21 results on '"van Dam, Teunis J. P."'
Search Results
2. Evolution of modular intraflagellar transport from a coatomer-like progenitor
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van Dam, Teunis J. P., Townsend, Matthew J., Turk, Martin, Schlessinger, Avner, Sali, Andrej, Field, Mark C., and Huynen, Martijn A.
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- 2013
3. OFIP/KIAA0753 forms a complex with OFD1 and FOR20 at pericentriolar satellites and centrosomes and is mutated in one individual with oral-facial-digital syndrome
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Chevrier, Véronique, Bruel, Ange-Line, Van Dam, Teunis J. P., Franco, Brunella, Lo Scalzo, Melissa, Lembo, Frédérique, Audebert, Stéphane, Baudelet, Emilie, Isnardon, Daniel, Bole, Angélique, Borg, Jean-Paul, Kuentz, Paul, Thevenon, Julien, Burglen, Lydie, Faivre, Laurence, Rivière, Jean-Baptiste, Huynen, Martijn A., Birnbaum, Daniel, Rosnet, Olivier, and Thauvin-Robinet, Christel
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- 2016
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4. Evolution of the TOR Pathway
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van Dam, Teunis J. P., Zwartkruis, Fried J. T., Bos, Johannes L., and Snel, Berend
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- 2011
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5. Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
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Deutekom, Eva S, Snel, Berend, van Dam, Teunis J P, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Theoretical Biology and Bioinformatics, and Sub Bioinformatics
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Genome evolution ,AcademicSubjects/SCI01060 ,Proteome ,Inference ,Computational biology ,Biology ,Genome ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,eukaryotes ,Similarity (network science) ,co-occurrence ,Databases, Protein ,Gene ,Molecular Biology ,Phylogeny ,030304 developmental biology ,Method Review ,0303 health sciences ,Internet ,Phylogenetic tree ,Co-occurrence ,Eukaryota ,Proteins ,Reproducibility of Results ,gene loss ,Genomics ,orthology inference ,Benchmarking ,Phylogenetic Pattern ,030217 neurology & neurosurgery ,Software ,Information Systems ,orthologous groups - Abstract
Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins. This manual analysis limits the possibility of including more protein-complex components, repeating the analyses for updated genome sets or expanding the analyses to larger scales. Automated orthology inference should allow such large-scale analyses, but substantial differences between orthologous groups generated by different approaches are observed. We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regard to genome evolution in eukaryotes. Specifically, we investigate phylogenetic profile similarity (co-occurrence of complexes), the last eukaryotic common ancestor’s gene content, pervasiveness of gene loss and the overlap with manually determined orthologous groups. Moreover, we compare the inferred orthologies to each other. We find that most orthology methods reconstruct a large last eukaryotic common ancestor, with substantial gene loss, and can predict interacting proteins reasonably well when applying phylogenetic co-occurrence. At the same time, derived orthologous groups show imperfect overlap with manually curated orthologous groups. There is no strong indication of which orthology method performs better than another on individual or all of these aspects. Counterintuitively, despite the orthology methods behaving similarly regarding large-scale evaluation, the obtained orthologous groups differ vastly from one another. Availability and implementation The data and code underlying this article are available in github and/or upon reasonable request to the corresponding author: https://github.com/ESDeutekom/ComparingOrthologies.
