiliation(s)
- Brendan O'Leary
- *Department of Biology, Queen's University, Kingston, ON, Canada K7L 3N6
| | - Srinath K. Rao
- *Department of Biology, Queen's University, Kingston, ON, Canada K7L 3N6
| | - William C. Plaxton
- *Department of Biology, Queen's University, Kingston, ON, Canada K7L 3N6
- †Department of Biochemistry, Queen's University, Kingston, ON, Canada K7L 3N6
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Panni S, Montecchi-Palazzi L, Kiemer L, Cabibbo A, Paoluzi S, Santonico E, Landgraf C, Volkmer-Engert R, Bachi A, Castagnoli L, Cesareni G. Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae
and H. sapiens. Proteomics 2010; 11:128-43. [DOI: 10.1002/pmic.201000030] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 09/24/2010] [Accepted: 10/09/2010] [Indexed: 11/08/2022]
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Ruan L, Torres CM, Qian J, Chen F, Mintz JD, Stepp DW, Fulton D, Venema RC. Pin1 prolyl isomerase regulates endothelial nitric oxide synthase. Arterioscler Thromb Vasc Biol 2010; 31:392-8. [PMID: 21051667 DOI: 10.1161/atvbaha.110.213181] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The Pin1 prolyl isomerase acts in concert with proline-directed protein kinases to regulate function of protein substrates through isomerization of peptide bonds that link phosphoserine or phosphothreonine to proline. We sought to determine whether Pin1 interacts with endothelial nitric oxide synthase (eNOS) in endothelial cells in a manner that depends on proline-directed phosphorylation of the eNOS enzyme and whether this interaction influences basal or agonist-stimulated eNOS activity. METHODS AND RESULTS Inhibitors of the extracellular-regulated kinase (ERK) 1/2 MAP kinases inhibit proline-directed phosphorylation of eNOS at serine 116 (Ser116) in bovine aortic endothelial cells (BAECs). Moreover, eNOS and Pin1 can be coimmunoprecipitated from BAECs only when Ser116 is phosphorylated. In addition, phosphomimetic Ser116Asp eNOS, but not wild-type eNOS, can be coimmunoprecipitated with Pin1 coexpressed in COS-7 cells. Inhibition of Pin1 in BAECs by juglone or by dominant negative Pin1 increases basal and agonist-stimulated NO release from the cells, whereas overexpression of wild-type Pin1 in BAECs suppresses basal and agonist-stimulated NO production. Overexpression of wild-type Pin1 in intact aortae also reduces agonist-induced relaxation of aortic rings. CONCLUSIONS Our results demonstrate a novel form of eNOS regulation in endothelial cells and blood vessels through Ser116 phosphorylation-dependent interaction of eNOS with Pin1.
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Affiliation(s)
- Ling Ruan
- Vascular Biology Center, Medical College of Georgia, Augusta, GA 30912-2500, USA
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Mok J, Kim PM, Lam HYK, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JLN, Sheu YJ, Sassi HE, Sopko R, Chan CSM, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal 2010; 3:ra12. [PMID: 20159853 DOI: 10.1126/scisignal.2000482] [Citation(s) in RCA: 274] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Phosphorylation is a universal mechanism for regulating cell behavior in eukaryotes. Although protein kinases target short linear sequence motifs on their substrates, the rules for kinase substrate recognition are not completely understood. We used a rapid peptide screening approach to determine consensus phosphorylation site motifs targeted by 61 of the 122 kinases in Saccharomyces cerevisiae. By correlating these motifs with kinase primary sequence, we uncovered previously unappreciated rules for determining specificity within the kinase family, including a residue determining P-3 arginine specificity among members of the CMGC [CDK (cyclin-dependent kinase), MAPK (mitogen-activated protein kinase), GSK (glycogen synthase kinase), and CDK-like] group of kinases. Furthermore, computational scanning of the yeast proteome enabled the prediction of thousands of new kinase-substrate relationships. We experimentally verified several candidate substrates of the Prk1 family of kinases in vitro and in vivo and identified a protein substrate of the kinase Vhs1. Together, these results elucidate how kinase catalytic domains recognize their phosphorylation targets and suggest general avenues for the identification of previously unknown kinase substrates across eukaryotes.
