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Byrne DP, Shrestha S, Galler M, Cao M, Daly LA, Campbell AE, Eyers CE, Veal EA, Kannan N, Eyers PA. Aurora A regulation by reversible cysteine oxidation reveals evolutionarily conserved redox control of Ser/Thr protein kinase activity. Sci Signal 2020; 13:eaax2713. [PMID: 32636306 DOI: 10.1126/scisignal.aax2713] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Reactive oxygen species (ROS) are physiological mediators of cellular signaling and play potentially damaging roles in human diseases. In this study, we found that the catalytic activity of the Ser/Thr kinase Aurora A was inhibited by the oxidation of a conserved cysteine residue (Cys290) that lies adjacent to Thr288, a critical phosphorylation site in the activation segment. Cys is present at the equivalent position in ~100 human Ser/Thr kinases, a residue that we found was important not only for the activity of human Aurora A but also for that of fission yeast MAPK-activated kinase (Srk1) and PKA (Pka1). Moreover, the presence of this conserved Cys predicted biochemical redox sensitivity among a cohort of human CAMK, AGC, and AGC-like kinases. Thus, we predict that redox modulation of the conserved Cys290 of Aurora A may be an underappreciated regulatory mechanism that is widespread in eukaryotic Ser/Thr kinases. Given the key biological roles of these enzymes, these findings have implications for understanding physiological and pathological responses to ROS and highlight the importance of protein kinase regulation through multivalent modification of the activation segment.
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Affiliation(s)
- Dominic P Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Martin Galler
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Min Cao
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Leonard A Daly
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Amy E Campbell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Elizabeth A Veal
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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Hirst NL, Nebel JC, Lawton SP, Walker AJ. Deep phosphoproteome analysis of Schistosoma mansoni leads development of a kinomic array that highlights sex-biased differences in adult worm protein phosphorylation. PLoS Negl Trop Dis 2020; 14:e0008115. [PMID: 32203512 PMCID: PMC7089424 DOI: 10.1371/journal.pntd.0008115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Although helminth parasites cause enormous suffering worldwide we know little of how protein phosphorylation, one of the most important post-translational modifications used for molecular signalling, regulates their homeostasis and function. This is particularly the case for schistosomes. Herein, we report a deep phosphoproteome exploration of adult Schistosoma mansoni, providing one of the richest phosphoprotein resources for any parasite so far, and employ the data to build the first parasite-specific kinomic array. Complementary phosphopeptide enrichment strategies were used to detect 15,844 unique phosphopeptides mapping to 3,176 proteins. The phosphoproteins were predicted to be involved in a wide range of biological processes and phosphoprotein interactome analysis revealed 55 highly interconnected clusters including those enriched with ribosome, proteasome, phagosome, spliceosome, glycolysis, and signalling proteins. 93 distinct phosphorylation motifs were identified, with 67 providing a ‘footprint’ of protein kinase activity; CaMKII, PKA and CK1/2 were highly represented supporting their central importance to schistosome function. Within the kinome, 808 phosphorylation sites were matched to 136 protein kinases, and 68 sites within 37 activation loops were discovered. Analysis of putative protein kinase-phosphoprotein interactions revealed canonical networks but also novel interactions between signalling partners. Kinomic array analysis of male and female adult worm extracts revealed high phosphorylation of transformation:transcription domain associated protein by both sexes, and CDK and AMPK peptides by females. Moreover, eight peptides including protein phosphatase 2C gamma, Akt, Rho2 GTPase, SmTK4, and the insulin receptor were more highly phosphorylated by female extracts, highlighting their possible importance to female worm function. We envision that these findings, tools and methodology will help drive new research into the functional biology of schistosomes and other helminth parasites, and support efforts to develop new therapeutics for their control. Schistosomes are formidable parasites that cause the debilitating and life-threatening disease human schistosomiasis. We need to better understand the cellular biology of these parasites to develop novel strategies for their control. Within cells, a process called protein phosphorylation controls many aspects of molecular communication or ‘signalling’ and is central to cellular function and homeostasis. Here, using complementary strategies, we have performed the first in-depth characterisation and functional annotation of protein phosphorylation events in schistosomes, providing one of the richest phosphoprotein resources for any parasite to date. Using this knowledge, we have developed a novel tool to simultaneously evaluate signalling processes in these worms and highlight sex-biased differences in adult worm protein phosphorylation. Several proteins were found to be more greatly phosphorylated by female worm extracts, suggesting their possible importance to female worm function. This work will help drive new research into the fundamental biology of schistosomes, as well as related parasites, and will support efforts to develop new drug or vaccine-based therapeutics for their control.
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Affiliation(s)
- Natasha L. Hirst
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Jean-Christophe Nebel
- School of Computer Science and Mathematics, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Scott P. Lawton
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Anthony J. Walker
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
- * E-mail:
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53
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Georgoulia PS, Bjelic S, Friedman R. Deciphering the molecular mechanism of FLT3 resistance mutations. FEBS J 2020; 287:3200-3220. [PMID: 31943770 DOI: 10.1111/febs.15209] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/13/2019] [Accepted: 01/09/2020] [Indexed: 12/18/2022]
Abstract
FMS-like tyrosine kinase 3 (FLT3) has been found to be mutated in ~ 30% of acute myeloid leukaemia patients. Small-molecule inhibitors targeting FLT3 that are currently approved or still undergoing clinical trials are subject to drug resistance due to FLT3 mutations. How these mutations lead to drug resistance is hitherto poorly understood. Herein, we studied the molecular mechanism of the drug resistance mutations D835N, Y842S and M664I, which confer resistance against the most advanced inhibitors, quizartinib and PLX3397 (pexidartinib), using enzyme kinetics and computer simulations. In vitro kinase assays were performed to measure the comparative catalytic activity of the native protein and the mutants, using a bacterial expression system developed to this aim. Our results reveal that the differential drug sensitivity profiles can be rationalised by the dynamics of the protein-drug interactions and perturbation of the intraprotein contacts upon mutations. Drug binding induced a single conformation in the native protein, whereas multiple conformations were observed otherwise (in the mutants or in the absence of drugs). The end-point kinetics measurements indicated that the three resistant mutants conferred catalytic activity that is at least as high as that of the reference without such mutations. Overall, our calculations and measurements suggest that the structural dynamics of the drug-resistant mutants that affect the active state and the increased conformational freedom of the remaining inactive drug-bound population are the two major factors that contribute to drug resistance in FLT3 harbouring cancer cells. Our results explain the mechanism of drug resistance mutations and can aid to the design of more effective tyrosine kinase inhibitors.
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Affiliation(s)
| | - Sinisa Bjelic
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
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54
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Mutations That Confer Drug-Resistance, Oncogenicity and Intrinsic Activity on the ERK MAP Kinases-Current State of the Art. Cells 2020; 9:cells9010129. [PMID: 31935908 PMCID: PMC7016714 DOI: 10.3390/cells9010129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/31/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
Unique characteristics distinguish extracellular signal-regulated kinases (Erks) from other eukaryotic protein kinases (ePKs). Unlike most ePKs, Erks do not autoactivate and they manifest no basal activity; they become catalysts only when dually phosphorylated on neighboring Thr and Tyr residues and they possess unique structural motifs. Erks function as the sole targets of the receptor tyrosine kinases (RTKs)-Ras-Raf-MEK signaling cascade, which controls numerous physiological processes and is mutated in most cancers. Erks are therefore the executers of the pathway’s biology and pathology. As oncogenic mutations have not been identified in Erks themselves, combined with the tight regulation of their activity, Erks have been considered immune against mutations that would render them intrinsically active. Nevertheless, several such mutations have been generated on the basis of structure-function analysis, understanding of ePK evolution and, mostly, via genetic screens in lower eukaryotes. One of the mutations conferred oncogenic properties on Erk1. The number of interesting mutations in Erks has dramatically increased following the development of Erk-specific pharmacological inhibitors and identification of mutations that cause resistance to these compounds. Several mutations have been recently identified in cancer patients. Here we summarize the mutations identified in Erks so far, describe their properties and discuss their possible mechanism of action.
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Kushnir T, Bar-Cohen S, Mooshayef N, Lange R, Bar-Sinai A, Rozen H, Salzberg A, Engelberg D, Paroush Z. An Activating Mutation in ERK Causes Hyperplastic Tumors in a scribble Mutant Tissue in Drosophila. Genetics 2020; 214:109-120. [PMID: 31740452 PMCID: PMC6944410 DOI: 10.1534/genetics.119.302794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022] Open
Abstract
Receptor tyrosine kinase signaling plays prominent roles in tumorigenesis, and activating oncogenic point mutations in the core pathway components Ras, Raf, or MEK are prevalent in many types of cancer. Intriguingly, however, analogous oncogenic mutations in the downstream effector kinase ERK have not been described or validated in vivo To determine if a point mutation could render ERK intrinsically active and oncogenic, we have assayed in Drosophila the effects of a mutation that confers constitutive activity upon a yeast ERK ortholog and has also been identified in a few human tumors. Our analyses indicate that a fly ERK ortholog harboring this mutation alone (RolledR80S), and more so in conjunction with the known sevenmaker mutation (RolledR80S+D334N), suppresses multiple phenotypes caused by loss of Ras-Raf-MEK pathway activity, consistent with an intrinsic activity that is independent of upstream signaling. Moreover, expression of RolledR80S and RolledR80S+D334N induces tissue overgrowth in an established Drosophila cancer model. Our findings thus demonstrate that activating mutations can bestow ERK with pro-proliferative, tumorigenic capabilities and suggest that Drosophila represents an effective experimental system for determining the oncogenicity of ERK mutants and their response to therapy.