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- 2020
6. Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences
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Deutekom, Eva S., primary, Vosseberg, Julian, additional, van Dam, Teunis J. P., additional, and Snel, Berend, additional
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- 2019
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7. CiliaCarta: An integrated and validated compendium of ciliary genes
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van Dam, Teunis J. P., primary, Kennedy, Julie, additional, van der Lee, Robin, additional, de Vrieze, Erik, additional, Wunderlich, Kirsten A., additional, Rix, Suzanne, additional, Dougherty, Gerard W., additional, Lambacher, Nils J., additional, Li, Chunmei, additional, Jensen, Victor L., additional, Leroux, Michel R., additional, Hjeij, Rim, additional, Horn, Nicola, additional, Texier, Yves, additional, Wissinger, Yasmin, additional, van Reeuwijk, Jeroen, additional, Wheway, Gabrielle, additional, Knapp, Barbara, additional, Scheel, Jan F., additional, Franco, Brunella, additional, Mans, Dorus A., additional, van Wijk, Erwin, additional, Képès, François, additional, Slaats, Gisela G., additional, Toedt, Grischa, additional, Kremer, Hannie, additional, Omran, Heymut, additional, Szymanska, Katarzyna, additional, Koutroumpas, Konstantinos, additional, Ueffing, Marius, additional, Nguyen, Thanh-Minh T., additional, Letteboer, Stef J. F., additional, Oud, Machteld M., additional, van Beersum, Sylvia E. C., additional, Schmidts, Miriam, additional, Beales, Philip L., additional, Lu, Qianhao, additional, Giles, Rachel H., additional, Szklarczyk, Radek, additional, Russell, Robert B., additional, Gibson, Toby J., additional, Johnson, Colin A., additional, Blacque, Oliver E., additional, Wolfrum, Uwe, additional, Boldt, Karsten, additional, Roepman, Ronald, additional, Hernandez-Hernandez, Victor, additional, and Huynen, Martijn A., additional
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- 2019
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8. Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts
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van der Lee, Robin, Wiel, Laurens, van Dam, Teunis J P, Huynen, Martijn A, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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0301 basic medicine ,Primates ,Genome evolution ,Evolution ,Gene Conversion ,Genomics ,Computational biology ,Major histocompatibility complex ,Genome ,Evolution, Molecular ,03 medical and health sciences ,Viral Proteins ,Genetic ,Receptors ,Genetics ,Journal Article ,Animals ,Humans ,Selection, Genetic ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,Gene ,Selection ,Selection (genetic algorithm) ,biology ,Immunity ,Molecular ,Genetic Variation ,Proteins ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,Acquired immune system ,Phenotype ,Virus ,030104 developmental biology ,Virus Diseases ,Multigene Family ,Host-Pathogen Interactions ,biology.protein ,Receptors, Virus ,Artifacts ,Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19] - Abstract
Hotspots of rapid genome evolution hold clues about human adaptation. We present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection in 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our new procedure is stringent and reveals substantial artefacts (20% of initial predictions) that have inflated previous estimates. The final 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immunity, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokines, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction and chromosome segregation (e.g. centromere-associated CENPO, CENPT), apolipoproteins, smell/taste receptors and mitochondrial proteins. Focusing on the virus–host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, tetherin) and predict 70 novel cases through integration with virus–human interaction data. Protein structure analysis further identifies positive selection in the interaction interfaces between viruses and their cellular receptors (CD4-HIV; CD46-measles, adenoviruses; CD55-picornaviruses). Finally, primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positive selection is a rich source for studying the genetics underlying human (antiviral) phenotypes. Procedures and data are available at https://github.com/robinvanderlee/positive-selection.
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- 2017
9. 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
10. Ciliary force-responsive striated fibers promote basal body connections and cortical interactions.
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Soh, Adam W. J., van Dam, Teunis J. P., Stemm-Wolf, Alexander J., Pham, Andrew T., Morgan, Garry P., O’Toole, Eileen T., and Pearson, Chad G.
