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Leung M, Steinman J, Li D, Lor A, Gruesen A, Sadah A, van Kuijk FJ, Montezuma SR, Kondkar AA, Radhakrishnan R, Lobo GP. The Logistical Backbone of Photoreceptor Cell Function: Complementary Mechanisms of Dietary Vitamin A Receptors and Rhodopsin Transporters. Int J Mol Sci 2024; 25:4278. [PMID: 38673863 PMCID: PMC11050646 DOI: 10.3390/ijms25084278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
In this review, we outline our current understanding of the mechanisms involved in the absorption, storage, and transport of dietary vitamin A to the eye, and the trafficking of rhodopsin protein to the photoreceptor outer segments, which encompasses the logistical backbone required for photoreceptor cell function. Two key mechanisms of this process are emphasized in this manuscript: ocular and systemic vitamin A membrane transporters, and rhodopsin transporters. Understanding the complementary mechanisms responsible for the generation and proper transport of the retinylidene protein to the photoreceptor outer segment will eventually shed light on the importance of genes encoded by these proteins, and their relationship on normal visual function and in the pathophysiology of retinal degenerative diseases.
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Affiliation(s)
- Matthias Leung
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Jeremy Steinman
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Dorothy Li
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Anjelynt Lor
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Andrew Gruesen
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Ahmed Sadah
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Frederik J. van Kuijk
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Sandra R. Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Altaf A. Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 12271, Saudi Arabia;
| | - Rakesh Radhakrishnan
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
| | - Glenn P. Lobo
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (J.S.); (D.L.); (A.L.); (A.G.); (A.S.); (F.J.v.K.); (S.R.M.)
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2
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Bu W, Di J, Zhao J, Liu R, Wu Y, Ran J, Li T. Dynein Light Intermediate Chains Exhibit Different Arginine Methylation Patterns. J Clin Lab Anal 2024; 38:e25030. [PMID: 38525916 PMCID: PMC11033342 DOI: 10.1002/jcla.25030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND The motor protein dynein is integral to retrograde transport along microtubules and interacts with numerous cargoes through the recruitment of cargo-specific adaptor proteins. This interaction is mediated by dynein light intermediate chain subunits LIC1 (DYNC1LI1) and LIC2 (DYNC1LI2), which govern the adaptor binding and are present in distinct dynein complexes with overlapping and unique functions. METHODS Using bioinformatics, we analyzed the C-terminal domains (CTDs) of LIC1 and LIC2, revealing similar structural features but diverse post-translational modifications (PTMs). The methylation status of LIC2 and the proteins involved in this modification were examined through immunoprecipitation and immunoblotting analyses. The specific methylation sites on LIC2 were identified through a site-directed mutagenesis analysis, contributing to a deeper understanding of the regulatory mechanisms of the dynein complex. RESULTS We found that LIC2 is specifically methylated at the arginine 397 residue, a reaction that is catalyzed by protein arginine methyltransferase 1 (PRMT1). CONCLUSIONS The distinct PTMs of the LIC subunits offer a versatile mechanism for dynein to transport diverse cargoes efficiently. Understanding how these PTMs influence the functions of LIC2, and how they differ from LIC1, is crucial for elucidating the role of dynein-related transport pathways in a range of diseases. The discovery of the arginine 397 methylation site on LIC2 enhances our insight into the regulatory PTMs of dynein functions.
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Affiliation(s)
- Weiwen Bu
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Jie Di
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Junkui Zhao
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Ruming Liu
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Yue Wu
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life SciencesShandong Normal UniversityJinanChina
| | - Jie Ran
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life SciencesShandong Normal UniversityJinanChina
| | - Te Li
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
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3
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Rao L, Gennerich A. Structure and Function of Dynein's Non-Catalytic Subunits. Cells 2024; 13:330. [PMID: 38391943 PMCID: PMC10886578 DOI: 10.3390/cells13040330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Dynein, an ancient microtubule-based motor protein, performs diverse cellular functions in nearly all eukaryotic cells, with the exception of land plants. It has evolved into three subfamilies-cytoplasmic dynein-1, cytoplasmic dynein-2, and axonemal dyneins-each differentiated by their cellular functions. These megadalton complexes consist of multiple subunits, with the heavy chain being the largest subunit that generates motion and force along microtubules by converting the chemical energy of ATP hydrolysis into mechanical work. Beyond this catalytic core, the functionality of dynein is significantly enhanced by numerous non-catalytic subunits. These subunits are integral to the complex, contributing to its stability, regulating its enzymatic activities, targeting it to specific cellular locations, and mediating its interactions with other cofactors. The diversity of non-catalytic subunits expands dynein's cellular roles, enabling it to perform critical tasks despite the conservation of its heavy chains. In this review, we discuss recent findings and insights regarding these non-catalytic subunits.
