13 results on '"Texier, Yves"'
Search Results
2. Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice
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Boldt, Karsten, Mans, Dorus A., Won, Jungyeon, van Reeuwijk, Jeroen, Vogt, Andreas, Kinkl, Norbert, Letteboer, Stef J.F., Hicks, Wanda L., Hurd, Ron E., Naggert, Jurgen K., Texier, Yves, den Hollander, Anneke I., Koenekoop, Robert K., Bennett, Jean, Cremers, Frans P.M., Gloeckner, Christian J., Nishina, Patsy M., Roepman, Ronald, and Ueffing, Marius
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Blindness ,Genetic disorders ,Health care industry - Abstract
The mutations that cause Leber congenital amaurosis (LCA) lead to photoreceptor cell death at an early age, causing childhood blindness. To unravel the molecular basis of LCA, we analyzed how [...]
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- 2011
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3. The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis
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Castaings, Loren, Camargo, Antonio, Pocholle, Delphine, Gaudon, Virginie, Texier, Yves, Boutet-Mercey, Stéphanie, Taconnat, Ludivine, Renou, Jean-Pierre, Daniel-Vedele, Françoise, Fernandez, Emilio, Meyer, Christian, and Krapp, Anne
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- 2009
4. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms
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Boldt, Karsten, van Reeuwijk, Jeroen, Dougherty, Gerard, Lamers, Ideke J C, Coene, Karlien L M, Arts, Heleen H, Betts, Matthew J, Beyer, Tina, Bolat, Emine, Gloeckner, Christian Johannes, Haidari, Khatera, Hetterschijt, Lisette, Lu, Qianhao, Iaconis, Daniela, Jenkins, Dagan, Klose, Franziska, Knapp, Barbara, Latour, Brooke, Letteboer, Stef J F, Marcelis, Carlo L, Mitic, Dragana, Morleo, Manuela, Oud, Machteld M, Koutroumpas, Konstantinos, Riemersma, Moniek, Rix, Susan, Terhal, Paulien A, Toedt, Grischa, van Dam, Teunis J P, de Vrieze, Erik, Wissinger, Yasmin, Wu, Ka Man, Apic, Gordana, Beales, Philip L, Nguyen, Thanh-Minh T, Blacque, Oliver E, Gibson, Toby J, Huynen, Martijn A, Katsanis, Nicholas, Kremer, Hannie, Omran, Heymut, van Wijk, Erwin, Wolfrum, Uwe, Kepes, François, Davis, Erica E, Texier, Yves, Franco, Brunella, Giles, Rachel H, Ueffing, Marius, Russell, Robert B, Roepman, Ronald, Group, UK10K Rare Diseases, Al-Turki, Saeed, Anderson, Carl, Antony, Dinu, Barroso, Inês, van Beersum, Sylvia E C, Bentham, Jamie, Bhattacharya, Shoumo, Carss, Keren, Chatterjee, Krishna, Cirak, Sebahattin, Cosgrove, Catherine, Danecek, Petr, Durbin, Richard, Fitzpatrick, David, Floyd, Jamie, Horn, Nicola, Reghan Foley, A., Franklin, Chris, Futema, Marta, Humphries, Steve E, Hurles, Matt, Joyce, Chris, McCarthy, Shane, Mitchison, Hannah M, Muddyman, Dawn, Muntoni, Francesco, Willer, Jason R, O'Rahilly, Stephen, Onoufriadis, Alexandros, Payne, Felicity, Plagnol, Vincent, Raymond, Lucy, Savage, David B, Scambler, Peter, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert, Mans, Dorus A, Serra, Eva, Stalker, Jim, van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Walter, Klaudia, Whittall, Ros, Williamson, Kathy, Boldt, K, van Reeuwijk, J, Lu, Q, Koutroumpas, K, Nguyen, Tmt, Texier, Y, van Beersum, Sec, Horn, N, Willer, Jr, Mans, Da, Dougherty, G, Lamers, Ijc, Coene, Klm, Arts, Hh, Betts, Mj, Beyer, T, Bolat, E, Gloeckner, Cj, Haidari, K, Hetterschijt, L, Iaconis, D, Jenkins, D, Klose, F, Knapp, B, Latour, B, Letteboer, Sjf, Marcelis, Cl, Mitic, D, Morleo, M, Oud, Mm, Riemersma, M, Rix, S, Terhal, Pa, Toedt, G, van Dam, Tjp, de Vrieze, E, Wissinger, Y, Wu, Km, Apic, G, Beales, Pl, Blacque, Oe, Gibson, Tj, Huynen, Ma, Katsanis, N, Kremer, H, Omran, H, van Wijk, E, Wolfrum, U, Kepes, F, Davis, Ee, Franco, B, Giles, Rh, Ueffing, M, Russell, Rb, Roepman, R, Boldt, Karsten, Van