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IMMOBILIZED proteins , *CILIA & ciliary motion , *FLUID flow , *FIBERS , *TETRAHYMENA , *ANCHORAGE - Abstract
Multi-ciliary arrays promote fluid flow and cellular motility using the polarized and coordinated beating of hundreds of motile cilia. Tetrahymena basal bodies (BBs) nucleate and position cilia, whereby BB-associated striated fibers (SFs) promote BB anchorage and orientation into ciliary rows. Mutants that shorten SFs cause disoriented BBs. In contrast to the cytotaxis model, we show that disoriented BBs with short SFs can regain normal orientation if SF length is restored. In addition, SFs adopt unique lengths by their shrinkage and growth to establish and maintain BB connections and cortical interactions in a ciliary force-dependent mechanism. Tetrahymena SFs comprise at least eight uniquely localizing proteins belonging to the SFassemblin family. Loss of different proteins that localize to the SF base disrupts either SF steady-state length or ciliary forceinduced SF elongation. Thus, the dynamic regulation of SFs promotes BB connections and cortical interactions to organize ciliary arrays. [ABSTRACT FROM AUTHOR]
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- 2020
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11. Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites
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Meerstein-Kessel, Lisette, primary, van der Lee, Robin, additional, Stone, Will, additional, Lanke, Kjerstin, additional, Baker, David A., additional, Alano, Pietro, additional, Silvestrini, Francesco, additional, Janse, Chris J., additional, Khan, Shahid M., additional, van de Vegte-Bolmer, Marga, additional, Graumans, Wouter, additional, Siebelink-Stoter, Rianne, additional, Kooij, Taco W. A., additional, Marti, Matthias, additional, Drakeley, Chris, additional, Campo, Joseph J., additional, van Dam, Teunis J. P., additional, Sauerwein, Robert, additional, Bousema, Teun, additional, and Huynen, Martijn A., additional
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- 2018
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12. The Gene Ontology of eukaryotic cilia and flagella
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Roncaglia, Paola, primary, van Dam, Teunis J. P., additional, Christie, Karen R., additional, Nacheva, Lora, additional, Toedt, Grischa, additional, Huynen, Martijn A., additional, Huntley, Rachael P., additional, Gibson, Toby J., additional, and Lomax, Jane, additional
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- 2017
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13. KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome
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Sanders, Anna A. W. M., de Vrieze, Erik, Alazami, Anas M., Alzahrani, Fatema, Malarkey, Erik B., Sorusch, Nasrin, Tebbe, Lars, Kuhns, Stefanie, van Dam, Teunis J. P., Alhashem, Amal, Tabarki, Brahim, Lu, Qianhao, Lambacher, Nils J., Kennedy, Julie E., Bowie, Rachel V., Hetterschijt, Lisette, van Beersum, Sylvia, van Reeuwijk, Jeroen, Boldt, Karsten, Kremer, Hannie, Kesterson, Robert A., Monies, Dorota, Abouelhoda, Mohamed, Roepman, Ronald, Huynen, Martijn H., Ueffing, Marius, Russell, Rob B., Wolfrum, Uwe, Yoder, Bradley K., van Wijk, Erwin, Alkuraya, Fowzan S., and Blacque, Oliver E.
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Adult ,Male ,K04F10.2 ,KIAA0556 ,Microtubule ,Microtubules ,Retina ,Mice ,Joubert syndrome ,Cerebellum ,Animals ,Humans ,Abnormalities, Multiple ,Exome ,Cilia ,Eye Abnormalities ,Sensory disorders Radboud Institute for Molecular Life Sciences [Radboudumc 12] ,Caenorhabditis elegans ,Child ,Cells, Cultured ,Adenosine Triphosphatases ,ADP-Ribosylation Factors ,Research ,Brain ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,Kidney Diseases, Cystic ,Basal Bodies ,Pedigree ,Mice, Inbred C57BL ,Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11] ,Basal body ,Child, Preschool ,Mutation ,Female ,Katanin ,Microtubule-Associated Proteins ,Protein Binding - Abstract
Background Joubert syndrome (JBTS) and related disorders are defined by cerebellar malformation (molar tooth sign), together with neurological symptoms of variable expressivity. The ciliary basis of Joubert syndrome related disorders frequently extends the phenotype to tissues such as the eye, kidney, skeleton and craniofacial structures. Results Using autozygome and exome analyses, we identified a null mutation in KIAA0556 in a multiplex consanguineous family with hallmark features of mild Joubert syndrome. Patient-derived fibroblasts displayed reduced ciliogenesis potential and abnormally elongated cilia. Investigation of disease pathophysiology revealed that Kiaa0556-/- null mice possess a Joubert syndrome-associated brain-restricted phenotype. Functional studies in Caenorhabditis elegans nematodes and cultured human cells support a conserved ciliary role for KIAA0556 linked to microtubule regulation. First, nematode KIAA0556 is expressed almost exclusively in ciliated cells, and the worm and human KIAA0556 proteins are enriched at the ciliary base. Second, C. elegans KIAA0056 regulates ciliary A-tubule number and genetically interacts with an ARL13B (JBTS8) orthologue to control cilium integrity. Third, human KIAA0556 binds to microtubules in vitro and appears to stabilise microtubule networks when overexpressed. Finally, human KIAA0556 biochemically interacts with ciliary proteins and p60/p80 katanins. The latter form a microtubule-severing enzyme complex that regulates microtubule dynamics as well as ciliary functions. Conclusions We have identified KIAA0556 as a novel microtubule-associated ciliary base protein mutated in Joubert syndrome. Consistent with the mild patient phenotype, our nematode, mice and human cell data support the notion that KIAA0556 has a relatively subtle and variable cilia-related function, which we propose is related to microtubule regulation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0858-z) contains supplementary material, which is available to authorized users.