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Affiliation(s)
- Janine Mok
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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37
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Cho DH, Seo J, Park JH, Jo C, Choi YJ, Soh JW, Jo I. Cyclin-Dependent Kinase 5 Phosphorylates Endothelial Nitric Oxide Synthase at Serine 116. Hypertension 2010; 55:345-52. [DOI: 10.1161/hypertensionaha.109.140210] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nitric oxide (NO) production in endothelial cells (EC) is regulated by multisite phosphorylation of specific serine and threonine residues in endothelial NO synthase (eNOS). Among these, eNOS-Ser116 is phosphorylated in the basal state, and its phosphorylation contributes to basal NO production. Here, we investigated the mechanism by which eNOS-Ser116 is phosphorylated during the basal state using bovine aortic EC. Although a previous study suggested that protein kinase C was involved in eNOS-Ser116 phosphorylation, overexpression of various protein kinase C isoforms did not affect eNOS-Ser116 phosphorylation. An in silico analysis using a motif scan revealed that the eNOS-Ser116 residue might be a substrate for proline-directed protein kinases. Roscovitine, a specific inhibitor of cyclin-dependent kinase (CDK), 1, 2, and 5, but not an inhibitor of mitogen-activated protein kinase kinase or glycogen synthase kinase 3β, inhibited eNOS-Ser116 phosphorylation dose dependently. Furthermore, purified CDK1, 2, or 5 directly phosphorylated eNOS-Ser116 in vitro. Ectopic expression of the dominant-negative CDK5 but not dominant-negative CDK1 or dominant-negative CDK2 repressed eNOS-Ser116 phosphorylation and increased NO production. In addition, CDK5 activity was detected in bovine aortic EC, and coimmunoprecipitation and confocal microscopy studies revealed a colocalization of eNOS and CDK5. Cotransfection of CDK5 and p25, the specific CDK5 activator, increased eNOS-Ser116 phosphorylation and decreased NO production, but its parent molecule, p35, and p39, another activator, were not detected in bovine aortic EC, which suggests the existence of a novel CDK5 activator. Overall, this is the first study to find that CDK5 is a physiological kinase responsible for eNOS-Ser116 phosphorylation and regulation of NO production.
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Affiliation(s)
- Du-Hyong Cho
- From the School of Medicine (D.-H.C.), Konkuk University, Seoul, South Korea; Department of Molecular Medicine and Ewha Medical Research Institute (J.S., I.J.), Ewha Womans University Medical School, Seoul, South Korea; Department of Biotechnology (J.-H.P.), Korea University, Seoul, South Korea; Center for Biomedical Sciences (C.J.), National Institute of Health, Seoul, South Korea; Department of Biochemistry (Y.J.C.), Seoul National University School of Medicine, Seoul, South Korea; Department of
| | - Jungwon Seo
- From the School of Medicine (D.-H.C.), Konkuk University, Seoul, South Korea; Department of Molecular Medicine and Ewha Medical Research Institute (J.S., I.J.), Ewha Womans University Medical School, Seoul, South Korea; Department of Biotechnology (J.-H.P.), Korea University, Seoul, South Korea; Center for Biomedical Sciences (C.J.), National Institute of Health, Seoul, South Korea; Department of Biochemistry (Y.J.C.), Seoul National University School of Medicine, Seoul, South Korea; Department of
| | - Jung-Hyun Park
- From the School of Medicine (D.-H.C.), Konkuk University, Seoul, South Korea; Department of Molecular Medicine and Ewha Medical Research Institute (J.S., I.J.), Ewha Womans University Medical School, Seoul, South Korea; Department of Biotechnology (J.-H.P.), Korea University, Seoul, South Korea; Center for Biomedical Sciences (C.J.), National Institute of Health, Seoul, South Korea; Department of Biochemistry (Y.J.C.), Seoul National University School of Medicine, Seoul, South Korea; Department of
| | - Chulman Jo
- From the School of Medicine (D.-H.C.), Konkuk University, Seoul, South Korea; Department of Molecular Medicine and Ewha Medical Research Institute (J.S., I.J.), Ewha Womans University Medical School, Seoul, South Korea; Department of Biotechnology (J.-H.P.), Korea University, Seoul, South Korea; Center for Biomedical Sciences (C.J.), National Institute of Health, Seoul, South Korea; Department of Biochemistry (Y.J.C.), Seoul National University School of Medicine, Seoul, South Korea; Department of
| | - Yoon Jung Choi
- From the School of Medicine (D.-H.C.), Konkuk University, Seoul, South Korea; Department of Molecular Medicine and Ewha Medical Research Institute (J.S., I.J.), Ewha Womans University Medical School, Seoul, South Korea; Department of Biotechnology (J.-H.P.), Korea University, Seoul, South Korea; Center for Biomedical Sciences (C.J.), National Institute of Health, Seoul, South Korea; Department of Biochemistry (Y.J.C.), Seoul National University School of Medicine, Seoul, South Korea; Department of
| | - Jae-Won Soh