Reeuwijk, Jeroen, Lu, Qianhao, Koutroumpas, Konstantino, Nguyen, Thanh Minh T., Texier, Yve, Van Beersum, Sylvia E. C., Horn, Nicola, Willer, Jason R., Mans, Dorus A., Dougherty, Gerard, Lamers, Ideke J. C., Coene, Karlien L. M., Arts, Heleen H., Betts, Matthew J., Beyer, Tina, Bolat, Emine, Gloeckner, Christian Johanne, Haidari, Khatera, Hetterschijt, Lisette, Iaconis, Daniela, Jenkins, Dagan, Klose, Franziska, Knapp, Barbara, Latour, Brooke, Letteboer, Stef J. F., Marcelis, Carlo L., Mitic, Dragana, Morleo, Manuela, Oud, Machteld M., Riemersma, Moniek, Rix, Susan, Terhal, Paulien A., Toedt, Grischa, Van Dam, Teunis J. P., De Vrieze, Erik, Wissinger, Yasmin, Wu, Ka Man, Al Turki, Saeed, Anderson, Carl, Antony, Dinu, Barroso, Inê, Bentham, Jamie, Bhattacharya, Shoumo, Carss, Keren, Chatterjee, Krishna, Cirak, Sebahattin, Cosgrove, Catherine, Danecek, Petr, Durbin, Richard, Fitzpatrick, David, Floyd, Jamie, Foley, A. Reghan, Franklin, Chri, Futema, Marta, Humphries, Steve E., Hurles, Matt, Joyce, Chri, Mccarthy, Shane, Mitchison, Hannah M., Muddyman, Dawn, Muntoni, Francesco, O'Rahilly, Stephen, Onoufriadis, Alexandro, Payne, Felicity, Plagnol, Vincent, Raymond, Lucy, Savage, David B., Scambler, Peter, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert, Serra, Eva, Stalker, Jim, Van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Walter, Klaudia, Whittall, Ro, Williamson, Kathy, Apic, Gordana, Beales, Philip L., Blacque, Oliver E., Gibson, Toby J., Huynen, Martijn A., Katsanis, Nichola, Kremer, Hannie, Omran, Heymut, Van Wijk, Erwin, Wolfrum, Uwe, Kepes, Françoi, Davis, Erica E., Franco, Brunella, Giles, Rachel H., Ueffing, Mariu, Russell, Robert B., and Roepman, Ronald
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Proteomics ,0301 basic medicine ,Systems Analysis ,DNA Mutational Analysis ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,General Physics and Astronomy ,Datasets as Topic ,methods [Chromatography, Affinity] ,Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12] ,Chromatography, Affinity ,Mass Spectrometry ,Protein Interaction Mapping ,therapy [Ciliopathies] ,genetics [Ciliopathies] ,methods [Molecular Targeted Therapy] ,Molecular Targeted Therapy ,Protein Interaction Maps ,Multidisciplinary ,Cilium ,Chemistry (all) ,abnormalities [Spine] ,pathology [Ciliopathies] ,genetics [Muscle Hypotonia] ,therapy [Muscle Hypotonia] ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,metabolism [Proteins] ,isolation & purification [Proteins] ,physiology [Biological Transport] ,3. Good health ,Cell biology ,Vesicular transport protein ,pathology [Dwarfism] ,metabolism [Cilia] ,Muscle Hypotonia ,ddc:500 ,pathology [Muscle Hypotonia] ,pathology [Spine] ,genetics [Dwarfism] ,Rare cancers Radboud Institute for Health Sciences [Radboudumc 9] ,Science ,Dwarfism ,Exocyst ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Physics and Astronomy (all) ,03 medical and health sciences ,Intraflagellar transport ,Ciliogenesis ,Organelle ,Humans ,Cilia ,Biochemistry, Genetics and Molecular Biology (all) ,Proteins ,Biological Transport ,General Chemistry ,therapy [Dwarfism] ,Fibroblasts ,genetics [Proteins] ,Ciliopathies ,Spine ,methods [Protein Interaction Mapping] ,Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11] ,030104 developmental biology ,Proteostasis ,HEK293 Cells ,methods [Proteomics] - Abstract
Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine., Mutations in proteins that localize to primary cilia cause devastating diseases, yet the primary cilium is a poorly understood organelle. Here the authors use interaction proteomics to identify a network of human ciliary proteins that provides new insights into several biological processes and diseases.