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Affiliation(s)
- Lu Rao
- Department of Biochemistry and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Arne Gennerich
- Department of Biochemistry and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Rahman F, Johnson JL, Zhang J, He J, Pestonjamasp K, Cherqui S, Catz SD. DYNC1LI2 regulates localization of the chaperone-mediated autophagy receptor LAMP2A and improves cellular homeostasis in cystinosis. Autophagy 2021; 18:1108-1126. [PMID: 34643468 PMCID: PMC9196850 DOI: 10.1080/15548627.2021.1971937] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The dynein motor protein complex is required for retrograde transport but the functions of the intermediate-light chains that form the cargo-binding complex are not elucidated and the importance of individual subunits in maintaining cellular homeostasis is unknown. Here, using mRNA arrays and protein analysis, we show that the dynein subunit, DYNC1LI2 (dynein, cytoplasmic 1 light intermediate chain 2) is downregulated in cystinosis, a lysosomal storage disorder caused by genetic defects in CTNS (cystinosin, lysosomal cystine transporter). Reconstitution of DYNC1LI2 expression in ctns-/- cells reestablished endolysosomal dynamics. Defective vesicular trafficking in cystinotic cells was rescued by DYNC1LI2 expression which correlated with decreased endoplasmic reticulum stress manifested as decreased expression levels of the chaperone HSPA5/GRP78, and the transcription factors ATF4 and DDIT3/CHOP. Mitochondrial fragmentation, membrane potential and endolysosomal-mitochondrial association in cystinotic cells were rescued by DYNC1LI2. Survival of cystinotic cells to oxidative stress was increased by DYNC1LI2 reconstitution but not by its paralog DYNC1LI1, which also failed to decrease ER stress and mitochondrial fragmentation. DYNC1LI2 expression rescued the localization of the chaperone-mediated autophagy (CMA) receptor LAMP2A, CMA activity, cellular homeostasis and LRP2/megalin expression in cystinotic proximal tubule cells, the primary cell type affected in cystinosis. DYNC1LI2 failed to rescue phenotypes in cystinotic cells when LAMP2A was downregulated or when co-expressed with dominant negative (DN) RAB7 or DN-RAB11, which impaired LAMP2A trafficking. DYNC1LI2 emerges as a regulator of cellular homeostasis and potential target to repair underlying trafficking and CMA in cystinosis, a mechanism that is not restored by lysosomal cystine depletion therapies. Abbreviations: ACTB: actin, beta; ATF4: activating transcription factor 4; CMA: chaperone-mediated autophagy; DYNC1LI1: dynein cytoplasmic 1 light intermediate chain 1; DYNC1LI2: dynein cytoplasmic 1 light intermediate chain 2; ER: endoplasmic reticulum; LAMP1: lysosomal associated membrane protein 1; LAMP2A: lysosomal associated membrane protein 2A; LIC: light-intermediate chains; LRP2/Megalin: LDL receptor related protein 2; PTCs: proximal tubule cells; RAB: RAB, member RAS oncogene family; RAB11FIP3: RAB11 family interacting protein 3; RILP: Rab interacting lysosomal protein
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Affiliation(s)
- Farhana Rahman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jennifer L Johnson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jinzhong Zhang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jing He
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kersi Pestonjamasp
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephanie Cherqui
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sergio D Catz
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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5
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Antony D, Brunner HG, Schmidts M. Ciliary Dyneins and Dynein Related Ciliopathies. Cells 2021; 10:cells10081885. [PMID: 34440654 PMCID: PMC8391580 DOI: 10.3390/cells10081885] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
Although ubiquitously present, the relevance of cilia for vertebrate development and health has long been underrated. However, the aberration or dysfunction of ciliary structures or components results in a large heterogeneous group of disorders in mammals, termed ciliopathies. The majority of human ciliopathy cases are caused by malfunction of the ciliary dynein motor activity, powering retrograde intraflagellar transport (enabled by the cytoplasmic dynein-2 complex) or axonemal movement (axonemal dynein complexes). Despite a partially shared evolutionary developmental path and shared ciliary localization, the cytoplasmic dynein-2 and axonemal dynein functions are markedly different: while cytoplasmic dynein-2 complex dysfunction results in an ultra-rare syndromal skeleto-renal phenotype with a high lethality, axonemal dynein dysfunction is associated with a motile cilia dysfunction disorder, primary ciliary dyskinesia (PCD) or Kartagener syndrome, causing recurrent airway infection, degenerative lung disease, laterality defects, and infertility. In this review, we provide an overview of ciliary dynein complex compositions, their functions, clinical disease hallmarks of ciliary dynein disorders, presumed underlying pathomechanisms, and novel developments in the field.