- From the School of Medicine (D.-H.C.), Konkuk University, Seoul, South Korea; Department of Molecular Medicine and Ewha Medical Research Institute (J.S., I.J.), Ewha Womans University Medical School, Seoul, South Korea; Department of Biotechnology (J.-H.P.), Korea University, Seoul, South Korea; Center for Biomedical Sciences (C.J.), National Institute of Health, Seoul, South Korea; Department of Biochemistry (Y.J.C.), Seoul National University School of Medicine, Seoul, South Korea; Department of
| | - Inho Jo
- From the School of Medicine (D.-H.C.), Konkuk University, Seoul, South Korea; Department of Molecular Medicine and Ewha Medical Research Institute (J.S., I.J.), Ewha Womans University Medical School, Seoul, South Korea; Department of Biotechnology (J.-H.P.), Korea University, Seoul, South Korea; Center for Biomedical Sciences (C.J.), National Institute of Health, Seoul, South Korea; Department of Biochemistry (Y.J.C.), Seoul National University School of Medicine, Seoul, South Korea; Department of
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Kumar N, Mohanty D. Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials. Bioinformatics 2009; 26:189-97. [DOI: 10.1093/bioinformatics/btp633] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Goldsmith EJ, Akella R, Min X, Zhou T, Humphreys JM. Substrate and docking interactions in serine/threonine protein kinases. Chem Rev 2007; 107:5065-81. [PMID: 17949044 PMCID: PMC4012561 DOI: 10.1021/cr068221w] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Elizabeth J Goldsmith
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA.
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Lack of evidence for direct phosphorylation of recombinantly expressed P2X(2) and P2X (3) receptors by protein kinase C. Purinergic Signal 2007; 3:377-88. [PMID: 18404451 PMCID: PMC2072911 DOI: 10.1007/s11302-007-9067-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 07/27/2007] [Indexed: 12/18/2022] Open
Abstract
P2X3 and P2X2+3 receptors are present on sensory neurons, where they contribute not only to transient nociceptive responses, but also to hypersensitivity underlying pathological pain states elicited by nerve injuries. Increased signalling through P2X3 and P2X2+3 receptors may arise from an increased routing to the plasma membrane and/or gain of function of pre-existing receptors. An obvious effector mechanism for functional modulation is protein kinase C (PKC)-mediated phosphorylation, since all P2X family members share a conserved consensus sequence for PKC, TXR/K, within the intracellularly located N-terminal domain. Contradictory reports have been published regarding the exact role of this motif. In the present study, we confirm that site-directed elimination of the potential phosphor-acceptor threonine or the basic residue in the P+2 position of the TXR/K sequence accelerates desensitization of P2X2 receptors and abolishes P2X3 receptor function. Moreover, the PKC activator phorbol 12-myristate 13-acetate increased P2X3 (but not P2X2) receptor-mediated currents. Biochemically, however, we were unable to demonstrate by various experimental approaches a direct phosphorylation of wild-type P2X2 and P2X3 receptors expressed in both Xenopus laevis oocytes and HEK293 cells. In conclusion, our data support the view that the TXR/K motif plays an important role in P2X function and that phorbol 12-myristate 13-acetate is capable of modulating some P2X receptor subtypes. The underlying mechanism, however, is unlikely to involve direct PKC-mediated P2X receptor phosphorylation.
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Rennefahrt UEE, Deacon SW, Parker SA, Devarajan K, Beeser A, Chernoff J, Knapp S, Turk BE, Peterson JR. Specificity profiling of Pak kinases allows identification of novel phosphorylation sites. J Biol Chem 2007; 282:15667-78. [PMID: 17392278 DOI: 10.1074/jbc.m700253200] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The p21-activated kinases (Paks) serve as effectors of the Rho family GTPases Rac and Cdc42. The six human Paks are divided into two groups based on sequence similarity. Group I Paks (Pak1 to -3) phosphorylate a number of substrates linking this group to regulation of the cytoskeleton and both proliferative and anti-apoptotic signaling. Group II Paks (Pak4 to -6) are thought to play distinct functional roles, yet their few known substrates are also targeted by Group I Paks. To determine if the two groups recognize distinct target sequences, we used a degenerate peptide library method to comprehensively characterize the consensus phosphorylation motifs of Group I and II Paks. We find that Pak1 and Pak2 exhibit virtually identical substrate specificity that is distinct from that of Pak4. Based on structural comparisons and mutagenesis, we identified two key amino acid residues that mediate the distinct specificities of Group I and II Paks and suggest a structural basis for these differences. These results implicate, for the first time, residues from the small lobe of a kinase in substrate selectivity. Finally, we utilized the Pak1 consensus motif to predict a novel Pak1 phosphorylation site in Pix (Pak-interactive exchange factor) and demonstrate that Pak1 phosphorylates this site both in vitro and in cultured cells. Collectively, these results elucidate the specificity of Pak kinases and illustrate a general method for the identification of novel sites phosphorylated by Paks.
