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Makarov D, Kielkowski P. Chemical Proteomics Reveals Protein Tyrosination Extends Beyond the Alpha-Tubulins in Human Cells. Chembiochem 2022; 23:e202200414. [PMID: 36218090 PMCID: PMC10099736 DOI: 10.1002/cbic.202200414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/10/2022] [Indexed: 01/25/2023]
Abstract
Tubulin detyrosination-tyrosination cycle regulates the stability of microtubules. With respect to α-tubulins, the tyrosination level is maintained by a single tubulin-tyrosine ligase (TTL). However, the precise dynamics and tubulin isoforms which undergo (de)tyrosination in neurons are unknown. Here, we exploit the substrate promiscuity of the TTL to introduce an O-propargyl-l-tyrosine to neuroblastoma cells and neurons. Mass spectrometry-based chemical proteomics in neuroblastoma cells using the O-propargyl-l-tyrosine probe revealed previously discussed tyrosination of TUBA4A, MAPRE1, and other non-tubulin proteins. This finding was further corroborated in differentiating neurons. Together we present the method for tubulin tyrosination profiling in living cells. Our results show that detyrosination-tyrosination is not restricted to α-tubulins with coded C-terminal tyrosine and is thus involved in fine-tuning of the tubulin and non-tubulin proteins during neuronal differentiation.
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Affiliation(s)
- Dmytro Makarov
- LMU München, Department of Chemistry, Institute for Chemical Epigenetics - Munich (ICEM), Würmtalstrasse 201, 81375, Munich, Germany
| | - Pavel Kielkowski
- LMU München, Department of Chemistry, Institute for Chemical Epigenetics - Munich (ICEM), Würmtalstrasse 201, 81375, Munich, Germany
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Aillaud C, Bosc C, Peris L, Bosson A, Heemeryck P, Van Dijk J, Le Friec J, Boulan B, Vossier F, Sanman LE, Syed S, Amara N, Couté Y, Lafanechère L, Denarier E, Delphin C, Pelletier L, Humbert S, Bogyo M, Andrieux A, Rogowski K, Moutin MJ. Vasohibins/SVBP are tubulin carboxypeptidases (TCPs) that regulate neuron differentiation. Science 2017; 358:1448-1453. [PMID: 29146868 DOI: 10.1126/science.aao4165] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/03/2017] [Indexed: 12/28/2022]
Abstract
Reversible detyrosination of α-tubulin is crucial to microtubule dynamics and functions, and defects have been implicated in cancer, brain disorganization, and cardiomyopathies. The identity of the tubulin tyrosine carboxypeptidase (TCP) responsible for detyrosination has remained unclear. We used chemical proteomics with a potent irreversible inhibitor to show that the major brain TCP is a complex of vasohibin-1 (VASH1) with the small vasohibin binding protein (SVBP). VASH1 and its homolog VASH2, when complexed with SVBP, exhibited robust and specific Tyr/Phe carboxypeptidase activity on microtubules. Knockdown of vasohibins or SVBP and/or inhibitor addition in cultured neurons reduced detyrosinated α-tubulin levels and caused severe differentiation defects. Furthermore, knockdown of vasohibins disrupted neuronal migration in developing mouse neocortex. Thus, vasohibin/SVBP complexes represent long-sought TCP enzymes.
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Affiliation(s)
- Chrystelle Aillaud
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Christophe Bosc
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Leticia Peris
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Anouk Bosson
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Pierre Heemeryck
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Juliette Van Dijk
- Institut de Génétique Humaine (IGH), Université Montpellier, CNRS UMR9002, 34000 Montpellier, France.,Centre de Recherche en Biochimie Macromoléculaire (CRBM), Université Montpellier, CNRS UMR5237, 34000 Montpellier, France
| | - Julien Le Friec
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Benoit Boulan
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Frédérique Vossier
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Laura E Sanman
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Salahuddin Syed
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neri Amara
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yohann Couté
- Institut de Biosciences et Biotechnologies de Grenoble (BIG)-Laboratoire Biologie à Grande Échelle, Université Grenoble Alpes, CEA, INSERM, F-38000 Grenoble, France
| | - Laurence Lafanechère
- Team Regulation and Pharmacology of the Cytoskeleton, Institute for Advanced Biosciences, INSERM U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Eric Denarier
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France.,BIG-Physiopathologie du Cytosquelette, CEA, F-38000 Grenoble, France
| | - Christian Delphin
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Laurent Pelletier
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Sandrine Humbert
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Annie Andrieux
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France. .,Inserm, U1216, F-38000 Grenoble, France.,BIG-Physiopathologie du Cytosquelette, CEA, F-38000 Grenoble, France
| | - Krzysztof Rogowski
- Institut de Génétique Humaine (IGH), Université Montpellier, CNRS UMR9002, 34000 Montpellier, France
| | - Marie-Jo Moutin
- Grenoble Institut des Neurosciences (GIN), Université Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
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Li MD, Burns TC, Morgan AA, Khatri P. Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases. Acta Neuropathol Commun 2014; 2:93. [PMID: 25187168 PMCID: PMC4167139 DOI: 10.1186/s40478-014-0093-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 01/11/2023] Open