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- 2015
14. OFIP/KIAA0753 forms a complex with OFD1 and FOR20 at pericentriolar satellites and centrosomes and is mutated in one individual with oral-facial-digital syndrome
- Author
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Chevrier, Véronique, primary, Bruel, Ange-Line, additional, Van Dam, Teunis J. P., additional, Franco, Brunella, additional, Lo Scalzo, Melissa, additional, Lembo, Frédérique, additional, Audebert, Stéphane, additional, Baudelet, Emilie, additional, Isnardon, Daniel, additional, Bole, Angélique, additional, Borg, Jean-Paul, additional, Kuentz, Paul, additional, Thevenon, Julien, additional, Burglen, Lydie, additional, Faivre, Laurence, additional, Rivière, Jean-Baptiste, additional, Huynen, Martijn A., additional, Birnbaum, Daniel, additional, Rosnet, Olivier, additional, and Thauvin-Robinet, Christel, additional
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- 2015
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15. Protein Complex Evolution Does Not Involve Extensive Network Rewiring
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van Dam, Teunis J. P., primary and Snel, Berend, additional
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- 2008
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16. CiliaCarta: An integrated and validated compendium of ciliary genes
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Gerard W. Dougherty, Victor L. Jensen, Jan Frederik Scheel, Katarzyna Szymanska, Uwe Wolfrum, Radek Szklarczyk, Miriam Schmidts, Julie Kennedy, Erwin van Wijk, Brunella Franco, Toby J. Gibson, Machteld M. Oud, Chunmei Li, Nils J. Lambacher, Erik de Vrieze, Grischa Toedt, Teunis J. P. van Dam, Karsten Boldt, Heymut Omran, Yves Texier, Rachel H. Giles, Ronald Roepman, Kirsten A. Wunderlich, Sylvia E. C. van Beersum, Oliver E. Blacque, Thanh-Minh T. Nguyen, Konstantinos Koutroumpas, Hannie Kremer, Nicola Horn, Martijn A. Huynen, Michel R. Leroux, Gabrielle Wheway, Rim Hjeij, Philip L. Beales, Gisela G. Slaats, Robert B. Russell, Robin van der Lee, François Képès, Yasmin Wissinger, Barbara Knapp, Dorus A. Mans, Suzanne Rix, Marius Ueffing, Colin A. Johnson, Stef J.F. Letteboer, Victor Hernandez-Hernandez, Qianhao Lu, Jeroen van Reeuwijk, Sub Bioinformatics, Theoretical Biology and Bioinformatics, MUMC+: DA KG Lab Centraal Lab (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, 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, Yve, Wissinger, Yasmin, van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F, Franco, Brunella, Mans, Dorus A, van Wijk, Erwin, Képès, Françoi, Slaats, Gisela G, Toedt, Grischa, Kremer, Hannie, Omran, Heymut, Szymanska, Katarzyna, Koutroumpas, Konstantino, Ueffing, Mariu, Nguyen, Thanh-Minh T, Letteboer, Stef J F, Oud, Machteld M, van Beersum, Sylvia E C, Schmidts, Miriam, Beales, Philip L, Lu, Qianhao, Giles, Rachel H, Szklarczyk, Radek, Russell, Robert B, Gibson, Toby J, Johnson, Colin A, Blacque, Oliver E, Wolfrum, Uwe, Boldt, Karsten, Roepman, Ronald, Hernandez-Hernandez, Victor, and Huynen, Martijn A