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Affiliation(s)
- Ulrike E E Rennefahrt
- Division of Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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Koga S, Yamaguchi N, Abe T, Minegishi M, Tsuchiya S, Yamamoto M, Minegishi N. Cell-cycle-dependent oscillation of GATA2 expression in hematopoietic cells. Blood 2007; 109:4200-8. [PMID: 17255359 DOI: 10.1182/blood-2006-08-044149] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In vitro manipulation of hematopoietic stem cells (HSCs) is a key issue in both transplantation therapy and regenerative medicine, and thus new methods are required to achieve HSC expansion with self-renewal. GATA2 is a transcription factor controlling pool size of HSCs. Of interest, continuous overexpression of GATA2 does not induce HSC proliferation. In this report, we demonstrate that GATA2 expression, in leukemic and normal hematopoietic cells, oscillates during the cell cycle, such that expression is high in S phase but low in G(1)/S and M phase. GATA2 binding to target Bcl-X gene also oscillates in accordance with GATA2 expression. Using a green fluorescent protein (GFP)-GATA2 fusion protein, we demonstrate cell-cycle-specific activity of proteasome-dependent degradation of GATA2. Immunoprecipitation/immunoblotting analysis demonstrated phosphorylation of GATA2 at cyclin-dependent kinase (Cdk)-consensus motifs, S/T(0)P(+1), and interaction of GATA2 with Cdk2/cyclin A2-, Cdk2/cyclin A2-, and Cdk4/cyclin D1-phosphorylated GATA2 in vitro. Mutants in phosphorylation motifs exhibited altered expression profiles of GFP-GATA2 domain fusion proteins. These results indicate that GATA2 phosphorylation by Cdk/cyclin systems is responsible for the cell-cycle-dependent regulation of GATA2 expression, and suggest the possibility that a cell-cycle-specific "on-off" response of GATA2 expression may control hematopoietic-cell proliferation and survival.
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Affiliation(s)
- Shinichiro Koga
- Tohoku University Biomedical Engineering Research Organization, Tohoku University, Sendai, Japan
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Avruch J. MAP kinase pathways: the first twenty years. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1773:1150-60. [PMID: 17229475 PMCID: PMC2043147 DOI: 10.1016/j.bbamcr.2006.11.006] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 11/02/2006] [Accepted: 11/07/2006] [Indexed: 10/23/2022]
Abstract
The MAP kinases, discovered approximately 20 years ago, together with their immediate upstream regulators, are among the most highly studied signal transduction molecules. This body of work has shaped many aspects of our present views of signal transduction by protein kinases. The effort expended in this area reflects the extensive participation of these regulatory modules in the control of cell fate decisions, i.e., proliferation, differentiation and death, across all eukaryotic phylla and in all tissues of metazoans. The discovery of these kinases is reviewed, followed by a discussion of some of the features of this signaling module that account for its broad impact on cell function and its enormous interest to many investigators.
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Affiliation(s)
- Joseph Avruch
- Department of Molecular Biology and the Diabetes Unit, Medical Services, Massachusetts General Hospital, and Department of Medicine, Harvard Medical School, 185 Cambridge St., Boston, MA 02114-2790, USA.
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Monick MM, Powers LS, Gross TJ, Flaherty DM, Barrett CW, Hunninghake GW. Active ERK contributes to protein translation by preventing JNK-dependent inhibition of protein phosphatase 1. THE JOURNAL OF IMMUNOLOGY 2006; 177:1636-45. [PMID: 16849472 DOI: 10.4049/jimmunol.177.3.1636] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human alveolar macrophages, central to immune responses in the lung, are unique in that they have an extended life span in contrast to precursor monocytes. We have shown previously that the ERK MAPK (ERK) pathway is constitutively active in human alveolar macrophages and contributes to the prolonged survival of these cells. We hypothesized that ERK maintains survival, in part, by positively regulating protein translation. In support of this hypothesis, we have found novel links among ERK, JNK, protein phosphatase 1 (PP1), and the eukaryotic initiation factor (eIF) 2alpha. eIF2alpha is active when hypophosphorylated and is essential for initiation of protein translation (delivery of initiator tRNA charged with methionine to the ribosome). Using [(35)S]methionine labeling, we found that ERK inhibition significantly decreased protein translation rates in alveolar macrophages. Decreased protein translation resulted from phosphorylation (and inactivation) of eIF2alpha. We found that ERK inhibition increased JNK activity. JNK in turn inactivated (via phosphorylation) PP1, the phosphatase responsible for maintaining the hypophosphorylated state of eIF2alpha. As a composite, our data demonstrate that in human alveolar macrophages, constitutive ERK activity positively regulates protein translation via the following novel pathway: active ERK inhibits JNK, leading to activation of PP1alpha, eIF2alpha dephosphorylation, and translation initiation. This new role for ERK in alveolar macrophage homeostasis may help to explain the survival characteristic of these cells within their unique high oxygen and stress microenvironment.
