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Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024:10.1038/s41589-024-01599-0. [PMID: 38658656 DOI: 10.1038/s41589-024-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
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Affiliation(s)
- Kishore K Mahalingan
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry & Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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2
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Funk L, Su KC, Ly J, Feldman D, Singh A, Moodie B, Blainey PC, Cheeseman IM. The phenotypic landscape of essential human genes. Cell 2022; 185:4634-4653.e22. [PMID: 36347254 PMCID: PMC10482496 DOI: 10.1016/j.cell.2022.10.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/01/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
Understanding the basis for cellular growth, proliferation, and function requires determining the roles of essential genes in diverse cellular processes, including visualizing their contributions to cellular organization and morphology. Here, we combined pooled CRISPR-Cas9-based functional screening of 5,072 fitness-conferring genes in human HeLa cells with microscopy-based imaging of DNA, the DNA damage response, actin, and microtubules. Analysis of >31 million individual cells identified measurable phenotypes for >90% of gene knockouts, implicating gene targets in specific cellular processes. Clustering of phenotypic similarities based on hundreds of quantitative parameters further revealed co-functional genes across diverse cellular activities, providing predictions for gene functions and associations. By conducting pooled live-cell screening of ∼450,000 cell division events for 239 genes, we additionally identified diverse genes with functional contributions to chromosome segregation. Our work establishes a resource detailing the consequences of disrupting core cellular processes that represents the functional landscape of essential human genes.
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Affiliation(s)
- Luke Funk
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kuan-Chung Su
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jimmy Ly
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - David Feldman
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Brittania Moodie
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA.
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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3
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Hotta T, McAlear TS, Yue Y, Higaki T, Haynes SE, Nesvizhskii AI, Sept D, Verhey KJ, Bechstedt S, Ohi R. EML2-S constitutes a new class of proteins that recognizes and regulates the dynamics of tyrosinated microtubules. Curr Biol 2022; 32:3898-3910.e14. [PMID: 35963242 PMCID: PMC9530018 DOI: 10.1016/j.cub.2022.07.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/13/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023]
Abstract
Tubulin post-translational modifications (PTMs) alter microtubule properties by affecting the binding of microtubule-associated proteins (MAPs). Microtubule detyrosination, which occurs by proteolytic removal of the C-terminal tyrosine from ɑ-tubulin, generates the oldest known tubulin PTM, but we lack comprehensive knowledge of MAPs that are regulated by this PTM. We developed a screening pipeline to identify proteins that discriminate between Y- and ΔY-microtubules and found that echinoderm microtubule-associated protein-like 2 (EML2) preferentially interacts with Y-microtubules. This activity depends on a Y-microtubule interaction motif built from WD40 repeats. We show that EML2 tracks the tips of shortening microtubules, a behavior not previously seen among human MAPs in vivo, and influences dynamics to increase microtubule stability. Our screening pipeline is readily adapted to identify proteins that specifically recognize a wide range of microtubule PTMs.
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Affiliation(s)
- Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Thomas S McAlear
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Takumi Higaki
- Faculty of Advanced Science and Technology (FAST), Kumamoto University, Kumamoto, Japan; International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, Japan
| | - Sarah E Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Susanne Bechstedt
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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4
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Jijumon AS, Bodakuntla S, Genova M, Bangera M, Sackett V, Besse L, Maksut F, Henriot V, Magiera MM, Sirajuddin M, Janke C. Lysate-based pipeline to characterize microtubule-associated proteins uncovers unique microtubule behaviours. Nat Cell Biol 2022; 24:253-267. [PMID: 35102268 DOI: 10.1038/s41556-021-00825-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/23/2021] [Indexed: 12/22/2022]
Abstract
The microtubule cytoskeleton forms complex macromolecular assemblies with a range of microtubule-associated proteins (MAPs) that have fundamental roles in cell architecture, division and motility. Determining how an individual MAP modulates microtubule behaviour is an important step in understanding the physiological roles of various microtubule assemblies. To characterize how MAPs control microtubule properties and functions, we developed an approach allowing for medium-throughput analyses of MAPs in cell-free conditions using lysates of mammalian cells. Our pipeline allows for quantitative as well as ultrastructural analyses of microtubule-MAP assemblies. Analysing 45 bona fide and potential mammalian MAPs, we uncovered previously unknown activities that lead to distinct and unique microtubule behaviours such as microtubule coiling or hook formation, or liquid-liquid phase separation along the microtubule lattice that initiates microtubule branching. We have thus established a powerful tool for a thorough characterization of a wide range of MAPs and MAP variants, thus opening avenues for the determination of mechanisms underlying their physiological roles and pathological implications.
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Affiliation(s)
- A S Jijumon
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Satish Bodakuntla
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Mariya Genova
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Mamata Bangera
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Violet Sackett
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Laetitia Besse
- Institut Curie, Université Paris-Saclay, Centre d'Imagerie Multimodale INSERM US43, CNRS UMS2016, Orsay, France
| | - Fatlinda Maksut
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Veronique Henriot
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Maria M Magiera
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | | | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.
- Université Paris-Saclay, CNRS UMR3348, Orsay, France.
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5
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Melo-Hanchuk TD, Kobarg J. Polyglutamylase activity of tubulin tyrosine ligase-like 4 is negatively regulated by the never in mitosis gene A family kinase never in mitosis gene A -related kinase 5. World J Biol Chem 2021; 12:38-51. [PMID: 34084286 PMCID: PMC8160597 DOI: 10.4331/wjbc.v12.i3.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/06/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tubulins, building blocks of microtubules, are modified substrates of diverse post-translational modifications including phosphorylation, polyglycylation and polyglutamylation. Polyglutamylation of microtubules, catalyzed by enzymes from the tubulin tyrosine ligase-like (TTLL) family, can regulate interactions with molecular motors and other proteins. Due to the diversity and functional importance of microtubule modifications, strict control of the TTLL enzymes has been suggested.
AIM To characterize the interaction between never in mitosis gene A-related kinase 5 (NEK5) and TTLL4 proteins and the effects of TTLL4 phosphorylation.
METHODS The interaction between NEK5 and TTLL4 was identified by yeast two-hybrid screening using the C-terminus of NEK5 (a.a. 260–708) as bait and confirmed by immunoprecipitation. The phosphorylation sites of TTLL4 were identified by mass spectrometry and point mutations were introduced.