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Affiliation(s)
- Tatyana Kushnir
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shaked Bar-Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Navit Mooshayef
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Singapore-Hebrew University of Jerusalem Alliance for Research and Enterprise, Molecular Mechanisms of Inflammatory Diseases Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, 138602, Singapore
| | - Rotem Lange
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Allan Bar-Sinai
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Helit Rozen
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed 1311502, Israel
| | - Adi Salzberg
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109601, Israel
| | - David Engelberg
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Singapore-Hebrew University of Jerusalem Alliance for Research and Enterprise, Molecular Mechanisms of Inflammatory Diseases Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
| | - Ze'ev Paroush
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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56
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Wang T, Ma G, Ang CS, Korhonen PK, Stroehlein AJ, Young ND, Hofmann A, Chang BCH, Williamson NA, Gasser RB. The developmental phosphoproteome of Haemonchus contortus. J Proteomics 2019; 213:103615. [PMID: 31846766 DOI: 10.1016/j.jprot.2019.103615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 12/22/2022]
Abstract
Protein phosphorylation plays essential roles in many cellular processes. Despite recent progress in the genomics, transcriptomics and proteomics of socioeconomically important parasitic nematodes, there is scant phosphoproteomic data to underpin molecular biological discovery. Here, using the phosphopeptide enrichment-based LC-MS/MS and data-independent acquisition (DIA) quantitation, we characterised the first developmental phosphoproteome of the parasitic nematode Haemonchus contortus - one of the most pathogenic parasites of ruminant livestock. Totally, 1804 phosphorylated proteins with 4406 phosphorylation sites ('phosphosites') from different developmental stages/sexes were identified. Bioinformatic analyses of quantified 'phosphosites' exhibited distinctive stage- and sex-specific patterns during development, and identified a subset of phosphoproteins proposed to play crucial roles in processes such as spindle positioning, signal transduction and kinase activity. A sequence-based comparison of the phosphoproteome of H. contortus with those of two free-living nematode species (Caenorhabditis elegans and Pristionchus pacificus) suggested a limited number of common protein phosphorylation events among these species. Our findings infer active roles for protein phosphorylation in the adaptation of a parasitic nematode to a constantly changing external environment. The phosphoproteomic data set for H. contortus provides a basis to better understand phosphorylation and associated biological processes (e.g., regulation of signal transduction), and might enable the discovery of novel anthelmintic targets. SIGNIFICANCE: Here, we report the first phosphoproteome for a socioeconomically parasitic nematode (Haemonchus contortus). This phosphoproteome exhibits distinctive patterns during development, suggesting active roles of post-translational modification in the parasite's adaptation to changing environments within and outside of the host animal. This work sheds a light on the developmental phosphorylation in a parasitic nematode, and could enable the discovery of novel interventions against major pathogens.
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Affiliation(s)
- Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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57
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Ahiri A, Garmes H, Podlipnik C, Aboulmouhajir A. Insights into evolutionary interaction patterns of the 'Phosphorylation Activation Segment' in kinase. Bioinformation 2019; 15:666-677. [PMID: 31787816 PMCID: PMC6859708 DOI: 10.6026/97320630015666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
We are interested in studying the phosphorylation of the kinase activation loop, distinguishing the passage from the unphosphorylated to the phosphorylated form without allostery. We performed an interaction study to trace the change of interactions between the activation segment and the kinase catalytic core, before and after phosphorylation. Results show that the structural changes are mainly due to the attraction between the phosphate group and guanidine groups of the arginine side chains of RD-pocket, which are constituted mainly of guanidine groups of the catalytic loop, the β9, and the αC helix. This attraction causes propagation of structural variation of the activation segment, principally towards the N-terminal. The structural variations are not made on all the amino acids of the activation segment; they are conditioned by the existence of two beta sheets stabilizing the loop during phosphorylation. The first,β6-β9 sheet is usually present in most of the kinases; the second, β10-β11 is formed due to the interaction between the main chain amino acids of the activation loop and the αEF/αF loop.
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Affiliation(s)
- Adil Ahiri
- Modeling and Molecular Spectroscopy Team, Faculty of Sciences, University Chouaib Doukkali, El-Jadida, Morroco
| | - Hocine Garmes
- Analytical Chemistry and Environmental Sciences Team, Department of chemistry, Faculty of Science, University Chouaib Doukkali, El Jadida, Morroco
| | - Crtomir Podlipnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Aziz Aboulmouhajir
- Modeling and Molecular Spectroscopy Team, Faculty of Sciences, University Chouaib Doukkali, El-Jadida, Morroco
- Extraction, Spectroscopy and Valorization Team, Organic synthesis, Extraction and Valorization Laboratory, Faculty of Sciences of Ain Chock, Hassan II University, Casablanca, Morocco
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58
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Sang D, Pinglay S, Wiewiora RP, Selvan ME, Lou HJ, Chodera JD, Turk BE, Gümüş ZH, Holt LJ. Ancestral reconstruction reveals mechanisms of ERK regulatory evolution. eLife 2019; 8:38805. [PMID: 31407663 PMCID: PMC6692128 DOI: 10.7554/elife.38805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/03/2019] [Indexed: 01/21/2023] Open
Abstract
Protein kinases are crucial to coordinate cellular decisions and therefore their activities are strictly regulated. Previously we used ancestral reconstruction to determine how CMGC group kinase specificity evolved (Howard et al., 2014). In the present study, we reconstructed ancestral kinases to study the evolution of regulation, from the inferred ancestor of CDKs and MAPKs, to modern ERKs. Kinases switched from high to low autophosphorylation activity at the transition to the inferred ancestor of ERKs 1 and 2. Two synergistic amino acid changes were sufficient to induce this change: shortening of the β3-αC loop and mutation of the gatekeeper residue. Restoring these two mutations to their inferred ancestral state led to a loss of dependence of modern ERKs 1 and 2 on the upstream activating kinase MEK in human cells. Our results shed light on the evolutionary mechanisms that led to the tight regulation of a kinase that is central in development and disease.
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Affiliation(s)
- Dajun Sang
- Institute for Systems Genetics, New York University Langone Medical Center, New York, United States
| | - Sudarshan Pinglay
- Institute for Systems Genetics, New York University Langone Medical Center, New York, United States
| | - Rafal P Wiewiora
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States.,Memorial Sloan Kettering Cancer Center, New York, United States
| | - Myvizhi E Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - John D Chodera
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, United States
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Suzuki M, Yoshida I, Suto K, Desaki Y, Shibuya N, Kaku H. AtCERK1 Phosphorylation Site S493 Contributes to the Transphosphorylation of Downstream Components for Chitin-Induced Immune Signaling. PLANT & CELL PHYSIOLOGY 2019; 60:1804-1810. [PMID: 31119298 DOI: 10.1093/pcp/pcz096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/11/2019] [Indexed: 06/09/2023]
Abstract
While ligand-induced autophosphorylation of receptor-like kinases (RLKs) is known to be critical for triggering the downstream responses, biochemical mechanism by which each phosphorylation site contributes to the initiation of corresponding signaling cascades is only poorly understood, except the involvement of some phosphorylation sites in the regulation of catalytic activity of these RLKs. In this article, we first confirmed that the phosphorylation of S493 of AtCERK1 is involved in the regulation of chitin-induced defense responses by the complementation of an atcerk1 mutant with AtCERK1(S493A) cDNA. In vitro kinase assay with the heterologously expressed kinase domain of AtCERK1, GST-AtCERK1cyt, showed that the S493A mutation did not affect the autophosphorylation of AtCERK1 itself but diminished the transphosphorylation of downstream signaling components, PBL27 and PUB4. On the other hand, a phosphomimetic mutant, GST-AtCERK1(S493D)cyt, transphosphorylated these substrates as similar to the wild type AtCERK1. These results suggested that the phosphorylation of S493 does not contribute to the regulation of catalytic activity but plays an important role for the transphosphorylation of the downstream signaling components, thus contributing to the initiation of chitin signaling. To our knowledge, it is a novel finding that a specific phosphorylation site contributes to the regulation of transphosphorylation activity of RLKs. Further studies on the structural basis by which S493 phosphorylation contributes to the regulation of transphosphorylation would contribute to the understanding how the ligand-induced autophosphorylation of RLKs properly regulates the downstream signaling.
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Affiliation(s)
- Maruya Suzuki
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Issei Yoshida
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Kenkichi Suto
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
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Mayo CB, Erlandsen H, Mouser DJ, Feinstein AG, Robinson VL, May ER, Cole JL. Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry 2019; 58:2967-2977. [PMID: 31246429 DOI: 10.1021/acs.biochem.9b00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The RNA-activated protein kinase, PKR, is a key mediator of the innate immunity response to viral infection. Viral double-stranded RNAs induce PKR dimerization and autophosphorylation. The PKR kinase domain forms a back-to-back dimer. However, intermolecular ( trans) autophosphorylation is not feasible in this arrangement. We have obtained PKR kinase structures that resolves this dilemma. The kinase protomers interact via the known back-to-back interface as well as a front-to-front interface that is formed by exchange of activation segments. Mutational analysis of the front-to-front interface support a functional role in PKR activation. Molecular dynamics simulations reveal that the activation segment is highly dynamic in the front-to-front dimer and can adopt conformations conducive to phosphoryl transfer. We propose a mechanism where back-to-back dimerization induces a conformational change that activates PKR to phosphorylate a "substrate" kinase docked in a front-to-front geometry. This mechanism may be relevant to related kinases that phosphorylate the eukaryotic initiation factor eIF2α.