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- 2016
5. CiliaCarta: An integrated and validated compendium of ciliary genes.
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van Dam, Teunis J. P., Kennedy, Julie, van der Lee, Robin, de Vrieze, Erik, Wunderlich, Kirsten A., Rix, Suzanne, Dougherty, Gerard W., Lambacher, Nils J., Li, Chunmei, Jensen, Victor L., Leroux, Michel R., Hjeij, Rim, Horn, Nicola, Texier, Yves, Wissinger, Yasmin, van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F., and Franco, Brunella
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CILIA & ciliary motion ,DEVELOPMENTAL biology ,CYTOLOGY ,GENES ,LIFE sciences ,OUTLINES - Abstract
The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at . [ABSTRACT FROM AUTHOR]
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- 2019
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6. Quantitative analysis of ciliary protein networks - Characterization of the intraflagellar transport complex B
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Texier, Yves Stephan, Hrabé de Angelis, Martin (Prof. Dr.), Adamski, Jerzy (Prof. Dr.), and Ueffing, Marius (Prof. Dr.)
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Biowissenschaften, Biologie ,ddc:570 - Abstract
The intraflagellar transport (IFT) complex is essential for ciliary transport. To gain insight into the function of the IFT complex, a method to determine its sub-structure was developed. The components of the IFT complex B (IFT-B) and its sub-structure were determined using different biochemical and mass spectrometric methods. Furthermore, the centrosomal protein 170 was identified to be associated to the IFT-B and shown to be essential for its ciliary localization. Der Intraflagellare Transport (IFT) Komplex ist essentiell für den ziliären Transport. Um mehr über die Funktion des IFT-Komplexes zu erfahren, wurde eine Methode zur Bestimmung seiner Sub-Struktur entwickelt. Unter Verwendung verschiedener biochemischer und massenspektrometrischer Methoden, wurden die Komponenten des IFT-Komplexes B (IFT-B) bestimmt, sowie seine Sub-Struktur analysiert. Des Weiteren wurde die Assoziation des Zentrosomalen Proteins 170 an den IFT-B, sowie die essentielle Funktion für dessen ziliäre Lokalisation gezeigt.
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- 2014
7. NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish.
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Dona, Margo, Bachmann-Gagescu, Ruxandra, Texier, Yves, Toedt, Grischa, Hetterschijt, Lisette, Tonnaer, Edith L., Peters, Theo A., van Beersum, Sylvia E. C., Bergboer, Judith G. M., Horn, Nicola, de Vrieze, Erik, Slijkerman, Ralph W. N., van Reeuwijk, Jeroen, Flik, Gert, Keunen, Jan E., Ueffing, Marius, Gibson, Toby J., Roepman, Ronald, Boldt, Karsten, and Kremer, Hannie
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PHOTORECEPTORS ,CILIOPATHY ,CELLULAR pathology ,ZEBRA danio ,MENDEL'S law ,GENETICS of retinal degeneration - Abstract
Ciliopathies are Mendelian disorders caused by dysfunction of cilia, ubiquitous organelles involved in fluid propulsion (motile cilia) or signal transduction (primary cilia). Retinal dystrophy is a common phenotypic characteristic of ciliopathies since photoreceptor outer segments are specialized primary cilia. These ciliary structures heavily rely on intracellular minus-end directed transport of cargo, mediated at least in part by the cytoplasmic dynein 1 motor complex, for their formation, maintenance and function. Ninein-like protein (NINL) is known to associate with this motor complex and is an important interaction partner of the ciliopathy-associated proteins lebercilin, USH2A and CC2D2A. Here, we scrutinize the function of NINL with combined proteomic and zebrafish in vivo approaches. We identify Double Zinc Ribbon and Ankyrin Repeat domains 1 (DZANK1) as a novel interaction partner of NINL and show that loss of Ninl, Dzank1 or both synergistically leads to dysmorphic photoreceptor outer segments, accumulation of trans-Golgi-derived vesicles and mislocalization of Rhodopsin and Ush2a in zebrafish. In addition, retrograde melanosome transport is severely impaired in zebrafish lacking Ninl or Dzank1. We further demonstrate that NINL and DZANK1 are essential for intracellular dynein-based transport by associating with complementary subunits of the cytoplasmic dynein 1 motor complex, thus shedding light on the structure and stoichiometry of this important motor complex. Altogether, our results support a model in which the NINL-DZANK1 protein module is involved in the proper assembly and folding of the cytoplasmic dynein 1 motor complex in photoreceptor cells, a process essential for outer segment formation and function. [ABSTRACT FROM AUTHOR]
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- 2015
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8. Applying SILAC for the Differential Analysis of Protein Complexes.