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Affiliation(s)
- Martha M Monick
- University of Iowa Carver College of Medicine, Veterans Administration Medical Center, Iowa City, IA 52242, USA.
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45
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Cheng KY, Noble MEM, Skamnaki V, Brown NR, Lowe ED, Kontogiannis L, Shen K, Cole PA, Siligardi G, Johnson LN. The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition. J Biol Chem 2006; 281:23167-79. [PMID: 16707497 DOI: 10.1074/jbc.m600480200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the catalytic site. The role of this recruitment site, which enhances substrate affinity and catalytic efficiency, has been investigated using peptides derived from the natural substrates, namely CDC6 and p107, and a bispeptide inhibitor in which the gamma-phosphate of ATP is covalently attached by a linker to the CDC6 substrate peptide. X-ray studies with a 30-residue CDC6 peptide in complex with pCDK2/cyclin A showed binding of a dodecamer peptide at the recruitment site and a heptapeptide at the catalytic site, but no density for the linking 11 residues. Kinetic studies established that the CDC6 peptide had an 18-fold lower Km compared with heptapeptide substrate and that this effect required the recruitment peptide to be covalently linked to the substrate peptide. X-ray studies with the CDC6 bispeptide showed binding of the dodecamer at the recruitment site and the modified ATP in two alternative conformations at the catalytic site. The CDC6 bispeptide was a potent inhibitor competitive with both ATP and peptide substrate of pCDK2/cyclin A activity against a heptapeptide substrate (Ki = 0.83 nm) but less effective against RXL-containing substrates. We discuss how localization at the recruitment site (KD 0.4 microm) leads to increased catalytic efficiency and the design of a potent inhibitor. The notion of a flexible linker between the sites, which must have more than a minimal number of residues, provides an explanation for recognition and discrimination against different substrates.
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Affiliation(s)
- Kin-Yip Cheng
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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Bullock AN, Debreczeni J, Amos AL, Knapp S, Turk BE. Structure and substrate specificity of the Pim-1 kinase. J Biol Chem 2005; 280:41675-82. [PMID: 16227208 DOI: 10.1074/jbc.m510711200] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Pim kinases are a family of three vertebrate protein serine/threonine kinases (Pim-1, -2, and -3) belonging to the CAMK (calmodulin-dependent protein kinase-related) group. Pim kinases are emerging as important mediators of cytokine signaling pathways in hematopoietic cells, and they contribute to the progression of certain leukemias and solid tumors. A number of cytoplasmic and nuclear proteins are phosphorylated by Pim kinases and may act as their effectors in normal physiology and in disease. Recent crystallographic studies of Pim-1 have identified unique structural features but have not provided insight into how the kinase recognizes its target substrates. Here, we have conducted peptide library screens to exhaustively determine the sequence specificity of active site-mediated phosphorylation by Pim-1 and Pim-3. We have identified the major site of Pim-1 autophosphorylation and find surprisingly that it maps to a novel site that diverges from its consensus phosphorylation motif. We have solved the crystal structure of Pim-1 bound to a high affinity peptide substrate in complexes with either the ATP analog AMP-PNP or the bisindolylmaleimide kinase inhibitor 2-[1-(3-dimethylaminopropyl)-1H-indol-3-yl]-3-(1H-indol-3-yl)maleimide HCl. These structures reveal an unanticipated mode of recognition for basic residues upstream of the phosphorylation site, distinct from that of other kinases with similar substrate specificity. The structures provide a rationale for the unusually high affinity of Pim kinases for peptide substrates and suggest a general mode for substrate binding to members of the CAMK group.
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Affiliation(s)
- Alex N Bullock
- Oxford University, Centre for Structural Genomics, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
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