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61
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Akizuki K, Kinumi T, Ono A, Senga Y, Osawa J, Shigeri Y, Ishida A, Kameshita I, Sueyoshi N. Autoactivation of C-terminally truncated Ca2+/calmodulin-dependent protein kinase (CaMK) Iδ via CaMK kinase-independent autophosphorylation. Arch Biochem Biophys 2019; 668:29-38. [DOI: 10.1016/j.abb.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 01/01/2023]
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62
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Fraga JS, Sárkány Z, Silva A, Correia I, Pereira PJB, Macedo-Ribeiro S. Genetic code ambiguity modulates the activity of a C. albicans MAP kinase linked to cell wall remodeling. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:654-661. [PMID: 30797104 DOI: 10.1016/j.bbapap.2019.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 12/28/2022]
Abstract
The human fungal pathogen Candida albicans ambiguously decodes the universal leucine CUG codon predominantly as serine but also as leucine. C. albicans has a high capacity to survive and proliferate in adverse environments but the rate of leucine incorporation fluctuates in response to different stress conditions. C. albicans is adapted to tolerate this ambiguous translation through a mechanism that combines drastic decrease in CUG usage and reduction of CUG-encoded residues in conserved positions in the protein sequences. However, in a few proteins, the residues encoded by CUG codons are found in strictly conserved positions, suggesting that this genetic code alteration might have a functional impact. One such example is Cek1, a central signaling protein kinase that contains a single CUG-encoded residue at a conserved position, whose identity might regulate the correct flow of information across the MAPK cascade. Here we show that insertion of a leucine at the CUG-encoded position decreases the stability of Cek1, apparently without major structural alterations. In contrast, incorporation of a serine residue at the CUG position induces the autophosphorylation of the conserved tyrosine residue of the Cek1 231TEY233 motif, and increases its intrinsic kinase activity in vitro. These findings show that CUG ambiguity modulates the activity of Cek1, a key kinase directly linked to morphogenesis and virulence in C. albicans.
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Affiliation(s)
- Joana S Fraga
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Zsuzsa Sárkány
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Alexandra Silva
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Inês Correia
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Pedro José Barbosa Pereira
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
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Arif A, Jia J, Willard B, Li X, Fox PL. Multisite Phosphorylation of S6K1 Directs a Kinase Phospho-code that Determines Substrate Selection. Mol Cell 2019; 73:446-457.e6. [PMID: 30612880 PMCID: PMC6415305 DOI: 10.1016/j.molcel.2018.11.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/16/2018] [Accepted: 11/15/2018] [Indexed: 01/02/2023]
Abstract
Multisite phosphorylation of kinases can induce on-off or graded regulation of catalytic activity; however, its influence on substrate specificity remains unclear. Here, we show that multisite phosphorylation of ribosomal protein S6 kinase 1 (S6K1) alters target selection. Agonist-inducible phosphorylation of glutamyl-prolyl tRNA synthetase (EPRS) by S6K1 in monocytes and adipocytes requires not only canonical phosphorylation at Thr389 by mTORC1 but also phosphorylation at Ser424 and Ser429 in the C terminus by cyclin-dependent kinase 5 (Cdk5). S6K1 phosphorylation at these additional sites induces a conformational switch and is essential for high-affinity binding and phosphorylation of EPRS, but not canonical S6K1 targets, e.g., ribosomal protein S6. Unbiased proteomic analysis identified additional targets phosphorylated by multisite phosphorylated S6K1 in insulin-stimulated adipocytes-namely, coenzyme A synthase, lipocalin 2, and cortactin. Thus, embedded within S6K1 is a target-selective kinase phospho-code that integrates signals from mTORC1 and Cdk5 to direct an insulin-stimulated, post-translational metabolon determining adipocyte lipid metabolism.
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Affiliation(s)
- Abul Arif
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Orthopedics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Jie Jia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Xiaoxia Li
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Nevenzal H, Noach-Hirsh M, Skornik-Bustan O, Brio L, Barbiro-Michaely E, Glick Y, Avrahami D, Lahmi R, Tzur A, Gerber D. A high-throughput integrated microfluidics method enables tyrosine autophosphorylation discovery. Commun Biol 2019; 2:42. [PMID: 30729180 PMCID: PMC6353932 DOI: 10.1038/s42003-019-0286-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 12/21/2018] [Indexed: 01/22/2023] Open
Abstract
Autophosphorylation of receptor and non-receptor tyrosine kinases is a common molecular switch with broad implications for pathogeneses and therapy of cancer and other human diseases. Technologies for large-scale discovery and analysis of autophosphorylation are limited by the inherent difficulty to distinguish between phosphorylation and autophosphorylation in vivo and by the complexity associated with functional assays of receptors kinases in vitro. Here, we report a method for the direct detection and analysis of tyrosine autophosphorylation using integrated microfluidics and freshly synthesized protein arrays. We demonstrate the efficacy of our platform in detecting autophosphorylation activity of soluble and transmembrane tyrosine kinases, and the dependency of in vitro autophosphorylation assays on membranes. Our method, Integrated Microfluidics for Autophosphorylation Discovery (IMAD), is high-throughput, requires low reaction volumes and can be applied in basic and translational research settings. To our knowledge, it is the first demonstration of posttranslational modification analysis of membrane protein arrays.
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Affiliation(s)
- Hadas Nevenzal
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Meirav Noach-Hirsh
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Or Skornik-Bustan
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Lev Brio
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Efrat Barbiro-Michaely
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Yair Glick
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Dorit Avrahami
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Roxane Lahmi
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Amit Tzur
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
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Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories. Proc Natl Acad Sci U S A 2018; 115:E12015-E12023. [PMID: 30509975 DOI: 10.1073/pnas.1717944115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The rotavirus (RV) genome is replicated and packaged into virus progeny in cytoplasmic inclusions called viroplasms, which require interactions between RV nonstructural proteins NSP2 and NSP5. How viroplasms form remains unknown. We previously found two forms of NSP2 in RV-infected cells: a cytoplasmically dispersed dNSP2, which interacts with hypophosphorylated NSP5; and a viroplasm-specific vNSP2, which interacts with hyperphosphorylated NSP5. Other studies report that CK1α, a ubiquitous cellular kinase, hyperphosphorylates NSP5, but requires NSP2 for reasons that are unclear. Here we show that silencing CK1α in cells before RV infection resulted in (i) >90% decrease in RV replication, (ii) disrupted vNSP2 and NSP5 interaction, (iii) dispersion of vNSP2 throughout the cytoplasm, and (iv) reduced vNSP2 protein levels. Together, these data indicate that CK1α directly affects NSP2. Accordingly, an in vitro kinase assay showed that CK1α phosphorylates serine 313 of NSP2 and triggers NSP2 octamers to form a lattice structure as demonstrated by crystallographic analysis. Additionally, a dual-specificity autokinase activity for NSP2 was identified and confirmed by mass spectrometry. Together, our studies show that phosphorylation of NSP2 involving CK1α controls viroplasm assembly. Considering that CK1α plays a role in the replication of other RNA viruses, similar phosphorylation-dependent mechanisms may exist for other virus pathogens that require cytoplasmic virus factories for replication.
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Gomes EV, Bortolossi JC, Sanches PR, Mendes NS, Martinez-Rossi NM, Rossi A. STE20/PAKA Protein Kinase Gene Releases an Autoinhibitory Domain through Pre-mRNA Alternative Splicing in the Dermatophyte Trichophyton rubrum. Int J Mol Sci 2018; 19:ijms19113654. [PMID: 30463281 PMCID: PMC6274995 DOI: 10.3390/ijms19113654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/30/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022] Open
Abstract
Signaling pathways are highly diverse in filamentous fungi, allowing the cells to receive and process ambient information. Interaction of components from different pathways results in signaling networks. The mitogen-activated protein kinase (MAPK) pathway is dependent on phosphorylation that is accomplished by kinase proteins. Thus, the STE/PAK protein kinase family plays essential roles in MAPK signal transduction, regulating several cellular functions. The STE/PAK protein displays an autoinhibitory (Cdc42/Rac interactive binding-CRIB) domain on its N-terminal portion, which interacts with the C-terminal catalytic kinase domain. Based on current knowledge, for the STE/PAK kinase to be activated, molecular signals (e.g., interaction with the activated form of Rac1 and Cdc42 proteins) or proteolytic cleavage by caspase 3 is necessary. Both mechanisms release the kinase domain from the CRIB interaction. Here, we hypothesize a novel molecular mechanism for the activation of STE20/PAKA kinase in Trichophyton rubrum based on an alternative pre-mRNA splicing process. Our data suggest that, because of the retention of intron 1 of this gene, it is theoretically possible that the translation of STE20/PAKA kinase will be free of its autoinhibitory CRIB domain. These findings indicate a rapid response system to environmental changes. Furthermore, STE20/PAKA may be a potential T. rubrum virulence factor and an interesting target for new drugs against dermatophytes.