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Proteomics ,Sensory Receptors ,Nematoda ,Social Sciences ,Ciliopathies ,Biochemistry ,Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12] ,Transcriptome ,0302 clinical medicine ,Animal Cells ,Psychology ,RETINAL PHOTORECEPTOR CELLS ,Exome ,Neurons ,0303 health sciences ,030302 biochemistry & molecular biology ,Eukaryota ,Genomics ,PRIMARY CILIUM ,thecilium ,3. Good health ,Nucleic acids ,Genetic interference ,Osteichthyes ,Medicine ,Epigenetics ,Cellular Structures and Organelles ,Cellular Types ,proteomic databases ,Sensory Receptor Cells ,Science ,education ,Ciliary genes ,LEBER CONGENITAL AMAUROSIS ,03 medical and health sciences ,Genetics ,Cilia ,Caenorhabditis elegans ,IDENTIFICATION ,MUTATIONS ,Embryos ,cilia ,Organisms ,Biology and Life Sciences ,Bayes Theorem ,Molecular Sequence Annotation ,medicine.disease ,Invertebrates ,Fish ,ciliary proteome ,Animal Studies ,Caenorhabditis ,Gene expression ,embryos ,030217 neurology & neurosurgery ,Developmental Biology ,Neuroscience ,Photoreceptors ,Candidate gene ,Embryology ,Oligonucleotides ,Morpholino ,Database and Informatics Methods ,RNA interference ,Bayesian classifier ,TRANSITION ZONE ,Zebrafish ,Antisense Oligonucleotides ,Multidisciplinary ,Spectrometric Identification of Proteins ,Proteomic Databases ,Nucleotides ,Cilium ,Stable Isotope Labeling by Amino Acids in Cell Culture ,photoreceptors ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,Animal Models ,Phenotype ,INTRAFLAGELLAR TRANSPORT ,DIFFERENTIATION ,Experimental Organism Systems ,Caenorhabditis Elegans ,Vertebrates ,Sensory Perception ,Research Article ,Signal Transduction ,EXPRESSION ,Stable isotope labeling by amino acids in cell culture ,Computational biology ,Biology ,Research and Analysis Methods ,SOLUTE-CARRIER-PROTEIN ,Model Organisms ,medicine ,Animals ,data integration ,030304 developmental biology ,Afferent Neurons ,Reproducibility of Results ,Cell Biology ,zebrafish ,biology.organism_classification ,Ciliopathy ,Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11] ,Biological Databases ,Cellular Neuroscience ,RNA ,OSCP1 ,CiliaCarta - 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 http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/. This work was supported by the European Community’s Seventh Framework Programme [241955, 278568 to MU and KB, 602273 to RS]; the Virgo consortium, funded by the Dutch government [FES0908 to TvD, RvdL and MAH]; the Netherlands Genomics Initiative [050-060-452 to TvD, RvdL and MAH]; the Canadian Institutes of Health Research [MOP-142243, MOP-82870 and PJT-156042 to MRL]; Michael Smith Foundation for Health Research to MRL and VLJ; Kidney Research Scientist Core Education and National Training fellowship to VLJ; The Foundation Fighting Blindness [PPA-0717-0719-RAD to UW, RR, and MU]; the Dutch Kidney Foundation “KOUNCIL” consortium [CP11.18 to RHG, PLB and RR]; The Deutsche Forschungsgemeinschaft [Excellence grant CellNetworks to RBR and QL, CRC1140 “Kidney Disease – From Genes to Mechanisms” to MS, collaborative research center grant SFB-1411 KIDGEM to MS]; Metakids Foundation to RS; the National Institute for Health Research to PLB and VH-H. PLB is an NIHR Senior Investigator; Radboudumc Hypatia Tenure Track Fellowship, Radboud Universiteit excellence fellowship, ERC starting grant TREATCilia, grant agreement no. 716344 to MS; and the Netherlands Organization for Scientific Research [NWO Vici-865.12.005 to RR].