Abstract
Introduction Neurodegenerative diseases share common pathologic features including neuroinflammation, mitochondrial dysfunction and protein aggregation, suggesting common underlying mechanisms of neurodegeneration. We undertook a meta-analysis of public gene expression data for neurodegenerative diseases to identify a common transcriptional signature of neurodegeneration. Results Using 1,270 post-mortem central nervous system tissue samples from 13 patient cohorts covering four neurodegenerative diseases, we identified 243 differentially expressed genes, which were similarly dysregulated in 15 additional patient cohorts of 205 samples including seven neurodegenerative diseases. This gene signature correlated with histologic disease severity. Metallothioneins featured prominently among differentially expressed genes, and functional pathway analysis identified specific convergent themes of dysregulation. MetaCore network analyses revealed various novel candidate hub genes (e.g. STAU2). Genes associated with M1-polarized macrophages and reactive astrocytes were strongly enriched in the meta-analysis data. Evaluation of genes enriched in neurons revealed 70 down-regulated genes, over half not previously associated with neurodegeneration. Comparison with aging brain data (3 patient cohorts, 221 samples) revealed 53 of these to be unique to neurodegenerative disease, many of which are strong candidates to be important in neuropathogenesis (e.g. NDN, NAP1L2). ENCODE ChIP-seq analysis predicted common upstream transcriptional regulators not associated with normal aging (REST, RBBP5, SIN3A, SP2, YY1, ZNF143, IKZF1). Finally, we removed genes common to neurodegeneration from disease-specific gene signatures, revealing uniquely robust immune response and JAK-STAT signaling in amyotrophic lateral sclerosis. Conclusions Our results implicate pervasive bioenergetic deficits, M1-type microglial activation and gliosis as unifying themes of neurodegeneration, and identify numerous novel genes associated with neurodegenerative processes. Electronic supplementary material The online version of this article (doi:10.1186/s40478-014-0093-y) contains supplementary material, which is available to authorized users.
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Rovini A, Gauthier G, Bergès R, Kruczynski A, Braguer D, Honoré S. Anti-migratory effect of vinflunine in endothelial and glioblastoma cells is associated with changes in EB1 C-terminal detyrosinated/tyrosinated status. PLoS One 2013; 8:e65694. [PMID: 23750272 PMCID: PMC3672205 DOI: 10.1371/journal.pone.0065694] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 05/01/2013] [Indexed: 12/26/2022] Open
Abstract
We previously showed that vinflunine, a microtubule-targeting drug of the Vinca-alkaloid family exerted its anti-angiogenic/anti-migratory activities through an increase in microtubule dynamics and an inhibition of microtubule targeting to adhesion sites. Such effect was associated with a reduction of EB1 comet length at microtubule (+) ends. In this work we first showed that the pro-angiogenic vascular endothelial growth factor VEGF suppressed microtubule dynamics in living Human Umbilical Vein Endothelial Cells (HUVECs), increased EB1 comet length by 40%, and induced EB1 to bind all along the microtubules, without modifying its expression level. Such microtubule (+) end stabilization occurred close to the plasma membrane in the vicinity of focal adhesion as shown by TIRF microscopy experiments. Vinflunine completely abolished the effect of VEGF on EB1 comets. Interestingly, we found a correlation between the reduction of EB1 comet length by vinflunine and the inhibition of cell migration. By using 2D gel electrophoresis we demonstrated for the first time that EB1 underwent several post-translational modifications in endothelial and tumor cells. Particularly, the C-terminal EEY sequence was poorly detectable in control and VEGF-treated HUVECs suggesting the existence of a non-tyrosinated form of EB1. By using specific antibodies that specifically recognized and discriminated the native tyrosinated form of EB1 and a putative C-terminal detyrosinated form, we showed that a detyrosinated form of EB1 exists in HUVECs and tumor cells. Interestingly, vinflunine decreased the level of the detyrosinated form and increased the native tyrosinated form of EB1. Using 3-L-Nitrotyrosine incorporation experiments, we concluded that the EB1 C-terminal modifications result from a detyrosination/retyrosination cycle as described for tubulin. Altogether, our results show that vinflunine inhibits endothelial cell migration through an alteration of EB1 comet length and EB1 detyrosination/retyrosination cycle.
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Affiliation(s)
- Amandine Rovini
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale UMR_S 911, Marseille, France
| | - Géraldine Gauthier
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale UMR_S 911, Marseille, France
- APHM, Hôpital Timone, Marseille, France
| | - Raphaël Bergès
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale UMR_S 911, Marseille, France
| | - Anna Kruczynski
- Centre de Recherche d'Oncologie Expérimentale, Institut de Recherche Pierre Fabre, Toulouse, France
| | - Diane Braguer
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale UMR_S 911, Marseille, France
- APHM, Hôpital Timone, Marseille, France
| | - Stéphane Honoré
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale UMR_S 911, Marseille, France
- APHM, Hôpital Timone, Marseille, France
- * E-mail:
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