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Affiliation(s)
- Eriston V Gomes
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
- Department of Biofunctional, Center of Higher Education Morgana Potrich Eireli, Morgana Potrich College, Mineiros, Goiás 75830-000, Brazil.
| | - Julio C Bortolossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Pablo R Sanches
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Niege S Mendes
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Nilce M Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
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67
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Adaptation to Endoplasmic Reticulum Stress Requires Transphosphorylation within the Activation Loop of Protein Kinases Kin1 and Kin2, Orthologs of Human Microtubule Affinity-Regulating Kinase. Mol Cell Biol 2018; 38:MCB.00266-18. [PMID: 30201804 DOI: 10.1128/mcb.00266-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/18/2018] [Indexed: 12/30/2022] Open
Abstract
Perturbations in endoplasmic reticulum (ER) homeostasis, a condition termed ER stress, activate the unfolded protein response (UPR), an intracellular network of signaling pathways. Recently, we have shown that protein kinase Kin1 and its paralog, Kin2, in the budding yeast Saccharomyces cerevisiae (orthologs of microtubule affinity-regulating kinase in humans) contribute to the UPR function. These Kin kinases contain a conserved kinase domain and an autoinhibitory kinase-associated 1 (KA1) domain separated by a long undefined domain. Here, we show that Kin1 or Kin2 protein requires minimally a kinase domain and an adjacent kinase extension region (KER) for UPR function. We also show that the functional mini-Kin2 protein is predominantly visualized inside the cells and precipitated with the cellular membrane fraction, suggesting its association with the cellular endomembrane system. Furthermore, we show that transphosphorylation of the Kin1 residue T302 and the analogous Kin2 residue T281 within the activation loop are important for full kinase activity. Collectively, our data suggest that, during ER stress, the Kin kinase domain is released from its autoinhibitory KA1 domain and is activated by transphosphorylation.
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68
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Yuan J, Ng WH, Lam PYP, Wang Y, Xia H, Yap J, Guan SP, Lee ASG, Wang M, Baccarini M, Hu J. The dimer-dependent catalytic activity of RAF family kinases is revealed through characterizing their oncogenic mutants. Oncogene 2018; 37:5719-5734. [PMID: 29930381 PMCID: PMC6202329 DOI: 10.1038/s41388-018-0365-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
Abstract
Although extensively studied for three decades, the molecular mechanisms that regulate the RAF/MEK/ERK kinase cascade remain ambiguous. Recent studies identified the dimerization of RAF as a key event in the activation of this cascade. Here, we show that in-frame deletions in the β3-αC loop activate ARAF as well as BRAF and other oncogenic kinases by enforcing homodimerization. By characterizing these RAF mutants, we find that ARAF has less allosteric and catalytic activity than the other two RAF isoforms, which arises from its non-canonical APE motif. Further, these RAF mutants exhibit a strong oncogenic potential, and a differential inhibitor resistance that correlates with their dimer affinity. Using these unique mutants, we demonstrate that active RAFs, including the BRAF(V600E) mutant, phosphorylate MEK in a dimer-dependent manner. This study characterizes a special category of oncogenic kinase mutations, and elucidates the molecular basis that underlies the differential ability of RAF isoforms to stimulate MEK-ERK pathway. Further, this study reveals a unique catalytic feature of RAF family kinases that can be exploited to control their activities for cancer therapies.
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Affiliation(s)
- Jimin Yuan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Paula Y P Lam
- Division of Cellular and Molecular Research, Singapore, Singapore
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Yu Wang
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Hongping Xia
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Jiajun Yap
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Shou Ping Guan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Ann S G Lee
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Office of Clinical & Academic Faculty Affairs, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Physiology, National University of Singapore, 2 Medical Drive, 117597, Singapore, Singapore
| | - Mei Wang
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Manuela Baccarini
- Max F. Perutz Laboratories, University of Vienna, Doktor-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, Singapore, Singapore.
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore.
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69
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Willems E, Dedobbeleer M, Digregorio M, Lombard A, Lumapat PN, Rogister B. The functional diversity of Aurora kinases: a comprehensive review. Cell Div 2018; 13:7. [PMID: 30250494 PMCID: PMC6146527 DOI: 10.1186/s13008-018-0040-6] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
Abstract
Aurora kinases are serine/threonine kinases essential for the onset and progression of mitosis. Aurora members share a similar protein structure and kinase activity, but exhibit distinct cellular and subcellular localization. AurA favors the G2/M transition by promoting centrosome maturation and mitotic spindle assembly. AurB and AurC are chromosome-passenger complex proteins, crucial for chromosome binding to kinetochores and segregation of chromosomes. Cellular distribution of AurB is ubiquitous, while AurC expression is mainly restricted to meiotically-active germ cells. In human tumors, all Aurora kinase members play oncogenic roles related to their mitotic activity and promote cancer cell survival and proliferation. Furthermore, AurA plays tumor-promoting roles unrelated to mitosis, including tumor stemness, epithelial-to-mesenchymal transition and invasion. In this review, we aim to understand the functional interplay of Aurora kinases in various types of human cells, including tumor cells. The understanding of the functional diversity of Aurora kinases could help to evaluate their relevance as potential therapeutic targets in cancer.
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Affiliation(s)
- Estelle Willems
- 1Laboratory of Nervous System Diseases and Therapy, GIGA-Neuroscience, University of Liège, Avenue Hippocrate, 15, 4000 Liège, Belgium
| | - Matthias Dedobbeleer
- 1Laboratory of Nervous System Diseases and Therapy, GIGA-Neuroscience, University of Liège, Avenue Hippocrate, 15, 4000 Liège, Belgium
| | - Marina Digregorio
- 1Laboratory of Nervous System Diseases and Therapy, GIGA-Neuroscience, University of Liège, Avenue Hippocrate, 15, 4000 Liège, Belgium
| | - Arnaud Lombard
- 1Laboratory of Nervous System Diseases and Therapy, GIGA-Neuroscience, University of Liège, Avenue Hippocrate, 15, 4000 Liège, Belgium.,2Department of Neurosurgery, CHU of Liège, Liège, Belgium
| | - Paul Noel Lumapat
- 1Laboratory of Nervous System Diseases and Therapy, GIGA-Neuroscience, University of Liège, Avenue Hippocrate, 15, 4000 Liège, Belgium.,3Department of Neurology, CHU of Liège, Liège, Belgium
| | - Bernard Rogister
- 1Laboratory of Nervous System Diseases and Therapy, GIGA-Neuroscience, University of Liège, Avenue Hippocrate, 15, 4000 Liège, Belgium.,3Department of Neurology, CHU of Liège, Liège, Belgium
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70
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Weil LE, Shmidov Y, Kublanovsky M, Morgenstern D, Feldman M, Bitton R, Levy D. Oligomerization and Auto-methylation of the Human Lysine Methyltransferase SETD6. J Mol Biol 2018; 430:4359-4368. [PMID: 30189201 DOI: 10.1016/j.jmb.2018.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/31/2018] [Accepted: 08/23/2018] [Indexed: 02/06/2023]
Abstract
Signaling via lysine methylation by protein lysine methyltransferases (PKMTs), has been linked to diverse biological and disease processes. The mono-methyltransferase SETD6 (SET-domain-containing protein 6) is a member of the PKMT family and was previously shown to regulate essential cellular processes such as the NF-κB, WNT and the oxidative stress pathways. However, on the biochemical level, little is known about the enzymatic mode of action of SETD6. Here we provide evidence that SETD6 forms high-molecular-weight structures. Specifically, we demonstrate that SETD6 monomeric, dimeric and trimeric forms are stabilized by the methyl donor, S-adenosyl-l-methionine. We then show that SETD6 has auto-methylation activity at K39 and K179, which serves as the major auto-methylation sites with a moderate auto-methylation activity toward K372. A point mutation at K179 but not at K39 and K372, located at the SET domain of SETD6, impaired SETD6 ability to form a trimer, strongly implying a link between the auto-methylation and the oligomerization state. Finally, by radioactive in vitro methylation experiments and biochemical kinetics analysis, we show that the auto-methylation at K39 and K179 increases the catalytic rate of SETD6. Collectively, our data support a model by which SETD6 auto-methylation and self-interaction positively regulate its enzymatic activity in vitro and may suggest that other PKMTs are regulated in the same manner.
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Affiliation(s)
- Lital Estrella Weil
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Yulia Shmidov
- Department of Chemical Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Margarita Kublanovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - David Morgenstern
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Ronit Bitton
- Department of Chemical Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel.
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71
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Regulation of Herpes Simplex Virus 2 Protein Kinase UL13 by Phosphorylation and Its Role in Viral Pathogenesis. J Virol 2018; 92:JVI.00807-18. [PMID: 29899106 DOI: 10.1128/jvi.00807-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
UL13 proteins are serine/threonine protein kinases encoded by herpes simplex virus 1 (HSV-1) and HSV-2. Although the downstream effects of the HSV protein kinases, mostly those of HSV-1 UL13, have been reported, there is a lack of information on how these viral protein kinases are regulated in HSV-infected cells. In this study, we used a large-scale phosphoproteomic analysis of HSV-2-infected cells to identify a physiological phosphorylation site in HSV-2 UL13 (i.e., Ser-18) and investigated the significance of phosphorylation of this site in HSV-2-infected cell cultures and mice. Our results were as follows. (i) An alanine substitution at UL13 Ser-18 (S18A) significantly reduced HSV-2 replication and cell-to-cell spread in U2OS cells to a level similar to those of the UL13-null and kinase-dead mutations. (ii) The UL13 S18A mutation significantly impaired phosphorylation of a cellular substrate of this viral protein kinase in HSV-2-infected U2OS cells. (iii) Following vaginal infection of mice, the UL13 S18A mutation significantly reduced mortality, HSV-2 replication in the vagina, and development of vaginal disease to levels similar to those of the UL13-null and the kinase-dead mutations. (iv) A phosphomimetic substitution at UL13 Ser-18 significantly restored the phenotype observed with the UL13 S18A mutation in U2OS cells and mice. Collectively, our results suggested that phosphorylation of UL13 Ser-18 regulated UL13 function in HSV-2-infected cells and that this regulation was critical for the functional activity of HSV-2 UL13 in vitro and in vivo and also for HSV-2 replication and pathogenesis.IMPORTANCE Based on studies on cellular protein kinases, it is obvious that the regulatory mechanisms of protein kinases are as crucial as their functional consequences. Herpesviruses each encode at least one protein kinase, but the mechanism by which these kinases are regulated in infected cells remains to be elucidated, with a few exceptions, although information on their functional effects has been accumulating. In this study, we have shown that phosphorylation of the HSV-2 UL13 protein kinase at Ser-18 regulated its function in infected cells, and this regulation was critical for HSV-2 replication and pathogenesis in vivo UL13 is conserved in all members of the family Herpesviridae, and this is the first report clarifying the regulatory mechanism of a conserved herpesvirus protein kinase that is involved in viral replication and pathogenesis in vivo Our study may provide insight into the regulatory mechanisms of the other conserved herpesvirus protein kinases.