RESULTS Here, we show that NEK5 interacts with TTLL4 and regulates its polyglutamylation activity. We further show that NEK5 can also interact with TTLL5 and TTLL7. The silencing of NEK5 increases the levels of polyglutamylation of proteins by increasing the activity of TTLL4. The same effects were observed after the expression of the catalytically inactive form of NEK5. This regulation of TTLL4 activity involves its phosphorylation at Y815 and S1136 amino acid residues.
CONCLUSION Our results demonstrate, for the first time, the regulation of TTLL activity through phosphorylation, pointing to NEK5 as a potential effector kinase. We also suggest a general control of tubulin polyglutamylation through NEK family members in human cells.
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Affiliation(s)
| | - Jörg Kobarg
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-862, Brazil
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6
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Gurkaslar HK, Culfa E, Arslanhan MD, Lince-Faria M, Firat-Karalar EN. CCDC57 Cooperates with Microtubules and Microcephaly Protein CEP63 and Regulates Centriole Duplication and Mitotic Progression. Cell Rep 2021; 31:107630. [PMID: 32402286 DOI: 10.1016/j.celrep.2020.107630] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 03/08/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Centrosomes function in key cellular processes ranging from cell division to cellular signaling. Their dysfunction is linked to cancer and developmental disorders. Here, we identify CCDC57 as a pleiotropic regulator of centriole duplication, mitosis, and ciliogenesis. Combining proximity mapping with superresolution imaging, we show that CCDC57 localizes to the proximal end of centrioles and interacts with the microcephaly protein CEP63, centriolar satellite proteins, and microtubules. Loss of CCDC57 causes defects in centriole duplication and results in a failure to localize CEP63 and CEP152 to the centrosome. Additionally, CCDC57 depletion perturbs mitotic progression both in wild-type and centriole-less cells. Importantly, its centrosome-targeting region is required for its interaction with CEP63 and functions during centriole duplication and cilium assembly, whereas the microtubule-targeting region is required for its mitotic functions. Together, our results identify CCDC57 as a critical interface between centrosome and microtubule-mediated cellular processes that are deregulated in microcephaly.
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Affiliation(s)
- H Kubra Gurkaslar
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul 34450, Turkey
| | - Efraim Culfa
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul 34450, Turkey
| | - Melis D Arslanhan
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul 34450, Turkey
| | - Mariana Lince-Faria
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul 34450, Turkey.
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7
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Stuck MW, Chong WM, Liao JC, Pazour GJ. Rab34 is necessary for early stages of intracellular ciliogenesis. Curr Biol 2021; 31:2887-2894.e4. [PMID: 33989524 DOI: 10.1016/j.cub.2021.04.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 01/04/2023]
Abstract
Primary cilia are sensory organelles present on most vertebrate cells and are critical for development and health. Ciliary dysfunction is associated with a large class of human pathologies collectively known as ciliopathies. These include cystic kidneys, blindness, obesity, skeletal malformations, and other organ anomalies. Using a proximity biotinylation with Ift27 as bait, we identified the small guanosine triphosphatase (GTPase) Rab34 as a ciliary protein. Rab34 localizes to the centrosomes near the mother centriole, the axoneme of developed cilia, and highly dynamic tubule structures in the centrosomal region. Rab34 is required for cilia formation in fibroblasts, where we find that Rab34 loss blocks ciliogenesis at an early step of ciliary vesicle formation. In inner medullary collecting duct (IMCD3) epithelial cells, the requirement is more complex, with Rab34 needed in cells grown at low density but becoming less important as cell density increases. Ciliogenesis can proceed by an internal pathway where cilia form in the cytoplasm before being displayed on the ciliary surface or cilia can assemble by an external pathway where the centriole docks on the plasma membrane before ciliary assembly. Fibroblasts are thought to use the internal pathway, although IMCD3 cells are thought to use the external pathway. However, we find that IMCD3 cells can use the internal assembly pathway and significant numbers of internally assembling cilia are observed in low-density cells. Together, our work indicates that Rab34 is required for internal assembly of cilia, but not for cilia built on the cell surface.
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Affiliation(s)
- Michael W Stuck
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, USA
| | - Weng Man Chong
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Jung-Chi Liao
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, USA.
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Bertiaux E, Balestra AC, Bournonville L, Louvel V, Maco B, Soldati-Favre D, Brochet M, Guichard P, Hamel V. Expansion microscopy provides new insights into the cytoskeleton of malaria parasites including the conservation of a conoid. PLoS Biol 2021; 19:e3001020. [PMID: 33705377 PMCID: PMC7951857 DOI: 10.1371/journal.pbio.3001020] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/21/2021] [Indexed: 12/17/2022] Open
Abstract
Malaria is caused by unicellular Plasmodium parasites. Plasmodium relies on diverse microtubule cytoskeletal structures for its reproduction, multiplication, and dissemination. Due to the small size of this parasite, its cytoskeleton has been primarily observable by electron microscopy (EM). Here, we demonstrate that the nanoscale cytoskeleton organisation is within reach using ultrastructure expansion microscopy (U-ExM). In developing microgametocytes, U-ExM allows monitoring the dynamic assembly of axonemes and concomitant tubulin polyglutamylation in whole cells. In the invasive merozoite and ookinete forms, U-ExM unveils the diversity across Plasmodium stages and species of the subpellicular microtubule arrays that confer cell rigidity. In ookinetes, we additionally identify an apical tubulin ring (ATR) that colocalises with markers of the conoid in related apicomplexan parasites. This tubulin-containing structure was presumed to be lost in Plasmodium despite its crucial role in motility and invasion in other apicomplexans. Here, U-ExM reveals that a divergent and considerably reduced form of the conoid is actually conserved in Plasmodium species.