- Published
- 2019
17. Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes.
- Author
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Deutekom ES, Snel B, and van Dam TJP
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- Databases, Protein, Eukaryota classification, Evolution, Molecular, Genome genetics, Genomics methods, Internet, Proteins metabolism, Proteome metabolism, Reproducibility of Results, Software, Benchmarking methods, Eukaryota genetics, Phylogeny, Proteins genetics, Proteome genetics
- Abstract
Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins. This manual analysis limits the possibility of including more protein-complex components, repeating the analyses for updated genome sets or expanding the analyses to larger scales. Automated orthology inference should allow such large-scale analyses, but substantial differences between orthologous groups generated by different approaches are observed. We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regard to genome evolution in eukaryotes. Specifically, we investigate phylogenetic profile similarity (co-occurrence of complexes), the last eukaryotic common ancestor's gene content, pervasiveness of gene loss and the overlap with manually determined orthologous groups. Moreover, we compare the inferred orthologies to each other. We find that most orthology methods reconstruct a large last eukaryotic common ancestor, with substantial gene loss, and can predict interacting proteins reasonably well when applying phylogenetic co-occurrence. At the same time, derived orthologous groups show imperfect overlap with manually curated orthologous groups. There is no strong indication of which orthology method performs better than another on individual or all of these aspects. Counterintuitively, despite the orthology methods behaving similarly regarding large-scale evaluation, the obtained orthologous groups differ vastly from one another. Availability and implementation The data and code underlying this article are available in github and/or upon reasonable request to the corresponding author: https://github.com/ESDeutekom/ComparingOrthologies., (© The Author(s) 2020. Published by Oxford University Press.)
- Published
- 2021
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18. TMEM70 functions in the assembly of complexes I and V.
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Sánchez-Caballero L, Elurbe DM, Baertling F, Guerrero-Castillo S, van den Brand M, van Strien J, van Dam TJP, Rodenburg R, Brandt U, Huynen MA, and Nijtmans LGJ
- Subjects
- Biotinylation, Evolution, Molecular, Gene Knockout Techniques, HEK293 Cells, Humans, Membrane Proteins deficiency, Membrane Proteins genetics, Mitochondrial Proteins deficiency, Mitochondrial Proteins genetics, Oxidative Phosphorylation, Protein Binding, Electron Transport Complex I metabolism, Membrane Proteins metabolism, Mitochondrial Proteins metabolism, Mitochondrial Proton-Translocating ATPases metabolism
- Abstract
Protein complexes from the oxidative phosphorylation (OXPHOS) system are assembled with the help of proteins called assembly factors. We here delineate the function of the inner mitochondrial membrane protein TMEM70, in which mutations have been linked to OXPHOS deficiencies, using a combination of BioID, complexome profiling and coevolution analyses. TMEM70 interacts with complex I and V and for both complexes the loss of TMEM70 results in the accumulation of an assembly intermediate followed by a reduction of the next assembly intermediate in the pathway. This indicates that TMEM70 has a role in the stability of membrane-bound subassemblies or in the membrane recruitment of subunits into the forming complex. Independent evidence for a role of TMEM70 in OXPHOS assembly comes from evolutionary analyses. The TMEM70/TMEM186/TMEM223 protein family, of which we show that TMEM186 and TMEM223 are mitochondrial in human as well, only occurs in species with OXPHOS complexes. Our results validate the use of combining complexome profiling with BioID and evolutionary analyses in elucidating congenital defects in protein complex assembly., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)
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- 2020
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19. Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts.