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Kasak L, Näks M, Eek P, Piirsoo A, Bhadoria R, Starkov P, Saarma M, Kasvandik S, Piirsoo M. Characterization of Protein Kinase ULK3 Regulation by Phosphorylation and Inhibition by Small Molecule SU6668. Biochemistry 2018; 57:5456-5465. [DOI: 10.1021/acs.biochem.8b00356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lagle Kasak
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Mihkel Näks
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Priit Eek
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Alla Piirsoo
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Rohit Bhadoria
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Pavel Starkov
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Merilin Saarma
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Marko Piirsoo
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
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73
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Vo TTL, Jeong CH, Lee S, Kim KW, Ha E, Seo JH. Versatility of ARD1/NAA10-mediated protein lysine acetylation. Exp Mol Med 2018; 50:1-13. [PMID: 30054464 PMCID: PMC6063952 DOI: 10.1038/s12276-018-0100-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 12/29/2022] Open
Abstract
Post-translational modifications (PTMs) are chemical alterations that occur in proteins that play critical roles in various cellular functions. Lysine acetylation is an important PTM in eukaryotes, and it is catalyzed by lysine acetyltransferases (KATs). KATs transfer acetyl-coenzyme A to the internal lysine residue of substrate proteins. Arrest defective 1 (ARD1) is a member of the KAT family. Since the identification of its KAT activity 15 years ago, many studies have revealed that diverse cellular proteins are acetylated by ARD1. ARD1-mediated lysine acetylation is a key switch that regulates the enzymatic activities and biological functions of proteins and influences cell biology from development to pathology. In this review, we summarize protein lysine acetylation mediated by ARD1 and describe the biological meanings of this modification. Enzymes that modify proteins by adding an acetyl group have profound effects on metabolism and development, as well as disease. This process, known as acetylation, is carried out by KAT proteins, which are present throughout the body. Although acetyl groups are small, acetylation can change a protein’s electrical charge and shape, and even alter its function. Ji Hae Seo at Keimyung University School of Medicine in Daegu, South Korea, and co-workers reviewed the roles of KAT proteins in health and disease. They report that KAT proteins control gene expression, switch metabolic pathways on or off, and regulate development. Malfunction can lead to various disorders, including neurodegeneration and tumor growth. The researchers highlight several KAT proteins, in particular an enzyme that acetylates the amino acid lysine, that are promising targets for treatment of diseases, including cancer.
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Affiliation(s)
- Tam Thuy Lu Vo
- College of Pharmacy, Keimyung University, Daegue, 42601, Republic of Korea
| | - Chul-Ho Jeong
- College of Pharmacy, Keimyung University, Daegue, 42601, Republic of Korea
| | - Sooyeun Lee
- College of Pharmacy, Keimyung University, Daegue, 42601, Republic of Korea
| | - Kyu-Won Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eunyoung Ha
- Department of Biochemistry, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea
| | - Ji Hae Seo
- Department of Biochemistry, Keimyung University School of Medicine, Daegu, 42601, Republic of Korea.
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74
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Cobbaut M, Derua R, Parker PJ, Waelkens E, Janssens V, Van Lint J. Protein kinase D displays intrinsic Tyr autophosphorylation activity: insights into mechanism and regulation. FEBS Lett 2018; 592:2432-2443. [PMID: 29933512 PMCID: PMC6099456 DOI: 10.1002/1873-3468.13171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/26/2018] [Accepted: 06/12/2018] [Indexed: 01/31/2023]
Abstract
The protein kinase D (PKD) family is regulated through multi-site phosphorylation, including autophosphorylation. For example, PKD displays in vivo autophosphorylation on Ser-742 (and Ser-738 in vitro) in the activation loop and Ser-910 in the C-tail (hPKD1 numbering). In this paper, we describe the surprising observation that PKD also displays in vitro autocatalytic activity towards a Tyr residue in the P + 1 loop of the activation segment. We define the molecular determinants for this unusual activity and identify a Cys residue (C705 in PKD1) in the catalytic loop as of utmost importance. In cells, PKD Tyr autophosphorylation is suppressed through the association of an inhibitory factor. Our findings provide important novel insights into PKD (auto)regulation.
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Affiliation(s)
- Mathias Cobbaut
- Laboratory of Protein Phosphorylation and ProteomicsDepartment of Cellular and Molecular MedicineFaculty of MedicineKU LeuvenBelgium
- Leuven Cancer Institute (LKI)KU LeuvenBelgium
- Present address:
Protein Phosphorylation LabThe Francis Crick InstituteLondonUK
| | - Rita Derua
- Laboratory of Protein Phosphorylation and ProteomicsDepartment of Cellular and Molecular MedicineFaculty of MedicineKU LeuvenBelgium
| | - Peter J. Parker
- Protein Phosphorylation LabThe Francis Crick InstituteLondonUK
- School of Cancer and Pharmaceutical SciencesKing's College LondonUK
| | - Etienne Waelkens
- Laboratory of Protein Phosphorylation and ProteomicsDepartment of Cellular and Molecular MedicineFaculty of MedicineKU LeuvenBelgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation and ProteomicsDepartment of Cellular and Molecular MedicineFaculty of MedicineKU LeuvenBelgium
- Leuven Cancer Institute (LKI)KU LeuvenBelgium
| | - Johan Van Lint
- Laboratory of Protein Phosphorylation and ProteomicsDepartment of Cellular and Molecular MedicineFaculty of MedicineKU LeuvenBelgium
- Leuven Cancer Institute (LKI)KU LeuvenBelgium
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75
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Katsura K, Tomabechi Y, Matsuda T, Yonemochi M, Mikuni J, Ohsawa N, Terada T, Yokoyama S, Kukimoto-Niino M, Takemoto C, Shirouzu M. Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression. Protein Expr Purif 2018; 150:92-99. [PMID: 29793032 DOI: 10.1016/j.pep.2018.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/10/2018] [Accepted: 05/10/2018] [Indexed: 01/07/2023]
Abstract
Since phosphorylation is involved in various physiological events, kinases and interacting factors can be potential targets for drug discovery. For the development and improvement of inhibitors from the point of view of mechanistic enzymology, a cell-free protein synthesis system would be advantageous, since it could prepare mutant proteins easily. However, especially in the case of protein kinase, product solubility remains one of the major challenges. To overcome this problem, we prepared a chaperone-supplemented extract from Escherichia coli BL21 cells harboring a plasmid encoding a set of chaperone genes, dnaK, dnaJ, and grpE. We explored cell-disruption procedures and constructed an efficient protein synthesis system. Employing this system, we produced the kinase domain of human hematopoietic cell kinase (HCK) to obtain further structural information about its molecular interaction with one of its inhibitors, previously developed by our group (RK-20449). Lower reaction temperature improved the solubility, and addition of a protein phosphatase (YpoH) facilitated the homogeneous production of the non-phosphorylated kinase domain. Crystals of the purified product were obtained and the kinase-inhibitor complex structure was solved at 1.7 Å resolution. In addition, results of kinase activity measurement, using a synthetic substrate, showed that the kinase activity was facilitated by autophosphorylation at Tyr416, as confirmed by the peptide mass mapping.
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Affiliation(s)
- Kazushige Katsura
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuri Tomabechi
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takayoshi Matsuda
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mayumi Yonemochi
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Junko Mikuni
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Noboru Ohsawa
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takaho Terada
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mutsuko Kukimoto-Niino
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Chie Takemoto
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Mikako Shirouzu
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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76
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Su D, Devarenne TP. In vitro activity characterization of the tomato SnRK1 complex proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:857-864. [PMID: 29777861 DOI: 10.1016/j.bbapap.2018.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/28/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Plant Sucrose non-Fermenting 1-Related Protein Kinase1 (SnRK1) complexes are members of the Snf1/AMPK/SnRK protein kinase family and play important roles in many aspects of metabolism. In tomato (Solanum lycopersicum, Sl), only one α-subunit of the SnRK1 complex, SlSnRK1.1, has been characterized to date. In this study, the phylogenetic placement and in vitro kinase activity of a second tomato SnRK1 α-subunit, SlSnRK1.2, were characterized. Interestingly, in the phylogenetic analysis of SnRK1 sequences from monocots and dicots SlSnRK1.2 clusters only with other Solanaceae SnRK1.2 sequences, suggesting possible functional divergence of these kinases from other SnRK1 kinases. For analysis of kinase activity, SlSnRK1.2 was able to autophosphorylate, phosphorylate the complex β-subunits, and phosphorylate the SnRK1 AMARA peptide substrate, all with drastically lower overall kinase activity compared to SlSnRK1.1. Activation by the upstream kinase SlSnAK was able to increase the kinase activity of both SlSnRK1.1 and SlSnRK1.2, although the increase is less dramatic for SlSnRK1.2. The highest kinase activity on the AMARA peptide for SlSnRK1.2 was seen when reconstituting the complex in vitro with SlSip1 as the β-subunit. In comparison, SlSnRK1.1 showed the lowest kinase activity on the AMARA peptide when SlSip1 was used. These studies suggest the SlSnRK1.2 phylogenetic divergence and lower SlSnRK1.2 kinase activity compared to SlSnRK1.1 may be indicative of different in vivo roles for each kinase.