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Affiliation(s)
- Eloïse Bertiaux
- University of Geneva, Department of Cell Biology, Faculty of Science, Geneva, Switzerland
| | - Aurélia C. Balestra
- University of Geneva, Department of Microbiology and Molecular Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Lorène Bournonville
- University of Geneva, Department of Cell Biology, Faculty of Science, Geneva, Switzerland
| | - Vincent Louvel
- University of Geneva, Department of Cell Biology, Faculty of Science, Geneva, Switzerland
| | - Bohumil Maco
- University of Geneva, Department of Microbiology and Molecular Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Dominique Soldati-Favre
- University of Geneva, Department of Microbiology and Molecular Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Mathieu Brochet
- University of Geneva, Department of Microbiology and Molecular Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Paul Guichard
- University of Geneva, Department of Cell Biology, Faculty of Science, Geneva, Switzerland
| | - Virginie Hamel
- University of Geneva, Department of Cell Biology, Faculty of Science, Geneva, Switzerland
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Tubulin modifying enzymes as target for the treatment oftau-related diseases. Pharmacol Ther 2020; 218:107681. [PMID: 32961263 DOI: 10.1016/j.pharmthera.2020.107681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/09/2020] [Indexed: 01/17/2023]
Abstract
In the brain of patients with Alzheimer's disease (AD), the number and length of microtubules (MTs) are significantly and selectively reduced. MTs are involved in a wide range of cellular functions, and defects of the microtubular system have emerged as a unifying hypothesis for the heterogeneous and variable clinical presentations of AD. MTs orchestrate their numerous functions through the spatiotemporal regulation of the binding of specialised microtubule-associated proteins (MAPs) and molecular motors. Covalent posttranslational modifications (PTMs) on the tubulin C-termini that protrude at the surface of MTs regulate the binding of these effectors. In neurons, MAP tau is highly abundant and its abnormal dissociation from MTs in the axon, cellular mislocalization and hyperphosphorylation, are primary events leading to neuronal death. Consequently, compounds targeting tau phosphorylation or aggregation are currently evaluated but their clinical significance has not been demonstrated yet. In this review, we discuss the emerging link between tubulin PTMs and tau dysfunction. In neurons, high levels of glutamylation and detyrosination profoundly impact the physicochemical properties at the surface of MTs. Moreover, in patients with early-onset progressive neurodegeneration, deleterious mutations in enzymes involved in modifying MTs at the surface have recently been identified, underscoring the importance of this enzymatic machinery in neurology. We postulate that pharmacologically targeting the tubulin-modifying enzymes holds promise as therapeutic approach for the treatment of neurodegenerative diseases.
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10
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The emerging role of tubulin posttranslational modifications in cilia and ciliopathies. BIOPHYSICS REPORTS 2020. [DOI: 10.1007/s41048-020-00111-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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11
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Jahejo AR, Zhang D, Niu S, Mangi RA, Khan A, Qadir MF, Khan A, Chen HC, Tian WX. Transcriptome-based screening of intracellular pathways and angiogenesis related genes at different stages of thiram induced tibial lesions in broiler chickens. BMC Genomics 2020; 21:50. [PMID: 31941444 PMCID: PMC6964038 DOI: 10.1186/s12864-020-6456-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 01/07/2020] [Indexed: 01/21/2023] Open
Abstract
Background The Tibial dyschondroplasia (TD) in fast-growing chickens is mainly caused by improper blood circulation. The exact mechanism underlying angiogenesis and vascularization in tibial growth plate of broiler chickens remains unclear. Therefore, this research attempts to study genes involved in the regulation of angiogenesis in chicken red blood cells. Twenty-four broiler chickens were allotted into a control and thiram (Tetramethyl thiuram disulfide) group. Blood samples were collected on day 2, 6 (8- and 14-days old chickens) and 15 (23 days old chickens). Results Histopathology and hematoxylin and eosin (H&E) results showed that angiogenesis decreased on the 6th day of the experiment but started to recover on the 15th day of the experiment. Immunohistochemistry (IHC) results confirmed the expressions of integrin alpha-v precursor (ITGAV) and clusterin precursor (CLU). Transcriptome sequencing analysis evaluated 293 differentially expressed genes (DEGs), of which 103 up-regulated genes and 190 down-regulated genes were enriched in the pathways of neuroactive ligand receptor interaction, mitogen-activated protein kinase (MAPK), ribosome, regulation of actin cytoskeleton, focal adhesion, natural killer cell mediated cytotoxicity and the notch signalling pathways. DEGs (n = 20) related to angiogenesis of chicken erythrocytes in the enriched pathways were thromboxane A2 receptor (TBXA2R), interleukin-1 receptor type 1 precursor (IL1R1), ribosomal protein L17 (RPL17), integrin beta-3 precursor (ITGB3), ITGAV, integrin beta-2 precursor (ITGB2), ras-related C3 botulinum toxin substrate 2 (RAC2), integrin alpha-2 (ITGA2), IQ motif containing GTPase activating protein 2 (IQGAP2), ARF GTPase-activating protein (GIT1), proto-oncogene vav (VAV1), integrin alpha-IIb-like (ITGA5), ras-related protein Rap-1b precursor (RAP1B), tyrosine protein kinase Fyn-like (FYN), tyrosine-protein phosphatase non-receptor type 11 (PTPN11), protein patched homolog 1 (PTCH1), nuclear receptor corepressor 2 (NCOR2) and mastermind like protein 3 (MAML3) selected for further confirmation with qPCR. However, commonly DEGs were sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (ATP2A3), ubiquitin-conjugating enzyme E2 R2 (UBE2R2), centriole cilia and spindle-associated protein (CCSAP), coagulation factor XIII A chain protein (F13A1), shroom 2 isoform X6 (SHROOM2), ras GTPase-activating protein 3 (RASA3) and CLU. Conclusion We have found potential therapeutic genes concerned to erythrocytes and blood regulation, which regulated the angiogenesis in thiram induced TD chickens. This study also revealed the potential functions of erythrocytes. Graphical abstract 1. Tibial dyschondroplasia (TD) in chickens were more on day 6, which started recovering on day 15. 2. The enriched pathway observed in TD chickens on day 6 was ribosome pathway, on day 15 were regulation of actin cytoskeleton and focal adhesion pathway. 3. The genes involved in the ribosome pathways was ribosomal protein L17 (RPL17). regulation of actin cytoskeleton pathway were Ras-related C3 botulinum toxin substrate 2 (RAC2), Ras-related protein Rap-1b precursor (RAP1B), ARF GTPase-activating protein (GIT1), IQ motif containing GTPase activating protein 2 (IQGAP2), Integrin alpha-v precursor (ITGAV), Integrin alpha-2 (ITGA2), Integrin beta-2 precursor (ITGB2), Integrin beta-3 precursor (ITGB3), Integrin alpha-IIb-like (ITGA5). Focal adhesion Proto-oncogene vav (Vav-like), Tyrosine-protein kinase Fyn-like (FYN).
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Affiliation(s)
- Ali Raza Jahejo
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Ding Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Sheng Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Raza Ali Mangi
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Afrasyab Khan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Muhammad Farhan Qadir
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Ajab Khan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Huan-Chun Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen-Xia Tian
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China.