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Affiliation(s)
- Dinu Antony
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106 Freiburg, Germany;
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands;
- Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands
| | - Han G. Brunner
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands;
- Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands
| | - Miriam Schmidts
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106 Freiburg, Germany;
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands;
- Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands
- Correspondence: ; Tel.: +49-761-44391; Fax: +49-761-44710
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6
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Kumari A, Kumar C, Wasnik N, Mylavarapu SVS. Dynein light intermediate chains as pivotal determinants of dynein multifunctionality. J Cell Sci 2021; 134:268315. [PMID: 34014309 DOI: 10.1242/jcs.254870] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In animal cells, a single cytoplasmic dynein motor mediates microtubule minus-end-directed transport, counterbalancing dozens of plus-end-directed kinesins. The remarkable ability of dynein to interact with a diverse cargo spectrum stems from its tightly regulated recruitment of cargo-specific adaptor proteins, which engage the dynactin complex to make a tripartite processive motor. Adaptor binding is governed by the homologous dynein light intermediate chain subunits LIC1 (DYNC1LI1) and LIC2 (DYNC1LI2), which exist in mutually exclusive dynein complexes that can perform both unique and overlapping functions. The intrinsically disordered and variable C-terminal domains of the LICs are indispensable for engaging a variety of structurally divergent adaptors. Here, we hypothesize that numerous spatiotemporally regulated permutations of posttranslational modifications of the LICs, as well as of the adaptors and cargoes, exponentially expand the spectrum of dynein-adaptor-cargo complexes. We thematically illustrate the possibilities that could generate a vast set of biochemical variations required to support the wide range of dynein functions.
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Affiliation(s)
- Amrita Kumari
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Chandan Kumar
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Neeraj Wasnik
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Sivaram V S Mylavarapu
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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7
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Nakayama K, Katoh Y. Architecture of the IFT ciliary trafficking machinery and interplay between its components. Crit Rev Biochem Mol Biol 2020; 55:179-196. [PMID: 32456460 DOI: 10.1080/10409238.2020.1768206] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cilia and flagella serve as cellular antennae and propellers in various eukaryotic cells, and contain specific receptors and ion channels as well as components of axonemal microtubules and molecular motors to achieve their sensory and motile functions. Not only the bidirectional trafficking of specific proteins within cilia but also their selective entry and exit across the ciliary gate is mediated by the intraflagellar transport (IFT) machinery with the aid of motor proteins. The IFT-B complex, which is powered by the kinesin-2 motor, mediates anterograde protein trafficking from the base to the tip of cilia, whereas the IFT-A complex together with the dynein-2 complex mediates retrograde protein trafficking. The BBSome complex connects ciliary membrane proteins to the IFT machinery. Defects in any component of this trafficking machinery lead to abnormal ciliogenesis and ciliary functions, and results in a broad spectrum of disorders, collectively called the ciliopathies. In this review article, we provide an overview of the architectures of the components of the IFT machinery and their functional interplay in ciliary protein trafficking.
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Affiliation(s)
- Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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8
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Quintero-Ronderos P, Laissue P. Genetic Variants Contributing to Early Recurrent Pregnancy Loss Etiology Identified by Sequencing Approaches. Reprod Sci 2020; 27:1541-1552. [PMID: 32430708 DOI: 10.1007/s43032-020-00187-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recurrent pregnancy loss (RPL) affects up to 5% of couples. It is believed that genetic factors contribute to the disease's etiology and pathophysiology. Hundreds of genes represent coherent RPL candidates due to mammalian implantation's inherent complexity. Sanger sequencing (direct sequencing) of candidate genes has identified potential RPL causative genes (and variants), including those regulating embryo implantation and pregnancy maintenance. Although this approach is a reliable technique, the simultaneous analysis of large genomic regions is challenging. Next-generation sequencing (NGS) technology has thus emerged as a useful alternative for determining genetic variants and transcriptomic disturbances contributing to monogenic and polygenic diseases pathogenesis. However, interpreting results remains challenging as NGS experiments provide an enormous amount of complex data. The molecular aspects of specific diseases must be fully understood for accurate interpretation of NGS data. This review was thus aimed at describing (for the first time) the most relevant studies involving Sanger and NGS sequencing, leading to the description of variants related to RPL pathogenesis. Successful RPL-related NGS initiatives (including RNAseq-based studies) and future challenges are discussed. We consider that the information given here should be useful for clinicians, scientists, and students to enable a better understanding of RPL etiology. It may also provide a basis for the development of diagnostic/prognostic approaches contributing toward translational medicine.
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Affiliation(s)
- Paula Quintero-Ronderos
- Center For Research in Genetics and Genomics (CIGGUR), GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 N° 63C-69, Bogotá, 1100100, Colombia
| | - Paul Laissue
- Center For Research in Genetics and Genomics (CIGGUR), GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 N° 63C-69, Bogotá, 1100100, Colombia.