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Affiliation(s)
- Dongyin Su
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Timothy P Devarenne
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
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77
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Ito T, Ishida S, Takahashi Y. Autophosphorylation of Ser-6 via an intermolecular mechanism is important for the rapid reduction of NtCDPK1 kinase activity for substrate RSG. PLoS One 2018; 13:e0196357. [PMID: 29684069 PMCID: PMC5912773 DOI: 10.1371/journal.pone.0196357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/11/2018] [Indexed: 12/03/2022] Open
Abstract
Tobacco (Nicotiana tabacum) Ca2+-dependent protein kinase 1 (NtCDPK1) is involved in feedback regulation of the plant hormone gibberellin through the phosphorylation of the transcription factor, REPRESSION OF SHOOT GROWTH (RSG). Previously, Ser-6 and Thr-21 were identified as autophosphorylation sites in NtCDPK1. Autophosphorylation of Ser-6 and Thr-21 not only decreases the binding affinity of NtCDPK1 for RSG, but also inhibits the homodimerization of NtCDPK1. Furthermore, autophosphorylation decreases the phosphorylation efficiency of RSG. We demonstrated that Ser-6 and Thr-21 of NtCDPK1 are phosphorylated in response to GAs in plants. The substitution of these autophosphorylation sites with Ala enhances the NtCDPK1 overexpression-induced sensitization of seeds to a GA biosynthetic inhibitor during germination. These findings suggested that autophosphorylation of Ser-6 and Thr-21 prevents excessive phosphorylation of RSG. In this study, we attempted to determine which autophosphorylation site is responsible for the functional regulation of NtCDPK1. Ser-6 was autophosphorylated within 1 min, whereas Thr-21 required over 5 min to be completely autophosphorylated. Furthermore, we found that Ser-6 and Thr-21 were autophosphorylated by inter- and intramolecular mechanisms, respectively, which may be reflected in the faster autophosphorylation of Ser-6. Although both autophosphorylation sites were involved in the reduction of the binding affinity of NtCDPK1 for RSG and the inhibition of NtCDPK1 homodimerization, autophosphorylation of Ser-6 alone was sufficient to decrease the kinase activity of NtCDPK1 for RSG. These results suggest that autophosphorylation of Ser-6 is important for the rapid reduction of NtCDPK1 kinase activity for RSG, whereas that of Thr-21 may play an auxiliary role.
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Affiliation(s)
- Takeshi Ito
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sarahmi Ishida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yohsuke Takahashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
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78
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Bhoir S, Shaik A, Thiruvenkatam V, Kirubakaran S. High yield bacterial expression, purification and characterisation of bioactive Human Tousled-like Kinase 1B involved in cancer. Sci Rep 2018; 8:4796. [PMID: 29555908 PMCID: PMC5859067 DOI: 10.1038/s41598-018-22744-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 12/14/2022] Open
Abstract
Human Tousled-like kinases (TLKs) are highly conserved serine/threonine protein kinases responsible for cell proliferation, DNA repair, and genome surveillance. Their possible involvement in cancer via efficient DNA repair mechanisms have made them clinically relevant molecular targets for anticancer therapy. Innovative approaches in chemical biology have played a key role in validating the importance of kinases as molecular targets. However, the detailed understanding of the protein structure and the mechanisms of protein-drug interaction through biochemical and biophysical techniques demands a method for the production of an active protein of exceptional stability and purity on a large scale. We have designed a bacterial expression system to express and purify biologically active, wild-type Human Tousled-like Kinase 1B (hTLK1B) by co-expression with the protein phosphatase from bacteriophage λ. We have obtained remarkably high amounts of the soluble and homogeneously dephosphorylated form of biologically active hTLK1B with our unique, custom-built vector design strategy. The recombinant hTLK1B can be used for the structural studies and may further facilitate the development of new TLK inhibitors for anti-cancer therapy using a structure-based drug design approach.
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Affiliation(s)
- Siddhant Bhoir
- Dicipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Simkheda, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Althaf Shaik
- Dicipline of Chemistry, Indian Institute of Technology Gandhinagar, Simkheda, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Vijay Thiruvenkatam
- Dicipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Simkheda, Palaj, Gandhinagar, 382355, Gujarat, India.
- Dicipline of Physics, Indian Institute of Technology Gandhinagar, Simkheda, Palaj, Gandhinagar, 382355, Gujarat, India.
| | - Sivapriya Kirubakaran
- Dicipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Simkheda, Palaj, Gandhinagar, 382355, Gujarat, India.
- Dicipline of Chemistry, Indian Institute of Technology Gandhinagar, Simkheda, Palaj, Gandhinagar, 382355, Gujarat, India.
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79
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Combes G, Barysz H, Garand C, Gama Braga L, Alharbi I, Thebault P, Murakami L, Bryne DP, Stankovic S, Eyers PA, Bolanos-Garcia VM, Earnshaw WC, Maciejowski J, Jallepalli PV, Elowe S. Mps1 Phosphorylates Its N-Terminal Extension to Relieve Autoinhibition and Activate the Spindle Assembly Checkpoint. Curr Biol 2018; 28:872-883.e5. [PMID: 29502948 PMCID: PMC5863767 DOI: 10.1016/j.cub.2018.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/15/2018] [Accepted: 02/01/2018] [Indexed: 12/29/2022]
Abstract
Monopolar spindle 1 (Mps1) is a conserved apical kinase in the spindle assembly checkpoint (SAC) that ensures accurate segregation of chromosomes during mitosis. Mps1 undergoes extensive auto- and transphosphorylation, but the regulatory and functional consequences of these modifications remain unclear. Recent findings highlight the importance of intermolecular interactions between the N-terminal extension (NTE) of Mps1 and the Hec1 subunit of the NDC80 complex, which control Mps1 localization at kinetochores and activation of the SAC. Whether the NTE regulates other mitotic functions of Mps1 remains unknown. Here, we report that phosphorylation within the NTE contributes to Mps1 activation through relief of catalytic autoinhibition that is mediated by the NTE itself. Moreover, we find that this regulatory NTE function is independent of its role in Mps1 kinetochore recruitment. We demonstrate that the NTE autoinhibitory mechanism impinges most strongly on Mps1-dependent SAC functions and propose that Mps1 activation likely occurs sequentially through dimerization of a “prone-to-autophosphorylate” Mps1 conformer followed by autophosphorylation of the NTE prior to maximal kinase activation segment trans-autophosphorylation. Our observations underline the importance of autoregulated Mps1 activity in generation and maintenance of a robust SAC in human cells. Mps1 autophosphorylation at the NTE promotes activity independent of localization NTE phosphorylation relieves an NTE-dependent autoinhibition Mps1 autophosphorylation at its NTE is essential for the SAC, but not congression
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Affiliation(s)
- Guillaume Combes
- Programme in Molecular and Cellular Biology, Faculty of Medicine, Université Laval, 1050 Avenue de la Médecine, Bureau 4633, Université Laval, Québec, QC G1V0A6, Canada; Axe of Reproduction, Mother and Youth Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, QC G1V 4G2, Canada
| | - Helena Barysz
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chantal Garand
- Axe of Reproduction, Mother and Youth Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, QC G1V 4G2, Canada
| | - Luciano Gama Braga
- Programme in Molecular and Cellular Biology, Faculty of Medicine, Université Laval, 1050 Avenue de la Médecine, Bureau 4633, Université Laval, Québec, QC G1V0A6, Canada; Axe of Reproduction, Mother and Youth Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, QC G1V 4G2, Canada
| | - Ibrahim Alharbi
- Programme in Molecular and Cellular Biology, Faculty of Medicine, Université Laval, 1050 Avenue de la Médecine, Bureau 4633, Université Laval, Québec, QC G1V0A6, Canada; Axe of Reproduction, Mother and Youth Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, QC G1V 4G2, Canada
| | - Philippe Thebault
- Axe of Reproduction, Mother and Youth Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, QC G1V 4G2, Canada
| | - Luc Murakami
- Axe of Reproduction, Mother and Youth Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, QC G1V 4G2, Canada
| | - Dominic P Bryne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Stasa Stankovic
- Department of Biological and Medical Sciences - Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Victor M Bolanos-Garcia
- Department of Biological and Medical Sciences - Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Prasad V Jallepalli
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sabine Elowe
- Programme in Molecular and Cellular Biology, Faculty of Medicine, Université Laval, 1050 Avenue de la Médecine, Bureau 4633, Université Laval, Québec, QC G1V0A6, Canada; Axe of Reproduction, Mother and Youth Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, QC G1V 4G2, Canada.