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12
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Bompard G, van Dijk J, Cau J, Lannay Y, Marcellin G, Lawera A, van der Laan S, Rogowski K. CSAP Acts as a Regulator of TTLL-Mediated Microtubule Glutamylation. Cell Rep 2019; 25:2866-2877.e5. [PMID: 30517872 DOI: 10.1016/j.celrep.2018.10.095] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/22/2017] [Accepted: 10/25/2018] [Indexed: 01/22/2023] Open
Abstract
Tubulin glutamylation is a reversible posttranslational modification that accumulates on stable microtubules (MTs). While abnormally high levels of this modification lead to a number of disorders such as male sterility, retinal degeneration, and neurodegeneration, very little is known about the molecular mechanisms underlying the regulation of glutamylase activity. Here, we found that CSAP forms a complex with TTLL5, and we demonstrate that the two proteins regulate their reciprocal abundance. Moreover, we show that CSAP increases TTLL5-mediated glutamylation and identify the TTLL5-interacting domain. Deletion of this domain leads to complete loss of CSAP activating function without impacting its MT binding. Binding of CSAP to TTLL5 promotes relocalization of TTLL5 toward MTs. Finally, we show that CSAP binds and activates all of the remaining autonomously active TTLL glutamylases. As such, we present CSAP as a major regulator of tubulin glutamylation and associated functions.
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Affiliation(s)
- Guillaume Bompard
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Juliette van Dijk
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Julien Cau
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Yoann Lannay
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Guillaume Marcellin
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Aleksandra Lawera
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Siem van der Laan
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Krzysztof Rogowski
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France.
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13
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Holdgaard SG, Cianfanelli V, Pupo E, Lambrughi M, Lubas M, Nielsen JC, Eibes S, Maiani E, Harder LM, Wesch N, Foged MM, Maeda K, Nazio F, de la Ballina LR, Dötsch V, Brech A, Frankel LB, Jäättelä M, Locatelli F, Barisic M, Andersen JS, Bekker-Jensen S, Lund AH, Rogov VV, Papaleo E, Lanzetti L, De Zio D, Cecconi F. Selective autophagy maintains centrosome integrity and accurate mitosis by turnover of centriolar satellites. Nat Commun 2019; 10:4176. [PMID: 31519908 PMCID: PMC6744468 DOI: 10.1038/s41467-019-12094-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
The centrosome is the master orchestrator of mitotic spindle formation and chromosome segregation in animal cells. Centrosome abnormalities are frequently observed in cancer, but little is known of their origin and about pathways affecting centrosome homeostasis. Here we show that autophagy preserves centrosome organization and stability through selective turnover of centriolar satellite components, a process we termed doryphagy. Autophagy targets the satellite organizer PCM1 by interacting with GABARAPs via a C-terminal LIR motif. Accordingly, autophagy deficiency results in accumulation of large abnormal centriolar satellites and a resultant dysregulation of centrosome composition. These alterations have critical impact on centrosome stability and lead to mitotic centrosome fragmentation and unbalanced chromosome segregation. Our findings identify doryphagy as an important centrosome-regulating pathway and bring mechanistic insights to the link between autophagy dysfunction and chromosomal instability. In addition, we highlight the vital role of centriolar satellites in maintaining centrosome integrity.
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Affiliation(s)
- Søs Grønbæk Holdgaard
- Cell Stress and Survival Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Valentina Cianfanelli
- Cell Stress and Survival Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Emanuela Pupo
- Department of Oncology, University of Torino Medical School, Turin, 10100, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, 10060, Italy
| | - Matteo Lambrughi
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Michal Lubas
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Julie C Nielsen
- Center for Healthy Aging, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Susana Eibes
- Cell Division Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Emiliano Maiani
- Cell Stress and Survival Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Lea M Harder
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, 5230, Denmark
| | - Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Mads Møller Foged
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Francesca Nazio
- Department of Pediatric Hemato-Oncology and Cell and Gene therapy, IRCCS Bambino Gesù Children's Hospital, Rome, 00143, Italy
| | - Laura R de la Ballina
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0317, Oslo, Norway
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Andreas Brech
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0379, Oslo, Norway
| | - Lisa B Frankel
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark
- RNA and Autophagy group, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Franco Locatelli
- Department of Pediatric Hemato-Oncology and Cell and Gene therapy, IRCCS Bambino Gesù Children's Hospital, Rome, 00143, Italy
- Department of Gynecology/Obstetrics and Pediatrics, Sapienza University of Rome, Rome, 00185, Italy
| | - Marin Barisic
- Cell Division Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, 5230, Denmark
| | - Simon Bekker-Jensen
- Center for Healthy Aging, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Anders H Lund
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, 2100, Denmark
| | - Letizia Lanzetti
- Department of Oncology, University of Torino Medical School, Turin, 10100, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, 10060, Italy
| | - Daniela De Zio
- Cell Stress and Survival Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Francesco Cecconi
- Cell Stress and Survival Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, 2100, Denmark.
- Department of Pediatric Hemato-Oncology and Cell and Gene therapy, IRCCS Bambino Gesù Children's Hospital, Rome, 00143, Italy.
- Department of Biology, University of Tor Vergata, Rome, 00133, Italy.
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14
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Maurya AK, Rogers T, Sengupta P. A CCRK and a MAK Kinase Modulate Cilia Branching and Length via Regulation of Axonemal Microtubule Dynamics in Caenorhabditis elegans. Curr Biol 2019; 29:1286-1300.e4. [PMID: 30955935 PMCID: PMC6482063 DOI: 10.1016/j.cub.2019.02.062] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/06/2019] [Accepted: 02/28/2019] [Indexed: 02/06/2023]
Abstract
The diverse morphologies of primary cilia are tightly regulated as a function of cell type and cellular state. CCRK- and MAK-related kinases have been implicated in ciliary length control in multiple species, although the underlying mechanisms are not fully understood. Here, we show that in C. elegans, DYF-18/CCRK and DYF-5/MAK act in a cascade to generate the highly arborized cilia morphologies of the AWA olfactory neurons. Loss of kinase function results in dramatically elongated AWA cilia that lack branches. Intraflagellar transport (IFT) motor protein localization, but not velocities, in AWA cilia is altered upon loss of dyf-18. We instead find that axonemal microtubules are decorated by the EBP-2 end-binding protein along their lengths and that the tubulin load is increased and tubulin turnover is reduced in AWA cilia of dyf-18 mutants. Moreover, we show that predicted microtubule-destabilizing mutations in two tubulin subunits, as well as mutations in IFT proteins predicted to disrupt tubulin transport, restore cilia branching and suppress AWA cilia elongation in dyf-18 mutants. Loss of dyf-18 is also sufficient to elongate the truncated rod-like unbranched cilia of the ASH nociceptive neurons in animals carrying a microtubule-destabilizing mutation in a tubulin subunit. We suggest that CCRK and MAK activity tunes cilia length and shape in part via modulation of axonemal microtubule stability, suggesting that similar mechanisms may underlie their roles in ciliary length control in other cell types.