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van der Lee R, Wiel L, van Dam TJP, and Huynen MA
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- Animals, Artifacts, Gene Conversion, Genetic Variation, Genomics, Host-Pathogen Interactions genetics, Humans, Immunity genetics, Multigene Family, Primates genetics, Proteins genetics, Receptors, Virus chemistry, Viral Proteins chemistry, Virus Diseases genetics, Evolution, Molecular, Selection, Genetic
- Abstract
Hotspots of rapid genome evolution hold clues about human adaptation. We present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection in 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our new procedure is stringent and reveals substantial artefacts (20% of initial predictions) that have inflated previous estimates. The final 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immunity, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokines, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction and chromosome segregation (e.g. centromere-associated CENPO, CENPT), apolipoproteins, smell/taste receptors and mitochondrial proteins. Focusing on the virus-host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, tetherin) and predict 70 novel cases through integration with virus-human interaction data. Protein structure analysis further identifies positive selection in the interaction interfaces between viruses and their cellular receptors (CD4-HIV; CD46-measles, adenoviruses; CD55-picornaviruses). Finally, primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positive selection is a rich source for studying the genetics underlying human (antiviral) phenotypes. Procedures and data are available at https://github.com/robinvanderlee/positive-selection., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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- 2017
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20. The vertebrate mitotic checkpoint protein BUBR1 is an unusual pseudokinase.
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Suijkerbuijk SJ, van Dam TJ, Karagöz GE, von Castelmur E, Hubner NC, Duarte AM, Vleugel M, Perrakis A, Rüdiger SG, Snel B, and Kops GJ
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Biological Evolution, Chromosome Segregation, Gene Duplication, Humans, Lizards, Molecular Sequence Data, Mutation, Protein Conformation, Protein Serine-Threonine Kinases genetics, Sequence Alignment, Zebrafish Proteins genetics, M Phase Cell Cycle Checkpoints, Protein Serine-Threonine Kinases metabolism
- Abstract
Chromosomal stability is safeguarded by a mitotic checkpoint, of which BUB1 and Mad3/BUBR1 are core components. These paralogs have similar, but not identical, domain organization. We show that Mad3/BUBR1 and BUB1 paralogous pairs arose by nine independent gene duplications throughout evolution, followed by parallel subfunctionalization in which preservation of the ancestral, amino-terminal KEN box or kinase domain was mutually exclusive. In one exception, vertebrate BUBR1-defined by the KEN box-preserved the kinase domain but allowed nonconserved degeneration of catalytic motifs. Although BUBR1 evolved to a typical pseudokinase in some vertebrates, it retained the catalytic triad in humans. However, we show that putative catalysis by human BUBR1 is dispensable for error-free chromosome segregation. Instead, residues that interact with ATP in conventional kinases are essential for conformational stability in BUBR1. We propose that parallel evolution of BUBR1 orthologs rendered its kinase function dispensable in vertebrates, producing an unusual, triad-containing pseudokinase., (Copyright © 2012 Elsevier Inc. All rights reserved.)
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- 2012
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21. Evolution of the Ras-like small GTPases and their regulators.
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van Dam TJ, Bos JL, and Snel B
- Abstract
Small GTPases are molecular switches at the hub of many signaling pathways and the expansion of this protein family is interwoven with the origin of unique eukaryotic cell features. We have previously reported on the evolution of CDC25 Homology Domain containing proteins, which act as guanine nucleotide exchange factors (GEFs) for Ras-like proteins. We now report on the evolution of both the Ras-like small GTPases as well as the GTPase activating proteins (GAPs) for Ras-like small GTPases. We performed an in depth phylogenetic analysis in 64 genomes of diverse eukaryotic species. These analyses revealed that multiple ancestral Ras-like GTPases and GAPs were already present in the Last Eukaryotic Common Ancestor (LECA), compatible with the presence of RasGEFs in LECA . Furthermore, we endeavor to reconstruct in which order the different Ras-like GTPases diverged from each other. We identified striking differences between the expansion of the various types of Ras-like GTPases and their respective GAPs and GEFs. Altogether, our analysis forms an extensive evolutionary framework for Ras-like signaling pathways and provides specific predictions for molecular biologists and biochemists.
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- 2011
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