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80
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Schiel KA. A new etiologic model for Alzheimers Disease. Med Hypotheses 2018; 111:27-35. [DOI: 10.1016/j.mehy.2017.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/19/2017] [Accepted: 12/12/2017] [Indexed: 01/26/2023]
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81
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Revisiting paradigms of Ca2+ signaling protein kinase regulation in plants. Biochem J 2018; 475:207-223. [DOI: 10.1042/bcj20170022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/15/2022]
Abstract
Calcium (Ca2+) serves as a universal second messenger in eukaryotic signal transduction. Understanding the Ca2+ activation kinetics of Ca2+ sensors is critical to understanding the cellular signaling mechanisms involved. In this review, we discuss the regulatory properties of two sensor classes: the Ca2+-dependent protein kinases (CPKs/CDPKs) and the calcineurin B-like (CBL) proteins that control the activity of CBL-interacting protein kinases (CIPKs) and identify emerging topics and some foundational points that are not well established experimentally. Most plant CPKs are activated by physiologically relevant Ca2+ concentrations except for those with degenerate EF hands, and new results suggest that the Ca2+-dependence of kinase activation may be modulated by both protein–protein interactions and CPK autophosphorylation. Early results indicated that activation of plant CPKs by Ca2+ occurred by relief of autoinhibition. However, recent studies of protist CDPKs suggest that intramolecular interactions between CDPK domains contribute allosteric control to CDPK activation. Further studies are required to elucidate the mechanisms regulating plant CPKs. With CBL–CIPKs, the two major activation mechanisms are thought to be (i) binding of Ca2+-bound CBL to the CIPK and (ii) phosphorylation of residues in the CIPK activation loop. However, the relative importance of these two mechanisms in regulating CIPK activity is unclear. Furthermore, information detailing activation by physiologically relevant [Ca2+] is lacking, such that the paradigm of CBLs as Ca2+ sensors still requires critical, experimental validation. Developing models of CPK and CIPK regulation is essential to understand how these kinases mediate Ca2+ signaling and to the design of experiments to test function in vivo.
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82
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Lin B, Harris DR, Kirkman LMD, Perez AM, Qian Y, Schermerhorn JT, Hong MY, Winston DS, Xu L, Brandt GS. FIKK Kinase, a Ser/Thr Kinase Important to Malaria Parasites, Is Inhibited by Tyrosine Kinase Inhibitors. ACS OMEGA 2017; 2:6605-6612. [PMID: 30023525 PMCID: PMC6044879 DOI: 10.1021/acsomega.7b00997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/27/2017] [Indexed: 06/08/2023]
Abstract
A relatively high-affinity inhibitor of FIKK kinase from the malaria parasite Plasmodium vivax was identified by in vitro assay of recombinant kinase. The FIKK kinase family is unique to parasitic organisms of the Apicomplexan order and has been shown to be critical in malaria parasites. The recombinant kinase domain was expressed and screened against a small molecule library, revealing a number of tyrosine kinase inhibitors that block FIKK kinase activity. A family of tyrphostins was further investigated, to begin exploring the FIKK kinase pharmacophore. Finally, emodin was identified as a relatively high-affinity FIKK kinase inhibitor, identifying this family of anthraquinones as potential lead compounds for the development of antimalarials targeting the FIKK kinase.
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83
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Lin BC, Harris DR, Kirkman LMD, Perez AM, Qian Y, Schermerhorn JT, Hong MY, Winston DS, Xu L, Lieber AM, Hamilton M, Brandt GS. The anthraquinone emodin inhibits the non-exported FIKK kinase from Plasmodium falciparum. Bioorg Chem 2017; 75:217-223. [PMID: 28987877 DOI: 10.1016/j.bioorg.2017.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 01/08/2023]
Abstract
The FIKK family of kinases is unique to parasites of the Apicomplexan order, which includes all malaria parasites. Plasmodium falciparum, the most virulent form of human malaria, has a family of 19 FIKK kinases, most of which are exported into the host red blood cell during malaria infection. Here, we confirm that FIKK 8 is a non-exported member of the FIKK kinase family. Through expression and purification of the recombinant kinase domain, we establish that emodin is a relatively high-affinity (IC50=2μM) inhibitor of PfFk8. Closely related anthraquinones do not inhibit PfFk8, suggesting that the particular substitution pattern of emodin is critical to the inhibitory pharmacophore. This first report of a P. falciparum FIKK kinase inhibitor lays the groundwork for developing specific inhibitors of the various members of the FIKK kinase family in order to probe their physiological function.
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Affiliation(s)
- Benjamin C Lin
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Darcy R Harris
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Lucy M D Kirkman
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Astrid M Perez
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Yiwen Qian
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Janse T Schermerhorn
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Min Y Hong
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Dennis S Winston
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Lingyin Xu
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Alexander M Lieber
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Matthew Hamilton
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States.
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84
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Chen ESW, Weng JH, Chen YH, Wang SC, Liu XX, Huang WC, Matsui T, Kawano Y, Liao JH, Lim LH, Bessho Y, Huang KF, Wu WJ, Tsai MD. Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation. Biochemistry 2017; 56:5112-5124. [PMID: 28858528 DOI: 10.1021/acs.biochem.7b00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The vast majority of in vitro structural and functional studies of the activation mechanism of protein kinases use the kinase domain alone. Well-demonstrated effects of regulatory domains or allosteric factors are scarce for serine/threonine kinases. Here we use a site-specifically phosphorylated SCD1-FHA1-kinase three-domain construct of the serine/threonine kinase Rad53 to show the effect of phospho-priming, an in vivo regulatory mechanism, on the autophosphorylation intermediate and specificity. Unphosphorylated Rad53 is a flexible monomer in solution but is captured in an asymmetric enzyme:substrate complex in crystal with the two FHA domains separated from each other. Phospho-priming induces formation of a stable dimer via intermolecular pT-FHA binding in solution. Importantly, autophosphorylation of unprimed and phospho-primed Rad53 produced predominantly inactive pS350-Rad53 and active pT354-Rad53, respectively. The latter mechanism was also demonstrated in vivo. Our results show that, while Rad53 can display active conformations under various conditions, simulation of in vivo regulatory conditions confers functionally relevant autophosphorylation.
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Affiliation(s)
- Eric Sheng-Wen Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
| | - Yu-Hou Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Shun-Chang Wang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Xiao-Xia Liu
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, California 94025, United States
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Liang-Hin Lim
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
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85
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Nguyen HA, El Khoury T, Guiral S, Laaberki MH, Candusso MP, Galisson F, Foucher AE, Kesraoui S, Ballut L, Vallet S, Orelle C, Zucchini L, Martin J, Page A, Attieh J, Aghajari N, Grangeasse C, Jault JM. Expanding the Kinome World: A New Protein Kinase Family Widely Conserved in Bacteria. J Mol Biol 2017; 429:3056-3074. [PMID: 28890133 DOI: 10.1016/j.jmb.2017.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/20/2017] [Accepted: 08/21/2017] [Indexed: 12/31/2022]
Abstract
Fine tuning of signaling pathways is essential for cells to cope with sudden environmental variations. This delicate balance is maintained in particular by protein kinases that control the activity of target proteins by reversible phosphorylation. In addition to homologous eukaryotic enzymes, bacteria have evolved some specific Ser/Thr/Tyr protein kinases without any structural resemblance to their eukaryotic counterparts. Here, we show that a previously identified family of ATPases, broadly conserved among bacteria, is in fact a new family of protein kinases with a Ser/Thr/Tyr kinase activity. A prototypic member of this family, YdiB from Bacillus subtilis, is able to autophosphorylate and to phosphorylate a surrogate substrate, the myelin basic protein. Two crystal structures of YdiB were solved (1.8 and 2.0Å) that display a unique ATP-binding fold unrelated to known protein kinases, although a conserved HxD motif is reminiscent of that found in Hanks-type protein kinases. The effect of mutations of conserved residues further highlights the unique nature of this new protein kinase family that we name ubiquitous bacterial kinase. We investigated the cellular role of YdiB and showed that a ∆ydiB mutant was more sensitive to paraquat treatment than the wild type, with ~13% of cells with an aberrant morphology. In addition, YdiE, which is known to participate with both YdiC and YdiB in an essential chemical modification of some specific tRNAs, is phosphorylated in vitro by YdiB. These results expand the boundaries of the bacterial kinome and support the involvement of YdiB in protein translation and resistance to oxidative stress in B. subtilis.
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Affiliation(s)
- Hien-Anh Nguyen
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Takla El Khoury
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France; University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France; Department of Biology, Faculty of Sciences, University of Balamand, Lebanon
| | - Sébastien Guiral
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Maria-Halima Laaberki
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Marie-Pierre Candusso
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Frédéric Galisson
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Anne-Emmanuelle Foucher
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Salsabil Kesraoui
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Lionel Ballut
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Sylvain Vallet
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Laure Zucchini
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Juliette Martin
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France
| | - Jihad Attieh
- Department of Biology, Faculty of Sciences, University of Balamand, Lebanon
| | - Nushin Aghajari
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Christophe Grangeasse
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France.
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86
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Weinberg F, Reischmann N, Fauth L, Taromi S, Mastroianni J, Köhler M, Halbach S, Becker AC, Deng N, Schmitz T, Uhl FM, Herbener N, Riedel B, Beier F, Swarbrick A, Lassmann S, Dengjel J, Zeiser R, Brummer T. The Atypical Kinase RIOK1 Promotes Tumor Growth and Invasive Behavior. EBioMedicine 2017; 20:79-97. [PMID: 28499923 PMCID: PMC5478185 DOI: 10.1016/j.ebiom.2017.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 12/27/2022] Open
Abstract
Despite being overexpressed in different tumor entities, RIO kinases are hardly characterized in mammalian cells. We investigated the role of these atypical kinases in different cancer cells. Using isogenic colon-, breast- and lung cancer cell lines, we demonstrate that knockdown of RIOK1, but not of RIOK2 or RIOK3, strongly impairs proliferation and invasiveness in conventional and 3D culture systems. Interestingly, these effects were mainly observed in RAS mutant cancer cells. In contrast, growth of RAS wildtype Caco-2 and Bcr-Abl-driven K562 cells is not affected by RIOK1 knockdown, suggesting a specific requirement for RIOK1 in the context of oncogenic RAS signaling. Furthermore, we show that RIOK1 activates NF-κB signaling and promotes cell cycle progression. Using proteomics, we identified the pro-invasive proteins Metadherin and Stathmin1 to be regulated by RIOK1. Additionally, we demonstrate that RIOK1 promotes lung colonization in vivo and that RIOK1 is overexpressed in different subtypes of human lung- and breast cancer. Altogether, our data suggest RIOK1 as a potential therapeutic target, especially in RAS-driven cancers.