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Boldt, Karsten, Gloeckner, Christian J., Texier, Yves, von Zweydorf, Felix, and Ueffing, Marius
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- 2014
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9. Autophosphorylation on S614 inhibits the activity and the transforming potential of BRAF.
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Dernayka, Layal, Rauch, Nora, Jarboui, Mohamed-Ali, Zebisch, Armin, Texier, Yves, Horn, Nicola, Romano, David, Gloeckner, Christian Johannes, Kriegsheim, Alex von, Ueffing, Marius, Kolch, Walter, and Boldt, Karsten
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BRAF genes , *AUTOPHOSPHORYLATION , *GENETIC mutation , *THREONINE , *CELLULAR signal transduction - Abstract
The BRAF proto-oncogene serine/threonine-protein kinase, known as BRAF, belongs to the RAF kinase family. It regulates the MAPK/ERK signalling pathway affecting several cellular processes such as growth, survival, differentiation, and cellular transformation. BRAF is mutated in ~ 8% of all human cancers with the V600E mutation constituting ~ 90% of mutations. Here, we have used quantitative mass spectrometry to map and compare phosphorylation site patterns between BRAF and BRAF V600E. We identified sites that are shared as well as several quantitative differences in phosphorylation abundance. The highest difference is phosphorylation of S614 in the activation loop which is ~ 5fold enhanced in BRAF V600E. Mutation of S614 increases the kinase activity of both BRAF and BRAF V600E and the transforming ability of BRAF V600E. The phosphorylation of S614 is mitogen inducible and the result of autophosphorylation. These data suggest that phosphorylation at this site is inhibitory, and part of the physiological shut-down mechanism of BRAF signalling. [ABSTRACT FROM AUTHOR]
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- 2016
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10. Heptad-Specific Phosphorylation of RNA Polymerase II CTD.
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Schüller, Roland, Forné, Ignasi, Straub, Tobias, Schreieck, Amelie, Texier, Yves, Shah, Nilay, Decker, Tim-Michael, Cramer, Patrick, Imhof, Axel, and Eick, Dirk
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RNA polymerase II , *PHOSPHORYLATION , *C-terminal residues , *GENETIC transcription , *MASS spectrometry - Abstract
Summary The carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) consists of heptad repeats with the consensus motif Y 1 -S 2 -P 3 -T 4 -S 5 -P 6 -S 7 . Dynamic phosphorylation of the CTD coordinates Pol II progression through the transcription cycle. Here, we use genetic and mass spectrometric approaches to directly detect and map phosphosites along the entire CTD. We confirm phosphorylation of CTD residues Y 1 , S 2 , T 4 , S 5 , and S 7 in mammalian and yeast cells. Although specific phosphorylation signatures dominate, adjacent CTD repeats can be differently phosphorylated, leading to a high variation of coexisting phosphosites in mono- and di-heptad CTD repeats. Inhibition of CDK9 kinase specifically reduces S 2 phosphorylation levels within the CTD. [ABSTRACT FROM AUTHOR]
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- 2016
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11. Interplay between NIN-LIKE PROTEINs 6 and 7 in nitrate signaling.