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Affiliation(s)
- Ashish Kumar Maurya
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| | - Travis Rogers
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
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15
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van der Laan S, Dubra G, Rogowski K. Tubulin glutamylation: a skeleton key for neurodegenerative diseases. Neural Regen Res 2019; 14:1899-1900. [PMID: 31290441 PMCID: PMC6676872 DOI: 10.4103/1673-5374.259611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Siem van der Laan
- Institute of Human Genetics (IGH), Tubulin Code Team, Centre National de la Recherche Scientifique (CNRS)-University of Montpellier, Montpellier, France
| | - Geronimo Dubra
- Institute of Human Genetics (IGH), Tubulin Code Team, Centre National de la Recherche Scientifique (CNRS)-University of Montpellier, Montpellier, France
| | - Krzysztof Rogowski
- Institute of Human Genetics (IGH), Tubulin Code Team, Centre National de la Recherche Scientifique (CNRS)-University of Montpellier, Montpellier, France
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16
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Monda JK, Cheeseman IM. Dynamic regulation of dynein localization revealed by small molecule inhibitors of ubiquitination enzymes. Open Biol 2018; 8:rsob.180095. [PMID: 30257893 PMCID: PMC6170511 DOI: 10.1098/rsob.180095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/29/2018] [Indexed: 11/27/2022] Open
Abstract
Cytoplasmic dynein is a minus-end-directed microtubule-based motor that acts at diverse subcellular sites. During mitosis, dynein localizes simultaneously to the mitotic spindle, spindle poles, kinetochores and the cell cortex. However, it is unclear what controls the relative targeting of dynein to these locations. As dynein is heavily post-translationally modified, we sought to test a role for these modifications in regulating dynein localization. We find that dynein rapidly and strongly accumulates at mitotic spindle poles following treatment with NSC697923, a small molecule that inhibits the ubiquitin E2 enzyme, Ubc13, or treatment with PYR-41, a ubiquitin E1 inhibitor. Subsets of dynein regulators such as Lis1, ZW10 and Spindly accumulate at the spindle poles, whereas others do not, suggesting that NSC697923 differentially affects specific dynein populations. We additionally find that dynein relocalization induced by NSC697923 or PYR-41 can be suppressed by simultaneous treatment with the non-selective deubiquitinase inhibitor, PR-619. However, we did not observe altered dynein localization following treatment with the selective E1 inhibitor, TAK-243. Although it is possible that off-target effects of NSC697923 and PYR-41 are responsible for the observed changes in dynein localization, the rapid relocalization upon drug treatment highlights the highly dynamic nature of dynein regulation during mitosis.
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Affiliation(s)
- Julie K Monda
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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17
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Wloga D, Joachimiak E, Louka P, Gaertig J. Posttranslational Modifications of Tubulin and Cilia. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028159. [PMID: 28003186 DOI: 10.1101/cshperspect.a028159] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tubulin undergoes several highly conserved posttranslational modifications (PTMs) including acetylation, detyrosination, glutamylation, and glycylation. These PTMs accumulate on a subset of microtubules that are long-lived, including those in the basal bodies and axonemes. Tubulin PTMs are distributed nonuniformly. In the outer doublet microtubules of the axoneme, the B-tubules are highly enriched in the detyrosinated, polyglutamylated, and polyglycylated tubulin, whereas the A-tubules contain mostly unmodified tubulin. The nonuniform patterns of tubulin PTMs may functionalize microtubules in a position-dependent manner. Recent studies indicate that tubulin PTMs contribute to the assembly, disassembly, maintenance, and motility of cilia. In particular, tubulin glutamylation has emerged as a key PTM that affects ciliary motility through regulation of axonemal dynein arms and controls the stability and length of the axoneme.
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Affiliation(s)
- Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Panagiota Louka
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
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18
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Dias MDS, Hamel CP, Meunier I, Varin J, Blanchard S, Boyard F, Sahel JA, Zeitz C. Novel splice-site mutation in TTLL5 causes cone dystrophy in a consanguineous family. Mol Vis 2017; 23:131-139. [PMID: 28356705 PMCID: PMC5360453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/16/2017] [Indexed: 11/03/2022] Open
Abstract
PURPOSE To report the clinical and genetic findings of one family with autosomal recessive cone dystrophy (CD) and to identify the causative mutation. METHODS An institutional study of three family members from two generations. The clinical examination included best-corrected Snellen visual acuity measurement, fundoscopy, the Farnsworth D-15 color vision test, a full-field electroretinogram (ERG) that incorporated the International Society for Clinical Electrophysiology of Vision standards and methodology, fundus autofluorescence (FAF) and infrared (IR), and spectral-domain optical coherence tomography (SD-OCT). Genetic findings were achieved with DNA analysis using whole exome sequencing (WES) and Sanger sequencing. RESULTS The proband, a 9-year-old boy, presented with a condition that appeared to be congenital and stationary. The clinical presentation initially reflected incomplete congenital stationary night blindness (icCSNB) because of myopia, a decrease in visual acuity, abnormal oscillatory potentials, and reduced amplitudes on the 30 Hz flicker ERG but was atypical because there were no clear electronegative responses. However, no disease-causing mutations in the genes underlying icCSNB were identified. Following WES analysis of family members, a homozygous splice-site mutation in intron 3 of TTLL5 (c.182-3_182-1delinsAA) was found cosegregating within the phenotype in the family. CONCLUSIONS The distinction between icCSNB and CD phenotypes is not always straightforward in young patients. The patient was quite young, which most likely explains why the progression of the CD was not obvious. WES analysis provided prompt diagnosis for this family; thus, the use of this technique to refine the diagnosis is highlighted in this study.