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Affiliation(s)
- Florian Weinberg
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany
| | - Nadine Reischmann
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Lisa Fauth
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Sanaz Taromi
- Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Justin Mastroianni
- Faculty of Biology, ALU, Freiburg, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Martin Köhler
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Andrea C Becker
- Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany; Department of Dermatology, University Medical Center - ALU, Freiburg, Germany
| | - Niantao Deng
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Tatjana Schmitz
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany
| | - Franziska Maria Uhl
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Nicola Herbener
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Bianca Riedel
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Fabian Beier
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Alexander Swarbrick
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Silke Lassmann
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany; German Cancer Consortium (DKTK, Freiburg) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörn Dengjel
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany; Department of Dermatology, University Medical Center - ALU, Freiburg, Germany; Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Robert Zeiser
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; German Cancer Consortium (DKTK, Freiburg) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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87
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Pellegrini E, Signor L, Singh S, Boeri Erba E, Cusack S. Structures of the inactive and active states of RIP2 kinase inform on the mechanism of activation. PLoS One 2017; 12:e0177161. [PMID: 28545134 PMCID: PMC5436651 DOI: 10.1371/journal.pone.0177161] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
Innate immune receptors NOD1 and NOD2 are activated by bacterial peptidoglycans leading to recruitment of adaptor kinase RIP2, which, upon phosphorylation and ubiquitination, becomes a scaffold for downstream effectors. The kinase domain (RIP2K) is a pharmaceutical target for inflammatory diseases caused by aberrant NOD2-RIP2 signalling. Although structures of active RIP2K in complex with inhibitors have been reported, the mechanism of RIP2K activation remains to be elucidated. Here we analyse RIP2K activation by combining crystal structures of the active and inactive states with mass spectrometric characterization of their phosphorylation profiles. The active state has Helix αC inwardly displaced and the phosphorylated Activation Segment (AS) disordered, whilst in the inactive state Helix αC is outwardly displaced and packed against the helical, non-phosphorylated AS. Biophysical measurements show that the active state is a stable dimer whilst the inactive kinase is in a monomer-dimer equilibrium, consistent with the observed structural differences at the dimer interface. We conclude that RIP2 kinase auto-phosphorylation is intimately coupled to dimerization, similar to the case of BRAF. Our results will help drug design efforts targeting RIP2 as a potential treatment for NOD2-RIP2 related inflammatory diseases.
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Affiliation(s)
| | - Luca Signor
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Saurabh Singh
- European Molecular Biology Laboratory, Grenoble, France
| | - Elisabetta Boeri Erba
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France
- * E-mail:
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88
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Mechanisms Governing Precise Protein Biotinylation. Trends Biochem Sci 2017; 42:383-394. [DOI: 10.1016/j.tibs.2017.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/25/2017] [Accepted: 02/03/2017] [Indexed: 12/26/2022]
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89
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Benhamman R, Bai F, Drory SB, Loubert-Hudon A, Ellis B, Matton DP. The Arabidopsis Mitogen-Activated Protein Kinase Kinase Kinase 20 (MKKK20) Acts Upstream of MKK3 and MPK18 in Two Separate Signaling Pathways Involved in Root Microtubule Functions. FRONTIERS IN PLANT SCIENCE 2017; 8:1352. [PMID: 28848569 PMCID: PMC5550695 DOI: 10.3389/fpls.2017.01352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/19/2017] [Indexed: 05/04/2023]
Abstract
Mitogen-activated protein kinase (MAPK) signaling networks represent important means of signal transduction in plants and other eukaryotes, controlling intracellular signaling by linking perception of environmental or developmental cues to downstream targets. In the Arabidopsis MEKK subfamily, the MKKK19, 20, and 21 form a highly supported clade with the Solanaceous Fertilization-Related Kinases. In Arabidopsis, little is known about this group, except for MKKK20, which is involved in osmotic stress. Using a directed MKKK-MKK yeast two-hybrid (Y2H) screen, MKKK20 was found to interact only with MKK3, while a MKKK20 large-scale Y2H screen retrieved MPK18 as a direct interactant. In vitro phosphorylation assays showed that MKKK20 phosphorylates both MKK3 and MPK18. However, when all three kinases are combined, no synergistic effect is observed on MPK18 phosphorylation, suggesting a direct access to MPK18, consistent with the absence of interaction between MKK3 and MPK18 in protein-protein interaction assays. Since mpk18 mutant plants were previously shown to be defective in microtubule-related functions, phenotypes of mkkk20 single and mkkk20/mpk18 double mutants were investigated to determine if MKKK20 acts upstream of MPK18. This was the case, as mkkk20 root length was shorter than WT in media containing microtubule-disrupting drugs as previously observed for mpk18 plants. Surprisingly, mkk3 plants were also similarly affected, suggesting the presence of two non-complementary pathways involved in Arabidopsis cortical microtubule function, the first including MKKK20, MKK3 and an unknown MPK; the second, a non-canonical MAPK cascade made of MKKK20 and MPK18 that bypasses the need for an MKK intermediate.
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Affiliation(s)
- Rachid Benhamman
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, MontréalQC, Canada
| | - Fangwen Bai
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, MontréalQC, Canada
| | - Samuel B. Drory
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, MontréalQC, Canada
| | - Audrey Loubert-Hudon
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, MontréalQC, Canada
| | - Brian Ellis
- Michael Smith Laboratories, University of British Columbia, VancouverBC, Canada
| | - Daniel P. Matton
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, MontréalQC, Canada
- *Correspondence: Daniel P. Matton,
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90
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Grandellis C, Fantino E, Muñiz García MN, Bialer MG, Santin F, Capiati DA, Ulloa RM. StCDPK3 Phosphorylates In Vitro Two Transcription Factors Involved in GA and ABA Signaling in Potato: StRSG1 and StABF1. PLoS One 2016; 11:e0167389. [PMID: 27907086 PMCID: PMC5131985 DOI: 10.1371/journal.pone.0167389] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022] Open
Abstract
Calcium-dependent protein kinases, CDPKs, decode calcium (Ca2+) transients and initiate downstream responses in plants. In order to understand how CDPKs affect plant physiology, their specific target proteins must be identified. In tobacco, the bZIP transcription factor Repression of Shoot Growth (NtRSG) that modulates gibberellin (GA) content is a specific target of NtCDPK1. StCDPK3 from potato is homologous (88% identical) to NtCDPK1 even in its N-terminal variable domain. In this work, we observe that NtRSG is also phosphorylated by StCDPK3. The potato RSG family of transcription factors is composed of three members that share similar features. The closest homologue to NtRSG, which was named StRSG1, was amplified and sequenced. qRT-PCR data indicate that StRSG1 is mainly expressed in petioles, stems, lateral buds, and roots. In addition, GA treatment affected StRSG1 expression. StCDPK3 transcripts were detected in leaves, petioles, stolons, roots, and dormant tubers, and transcript levels were modified in response to GA. The recombinant StRSG1-GST protein was produced and tested as a substrate for StCDPK3 and StCDPK1. 6xHisStCDPK3 was able to phosphorylate the potato StRSG1 in a Ca2+-dependent way, while 6xHisStCDPK1 could not. StCDPK3 also interacts and phosphorylates the transcription factor StABF1 (ABRE binding factor 1) involved in ABA signaling, as shown by EMSA and phosphorylation assays. StABF1 transcripts were mainly detected in roots, stems, and stolons. Our data suggest that StCDPK3 could be involved in the cross-talk between ABA and GA signaling at the onset of tuber development.
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Affiliation(s)
- Carolina Grandellis
- Institute of Genetic Engineering and Molecular Biology (INGEBI), National Research Council (CONICET) Vuelta de Obligado, 2 piso, Buenos Aires, Argentina
| | - Elisa Fantino
- Institute of Genetic Engineering and Molecular Biology (INGEBI), National Research Council (CONICET) Vuelta de Obligado, 2 piso, Buenos Aires, Argentina
| | - María Noelia Muñiz García
- Institute of Genetic Engineering and Molecular Biology (INGEBI), National Research Council (CONICET) Vuelta de Obligado, 2 piso, Buenos Aires, Argentina
| | - Magalí Graciela Bialer
- Institute of Genetic Engineering and Molecular Biology (INGEBI), National Research Council (CONICET) Vuelta de Obligado, 2 piso, Buenos Aires, Argentina
| | - Franco Santin
- Institute of Genetic Engineering and Molecular Biology (INGEBI), National Research Council (CONICET) Vuelta de Obligado, 2 piso, Buenos Aires, Argentina
| | - Daniela Andrea Capiati
- Institute of Genetic Engineering and Molecular Biology (INGEBI), National Research Council (CONICET) Vuelta de Obligado, 2 piso, Buenos Aires, Argentina
- Biochemistry Department, School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Rita María Ulloa
- Institute of Genetic Engineering and Molecular Biology (INGEBI), National Research Council (CONICET) Vuelta de Obligado, 2 piso, Buenos Aires, Argentina
- Biochemistry Department, School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
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