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Cheng YH, Durand M, Brehaut V, Hsu FC, Kelemen Z, Texier Y, Krapp A, and Tsay YF
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- Nitrates metabolism, Transcription Factors metabolism, Nitrogen metabolism, Gene Expression Regulation, Plant, Plant Proteins metabolism, Arabidopsis Proteins metabolism, Arabidopsis metabolism, Ammonium Compounds metabolism
- Abstract
NLP7 (NIN-LIKE-PROTEIN 7) is the major transcriptional factor responsible for the primary nitrate response (PNR), but the role of its homolog, NLP6, in nitrogen signaling and the interplay between NLP6 and NLP7 remain to be elucidated. In this study, we show that, like NLP7, nuclear localization of NLP6 via a nuclear retention mechanism is nitrate dependent, but nucleocytosolic shuttling of both NLP6 and NLP7 is independent of each other. Compared with single mutants, the nlp6nlp7 double mutant displays a synergistic growth retardation phenotype in response to nitrate. The transcriptome analysis of the PNR showed that NLP6 and NLP7 govern ∼50% of nitrate-induced genes, with cluster analysis highlighting 2 distinct patterns. In the A1 cluster, NLP7 plays the major role, whereas in the A2 cluster, NLP6 and NLP7 are partially functionally redundant. Interestingly, comparing the growth phenotype and PNR under high- and low-nitrate conditions demonstrated that NLP6 and NLP7 exert a more dominant role in the response to high nitrate. Apart from nitrate signaling, NLP6 and NLP7 also participated in high ammonium conditions. Growth phenotypes and transcriptome data revealed that NLP6 and NLP7 are completely functionally redundant and may act as repressors in response to ammonium. Other NLP family members also participated in the PNR, with NLP2 and NLP7 acting as broader regulators and NLP4, -5, -6, and -8 regulating PNR in a gene-dependent manner. Thus, our findings indicate that multiple modes of interplay exist between NLP6 and NLP7 that differ depending on nitrogen sources and gene clusters., (© American Society of Plant Biologists 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2023
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12. Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry.
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Texier Y, Toedt G, Gorza M, Mans DA, van Reeuwijk J, Horn N, Willer J, Katsanis N, Roepman R, Gibson TJ, Ueffing M, and Boldt K
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- 14-3-3 Proteins chemistry, 14-3-3 Proteins isolation & purification, HEK293 Cells, Humans, Intracellular Signaling Peptides and Proteins, Mass Spectrometry economics, Proteins metabolism, Proteomics, Proto-Oncogene Proteins B-raf chemistry, Proto-Oncogene Proteins B-raf isolation & purification, Sodium Dodecyl Sulfate, Mass Spectrometry methods, Multiprotein Complexes chemistry, Multiprotein Complexes isolation & purification, Protein Subunits metabolism
- Abstract
Analyzing the molecular architecture of native multiprotein complexes via biochemical methods has so far been difficult and error prone. Protein complex isolation by affinity purification can define the protein repertoire of a given complex, yet, it remains difficult to gain knowledge of its substructure or modular composition. Here, we introduce SDS concentration gradient induced decomposition of protein complexes coupled to quantitative mass spectrometry and in silico elution profile distance analysis. By applying this new method to a cellular transport module, the IFT/lebercilin complex, we demonstrate its ability to determine modular composition as well as sensitively detect known and novel complex components. We show that the IFT/lebercilin complex can be separated into at least five submodules, the IFT complex A, the IFT complex B, the 14-3-3 protein complex and the CTLH complex, as well as the dynein light chain complex. Furthermore, we identify the protein TULP3 as a potential new member of the IFT complex A and showed that several proteins, classified as IFT complex B-associated, are integral parts of this complex. To further demonstrate EPASIS general applicability, we analyzed the modular substructure of two additional complexes, that of B-RAF and of 14-3-3-ε. The results show, that EPASIS provides a robust as well as sensitive strategy to dissect the substructure of large multiprotein complexes in a highly time- as well as cost-effective manner.
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- 2014
- Full Text
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13. Applying SILAC for the differential analysis of protein complexes.
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Boldt K, Gloeckner CJ, Texier Y, von Zweydorf F, and Ueffing M
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- Analytic Sample Preparation Methods, Cell Death, HEK293 Cells, Humans, Mass Spectrometry, Proteins isolation & purification, Amino Acids chemistry, Isotope Labeling methods, Proteins chemistry, Proteins metabolism, Proteomics methods
- Abstract
Pull-downs based on tag fusion proteins as well as immunoprecipitations (IP) are widely used methods to analyze protein interactions. Selectivity and specificity of both methods are compromised by nonspecific binding to the capture agent or carrier beads thereby generating false positives. Here, we provide a method combining stable isotope labeling of amino acids in cell culture (SILAC) with affinity purification, coupled to quantitative tandem mass spectrometry. It permits the analysis of protein interactions with high sensitivity, while being able to discriminate contaminants and nonspecific binders. Besides pruning out contaminants, high-resolution MS data combined with quantitative proteomics software allow the comparative analysis of protein interaction patterns of different protein variants, for example mutated versus normal protein variant or of regulatory changes in a given protein complex due to different states of activity.
- Published
- 2014
- Full Text
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