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Affiliation(s)
- Miguel de Sousa Dias
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
| | - Christian P. Hamel
- INSERM U 1051, Institut des Neurosciences de Montpellier, Hôpital Saint-Eloi, Montpellier, France,Affections Sensorielles Génétiques, CHU de Montpellier, 191 Avenue du Doyen Gaston Giraud, Montpellier, France,Université Montpellier, 163 Avenue Auguste Broussonnet, Montpellier, France
| | - Isabelle Meunier
- INSERM U 1051, Institut des Neurosciences de Montpellier, Hôpital Saint-Eloi, Montpellier, France,Affections Sensorielles Génétiques, CHU de Montpellier, 191 Avenue du Doyen Gaston Giraud, Montpellier, France,Université Montpellier, 163 Avenue Auguste Broussonnet, Montpellier, France
| | - Juliette Varin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
| | | | - Fiona Boyard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
| | - José-Alain Sahel
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, 28 rue de Charenton, Paris, France,Institute of Ophthalmology, University College of London, London EC1V 9EL, UK,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France,Academie des Sciences, Institut de France, Paris, France,Department of Ophthalmology, The University of Pittsburghschool of Medicine, Pittsburg, PA
| | - Christina Zeitz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
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19
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McKinley KL, Cheeseman IM. Large-Scale Analysis of CRISPR/Cas9 Cell-Cycle Knockouts Reveals the Diversity of p53-Dependent Responses to Cell-Cycle Defects. Dev Cell 2017; 40:405-420.e2. [PMID: 28216383 DOI: 10.1016/j.devcel.2017.01.012] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/23/2016] [Accepted: 01/23/2017] [Indexed: 12/20/2022]
Abstract
Defining the genes that are essential for cellular proliferation is critical for understanding organismal development and identifying high-value targets for disease therapies. However, the requirements for cell-cycle progression in human cells remain incompletely understood. To elucidate the consequences of acute and chronic elimination of cell-cycle proteins, we generated and characterized inducible CRISPR/Cas9 knockout human cell lines targeting 209 genes involved in diverse cell-cycle processes. We performed single-cell microscopic analyses to systematically establish the effects of the knockouts on subcellular architecture. To define variations in cell-cycle requirements between cultured cell lines, we generated knockouts across cell lines of diverse origins. We demonstrate that p53 modulates the phenotype of specific cell-cycle defects through distinct mechanisms, depending on the defect. This work provides a resource to broadly facilitate robust and long-term depletion of cell-cycle proteins and reveals insights into the requirements for cell-cycle progression.
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Affiliation(s)
- Kara L McKinley
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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20
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Kern DM, Nicholls PK, Page DC, Cheeseman IM. A mitotic SKAP isoform regulates spindle positioning at astral microtubule plus ends. J Cell Biol 2016; 213:315-28. [PMID: 27138257 PMCID: PMC4862331 DOI: 10.1083/jcb.201510117] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/30/2016] [Indexed: 12/14/2022] Open
Abstract
The Astrin/SKAP complex regulates mitotic chromosome alignment and centrosome integrity, but previous work found conflicting results for SKAP function. Here, Kern et al. demonstrate that a previously unappreciated short SKAP isoform mediates mitotic spindle positioning at astral microtubule plus ends. The Astrin/SKAP complex plays important roles in mitotic chromosome alignment and centrosome integrity, but previous work found conflicting results for SKAP function. Here, we demonstrate that SKAP is expressed as two distinct isoforms in mammals: a longer, testis-specific isoform that was used for the previous studies in mitotic cells and a novel, shorter mitotic isoform. Unlike the long isoform, short SKAP rescues SKAP depletion in mitosis and displays robust microtubule plus-end tracking, including localization to astral microtubules. Eliminating SKAP microtubule binding results in severe chromosome segregation defects. In contrast, SKAP mutants specifically defective for plus-end tracking facilitate proper chromosome segregation but display spindle positioning defects. Cells lacking SKAP plus-end tracking have reduced Clasp1 localization at microtubule plus ends and display increased lateral microtubule contacts with the cell cortex, which we propose results in unbalanced dynein-dependent cortical pulling forces. Our work reveals an unappreciated role for the Astrin/SKAP complex as an astral microtubule mediator of mitotic spindle positioning.
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Affiliation(s)
- David M Kern
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Peter K Nicholls
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - David C Page
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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21
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Ohta S, Hamada M, Sato N, Toramoto I. Polyglutamylated Tubulin Binding Protein C1orf96/CSAP Is Involved in Microtubule Stabilization in Mitotic Spindles. PLoS One 2015; 10:e0142798. [PMID: 26562023 PMCID: PMC4642972 DOI: 10.1371/journal.pone.0142798] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/27/2015] [Indexed: 12/13/2022] Open
Abstract
The centrosome-associated C1orf96/Centriole, Cilia and Spindle-Associated Protein (CSAP) targets polyglutamylated tubulin in mitotic microtubules (MTs). Loss of CSAP causes critical defects in brain development; however, it is unclear how CSAP association with MTs affects mitosis progression. In this study, we explored the molecular mechanisms of the interaction of CSAP with mitotic spindles. Loss of CSAP caused MT instability in mitotic spindles and resulted in mislocalization of Nuclear protein that associates with the Mitotic Apparatus (NuMA), with defective MT dynamics. Thus, CSAP overload in the spindles caused extensive MT stabilization and recruitment of NuMA. Moreover, MT stabilization by CSAP led to high levels of polyglutamylation on MTs. MT depolymerization by cold or nocodazole treatment was inhibited by CSAP binding. Live-cell imaging analysis suggested that CSAP-dependent MT-stabilization led to centrosome-free MT aster formation immediately upon nuclear envelope breakdown without γ-tubulin. We therefore propose that CSAP associates with MTs around centrosomes to stabilize MTs during mitosis, ensuring proper bipolar spindle formation and maintenance.
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Affiliation(s)
- Shinya Ohta
- From the Center for Innovative and Translational Medicine, Medical School, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
- * E-mail:
| | - Mayako Hamada
- From the Center for Innovative and Translational Medicine, Medical School, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
| | - Nobuko Sato
- From the Center for Innovative and Translational Medicine, Medical School, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
| | - Iyo Toramoto
- From the Center for Innovative and Translational Medicine, Medical School, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
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22
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Systematic proteomics of the VCP-UBXD adaptor network identifies a role for UBXN10 in regulating ciliogenesis. Nat Cell Biol 2015; 17:1356-69. [PMID: 26389662 PMCID: PMC4610257 DOI: 10.1038/ncb3238] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 08/13/2015] [Indexed: 02/07/2023]
Abstract
The AAA-ATPase VCP (also known as p97 or CDC48) uses ATP hydrolysis to 'segregate' ubiquitylated proteins from their binding partners. VCP acts through UBX-domain-containing adaptors that provide target specificity, but the targets and functions of UBXD proteins remain poorly understood. Through systematic proteomic analysis of UBXD proteins in human cells, we reveal a network of over 195 interacting proteins, implicating VCP in diverse cellular pathways. We have explored one such complex between an unstudied adaptor UBXN10 and the intraflagellar transport B (IFT-B) complex, which regulates anterograde transport into cilia. UBXN10 localizes to cilia in a VCP-dependent manner and both VCP and UBXN10 are required for ciliogenesis. Pharmacological inhibition of VCP destabilized the IFT-B complex and increased trafficking rates. Depletion of UBXN10 in zebrafish embryos causes defects in left-right asymmetry, which depends on functional cilia. This study provides a resource for exploring the landscape of UBXD proteins in biology and identifies an unexpected requirement for VCP-UBXN10 in ciliogenesis.
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Van de Mark D, Kong D, Loncarek J, Stearns T. MDM1 is a microtubule-binding protein that negatively regulates centriole duplication. Mol Biol Cell 2015; 26:3788-802. [PMID: 26337392 PMCID: PMC4626064 DOI: 10.1091/mbc.e15-04-0235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/28/2015] [Indexed: 12/03/2022] Open
Abstract
MDM1 is a microtubule-binding protein that localizes to centrioles. 3D-SIM microscopy shows MDM1 to be closely associated with the centriole barrel, likely residing in the centriole lumen. MDM1 overexpression and depletion experiments suggest that MDM1 is a negative regulator of centriole duplication. Mouse double-minute 1 (Mdm1) was originally identified as a gene amplified in transformed mouse cells and more recently as being highly up-regulated during differentiation of multiciliated epithelial cells, a specialized cell type having hundreds of centrioles and motile cilia. Here we show that the MDM1 protein localizes to centrioles of dividing cells and differentiating multiciliated cells. 3D-SIM microscopy showed that MDM1 is closely associated with the centriole barrel, likely residing in the centriole lumen. Overexpression of MDM1 suppressed centriole duplication, whereas depletion of MDM1 resulted in an increase in granular material that likely represents early intermediates in centriole formation. We show that MDM1 binds microtubules in vivo and in vitro. We identified a repeat motif in MDM1 that is required for efficient microtubule binding and found that these repeats are also present in CCSAP, another microtubule-binding protein. We propose that MDM1 is a negative regulator of centriole duplication and that its function is mediated through microtubule binding.
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Affiliation(s)
| | - Dong Kong
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research-Frederick, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Jadranka Loncarek
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research-Frederick, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA 94305 Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
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Inferring transient particle transport dynamics in live cells. Nat Methods 2015; 12:838-40. [PMID: 26192083 DOI: 10.1038/nmeth.3483] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 06/14/2015] [Indexed: 12/29/2022]
Abstract
Live-cell imaging and particle tracking provide rich information on mechanisms of intracellular transport. However, trajectory analysis procedures to infer complex transport dynamics involving stochastic switching between active transport and diffusive motion are lacking. We applied Bayesian model selection to hidden Markov modeling to infer transient transport states from trajectories of mRNA-protein complexes in live mouse hippocampal neurons and metaphase kinetochores in dividing human cells. The software is available at http://hmm-bayes.org/.
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Taylor SP, Dantas TJ, Duran I, Wu S, Lachman RS, Nelson SF, Cohn DH, Vallee RB, Krakow D. Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome. Nat Commun 2015; 6:7092. [PMID: 26077881 PMCID: PMC4470332 DOI: 10.1038/ncomms8092] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 04/02/2015] [Indexed: 12/16/2022] Open
Abstract
The short rib polydactyly syndromes (SRPSs) are a heterogeneous group of autosomal recessive, perinatal lethal skeletal disorders characterized primarily by short, horizontal ribs, short limbs and polydactyly. Mutations in several genes affecting intraflagellar transport (IFT) cause SRPS but they do not account for all cases. Here we identify an additional SRPS gene and further unravel the functional basis for IFT. We perform whole-exome sequencing and identify mutations in a new disease-producing gene, cytoplasmic dynein-2 light intermediate chain 1, DYNC2LI1, segregating with disease in three families. Using primary fibroblasts, we show that DYNC2LI1 is essential for dynein-2 complex stability and that mutations in DYNC2LI1 result in variable length, including hyperelongated, cilia, Hedgehog pathway impairment and ciliary IFT accumulations. The findings in this study expand our understanding of SRPS locus heterogeneity and demonstrate the importance of DYNC2LI1 in dynein-2 complex stability, cilium function, Hedgehog regulation and skeletogenesis.
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Affiliation(s)
- S Paige Taylor
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Tiago J Dantas
- Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| | - Ivan Duran
- Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Sulin Wu
- Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Ralph S Lachman
- International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | | | - Stanley F Nelson
- 1] Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA [2] Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Daniel H Cohn
- 1] Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA [2] International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, California 90095, USA [3] Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| | - Deborah Krakow
- 1] Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA [2] Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA [3] International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, California 90095, USA
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Potential role of tubulin tyrosine ligase-like enzymes in tumorigenesis and cancer cell resistance. Cancer Lett 2014; 350:1-4. [DOI: 10.1016/j.canlet.2014.04.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/22/2014] [Accepted: 04/26/2014] [Indexed: 12/27/2022]
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Abstract
Centrioles and basal bodies (CBBs) are microtubule-rich cylindrical structures that nucleate and organize centrosomes and cilia, respectively. Despite their apparent ninefold rotational symmetry, the nine sets of triplet microtubules in CBBs possess asymmetries in their morphology and in the structures that associate with them. These asymmetries define the position of nascent CBB assembly, the orientation of ciliary beating, the orientation of spindle poles and the maintenance of cellular geometry. For some of these functions, the orientation of CBBs is first established during new CBB biogenesis when the daughter structure is positioned adjacent to the mother. The mother CBB organizes the surrounding environment that nascent CBBs are born into, thereby providing a nest for the new CBB to develop. Protists, including ciliates and algae, highlight the importance of this environment with the formation of asymmetrically placed scaffolds onto which new basal bodies assemble and are positioned. Recent studies illuminate the positioning of nascent centrioles relative to a modular pericentriolar material (PCM) environment and suggest that, like ciliates, centrosomes organize an immediate environment surrounding centrioles for their biogenesis and positioning. In this Commentary, I will explore the positioning of nascent CBB assembly as the first event in building cellular asymmetries and describe how the environment surrounding both basal bodies and centrioles may define asymmetric assembly.
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Affiliation(s)
- Chad G Pearson
- University of Colorado, Anschutz Medical Campus, Department of Cell and Developmental Biology, 12801 E. 17th Avenue, Room 12104, Aurora, CO 80045, USA
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Sergouniotis PI, Chakarova C, Murphy C, Becker M, Lenassi E, Arno G, Lek M, MacArthur DG, Bhattacharya SS, Moore AT, Holder GE, Robson AG, Wolfrum U, Webster AR, Plagnol V. Biallelic variants in TTLL5, encoding a tubulin glutamylase, cause retinal dystrophy. Am J Hum Genet 2014; 94:760-9. [PMID: 24791901 PMCID: PMC4067560 DOI: 10.1016/j.ajhg.2014.04.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/02/2014] [Indexed: 12/30/2022] Open
Abstract
In a subset of inherited retinal degenerations (including cone, cone-rod, and macular dystrophies), cone photoreceptors are more severely affected than rods; ABCA4 mutations are the most common cause of this heterogeneous class of disorders. To identify retinal-disease-associated genes, we performed exome sequencing in 28 individuals with "cone-first" retinal disease and clinical features atypical for ABCA4 retinopathy. We then conducted a gene-based case-control association study with an internal exome data set as the control group. TTLL5, encoding a tubulin glutamylase, was highlighted as the most likely disease-associated gene; 2 of 28 affected subjects harbored presumed loss-of-function variants: c.[1586_1589delAGAG];[1586_1589delAGAG], p.[Glu529Valfs(∗)2];[Glu529Valfs(∗)2], and c.[401delT(;)3354G>A], p.[Leu134Argfs(∗)45(;)Trp1118(∗)]. We then inspected previously collected exome sequence data from individuals with related phenotypes and found two siblings with homozygous nonsense variant c.1627G>T (p.Glu543(∗)) in TTLL5. Subsequently, we tested a panel of 55 probands with retinal dystrophy for TTLL5 mutations; one proband had a homozygous missense change (c.1627G>A [p.Glu543Lys]). The retinal phenotype was highly similar in three of four families; the sibling pair had a more severe, early-onset disease. In human and murine retinae, TTLL5 localized to the centrioles at the base of the connecting cilium. TTLL5 has been previously reported to be essential for the correct function of sperm flagella in mice and play a role in polyglutamylation of primary cilia in vitro. Notably, genes involved in the polyglutamylation and deglutamylation of tubulin have been associated with photoreceptor degeneration in mice. The electrophysiological and fundus autofluorescence imaging presented here should facilitate the molecular diagnosis in further families.
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Affiliation(s)
| | | | | | - Mirjana Becker
- Institute of Zoology, Focus Program Translational Neurosciences, Johannes Gutenberg University of Mainz, Mainz 55099, Germany
| | - Eva Lenassi
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Anthony T Moore
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Graham E Holder
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anthony G Robson
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Uwe Wolfrum
- Institute of Zoology, Focus Program Translational Neurosciences, Johannes Gutenberg University of Mainz, Mainz 55099, Germany
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; Moorfields Eye Hospital, London EC1V 2PD, UK.
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Bosch Grau M, Gonzalez Curto G, Rocha C, Magiera MM, Marques Sousa P, Giordano T, Spassky N, Janke C. Tubulin glycylases and glutamylases have distinct functions in stabilization and motility of ependymal cilia. ACTA ACUST UNITED AC 2013; 202:441-51. [PMID: 23897886 PMCID: PMC3734080 DOI: 10.1083/jcb.201305041] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tubulin glutamylating enzymes are important for beating behavior of ependymal cilia in the brain, whereas glycylating enzymes are critical for stability and maintenance of these cilia. Microtubules are subject to a variety of posttranslational modifications that potentially regulate cytoskeletal functions. Two modifications, glutamylation and glycylation, are highly enriched in the axonemes of most eukaryotes, and might therefore play particularly important roles in cilia and flagella. Here we systematically analyze the dynamics of glutamylation and glycylation in developing mouse ependymal cilia and the expression of the corresponding enzymes in the brain. By systematically screening enzymes of the TTLL family for specific functions in ependymal cilia, we demonstrate that the glycylating enzymes TTLL3 and TTLL8 were required for stability and maintenance of ependymal cilia, whereas the polyglutamylase TTLL6 was necessary for coordinated beating behavior. Our work provides evidence for a functional separation of glutamylating and glycylating enzymes in mammalian ependymal cilia. It further advances the elucidation of the functions of tubulin posttranslational modifications in motile cilia of the mammalian brain and their potential importance in brain development and disease.
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Abstract
Zebrafish are ideally suited for analysis of genes required for ciliogenesis and cilia function. Combining genetic manipulation with high quality in vivo imaging, zebrafish embryos provide a high-throughput system for annotation of the cilia proteome. The specific advantages of the system are the availability of cilia mutants, the ability to target genes of unknown function using antisense methods, the feasibility of observing cilia in living embryos, and the ability to image fixed cilia in wholemount at high resolution. Techniques are described for analysis of mutants, gene knockdown using antisense morpholino oligos, visualizing cilia and cilia orientation in wholemount zebrafish embryos, live imaging cilia, and electron microscopy of zebrafish cilia.
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Schmidt KN, Kuhns S, Neuner A, Hub B, Zentgraf H, Pereira G. Cep164 mediates vesicular docking to the mother centriole during early steps of ciliogenesis. ACTA ACUST UNITED AC 2012; 199:1083-101. [PMID: 23253480 PMCID: PMC3529528 DOI: 10.1083/jcb.201202126] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cep164 provides a molecular link between the mother centriole and the ciliary membrane biogenesis machinery by interacting with the GEF Rabin8 and the GTPase Rab8. Cilia formation is a multi-step process that starts with the docking of a vesicle at the distal part of the mother centriole. This step marks the conversion of the mother centriole into the basal body, from which axonemal microtubules extend to form the ciliary compartment. How vesicles are stably attached to the mother centriole to initiate ciliary membrane biogenesis is unknown. Here, we investigate the molecular role of the mother centriolar component Cep164 in ciliogenesis. We show that Cep164 was indispensable for the docking of vesicles at the mother centriole. Using biochemical and functional assays, we identified the components of the vesicular transport machinery, the GEF Rabin8 and the GTPase Rab8, as interacting partners of Cep164. We propose that Cep164 is targeted to the apical domain of the mother centriole to provide the molecular link between the mother centriole and the membrane biogenesis machinery that initiates cilia formation.
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Affiliation(s)
- Kerstin N Schmidt
- DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
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