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Vuolo L, Stevenson NL, Mukhopadhyay AG, Roberts AJ, Stephens DJ. Cytoplasmic dynein-2 at a glance. J Cell Sci 2020; 133:133/6/jcs240614. [DOI: 10.1242/jcs.240614] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT
Cytoplasmic dynein-2 is a motor protein complex that drives the movement of cargoes along microtubules within cilia, facilitating the assembly of these organelles on the surface of nearly all mammalian cells. Dynein-2 is crucial for ciliary function, as evidenced by deleterious mutations in patients with skeletal abnormalities. Long-standing questions include how the dynein-2 complex is assembled, regulated, and switched between active and inactive states. A combination of model organisms, in vitro cell biology, live-cell imaging, structural biology and biochemistry has advanced our understanding of the dynein-2 motor. In this Cell Science at a Glance article and the accompanying poster, we discuss the current understanding of dynein-2 and its roles in ciliary assembly and function.
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Affiliation(s)
- Laura Vuolo
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Nicola L. Stevenson
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Aakash G. Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London WC1E 7HX, UK
| | - Anthony J. Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London WC1E 7HX, UK
| | - David J. Stephens
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
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Structure of the dynein-2 complex and its assembly with intraflagellar transport trains. Nat Struct Mol Biol 2019; 26:823-829. [PMID: 31451806 PMCID: PMC6774794 DOI: 10.1038/s41594-019-0286-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
Dynein-2 assembles with polymeric intraflagellar transport (IFT) trains to form a transport machinery that is crucial for cilia biogenesis and signaling. Here we recombinantly expressed the ~1.4-MDa human dynein-2 complex and solved its cryo-EM structure to near-atomic resolution. The two identical copies of the dynein-2 heavy chain are contorted into different conformations by a WDR60-WDR34 heterodimer and a block of two RB and six LC8 light chains. One heavy chain is steered into a zig-zag conformation, which matches the periodicity of the anterograde IFT-B train. Contacts between adjacent dyneins along the train indicate a cooperative mode of assembly. Removal of the WDR60-WDR34-light chain subcomplex renders dynein-2 monomeric and relieves autoinhibition of its motility. Our results converge on a model in which an unusual stoichiometry of non-motor subunits controls dynein-2 assembly, asymmetry, and activity, giving mechanistic insight into the interaction of dynein-2 with IFT trains and the origin of diverse functions in the dynein family.
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11
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Quintero-Ronderos P, Laissue P. Genetic Variants Contributing to Early Recurrent Pregnancy Loss Etiology Identified by Sequencing Approaches. Reprod Sci 2019:1933719119831769. [PMID: 30879428 DOI: 10.1177/1933719119831769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recurrent pregnancy loss (RPL) affects up to 5% of couples. It is believed that genetic factors contribute to the disease's etiology and pathophysiology. Hundreds of genes represent coherent RPL candidates due to mammalian implantation's inherent complexity. Sanger sequencing (direct sequencing) of candidate genes has identified potential RPL causative genes (and variants), including those regulating embryo implantation and pregnancy maintenance. Although this approach is a reliable technique, the simultaneous analysis of large genomic regions is challenging. Next-generation sequencing (NGS) technology has thus emerged as a useful alternative for determining genetic variants and transcriptomic disturbances contributing to monogenic and polygenic diseases pathogenesis. However, interpreting results remains challenging as NGS experiments provide an enormous amount of complex data. The molecular aspects of specific diseases must be fully understood for accurate interpretation of NGS data. This review was thus aimed at describing (for the first time) the most relevant studies involving Sanger and NGS sequencing, leading to the description of variants related to RPL pathogenesis. Successful RPL-related NGS initiatives (including RNAseq-based studies) and future challenges are discussed. We consider that the information given here should be useful for clinicians, scientists, and students to enable a better understanding of RPL etiology. It may also provide a basis for the development of diagnostic/prognostic approaches contributing toward translational medicine.
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Affiliation(s)
- Paula Quintero-Ronderos
- 1 Center For Research in Genetics and Genomics (CIGGUR), GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Paul Laissue
- 1 Center For Research in Genetics and Genomics (CIGGUR), GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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12
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Gonçalves JC, Dantas TJ, Vallee RB. Distinct roles for dynein light intermediate chains in neurogenesis, migration, and terminal somal translocation. J Cell Biol 2019; 218:808-819. [PMID: 30674581 PMCID: PMC6400572 DOI: 10.1083/jcb.201806112] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 11/21/2018] [Accepted: 01/02/2019] [Indexed: 12/16/2022] Open
Abstract
Cytoplasmic dynein participates in multiple aspects of neocortical development. These include neural progenitor proliferation, morphogenesis, and neuronal migration. The cytoplasmic dynein light intermediate chains (LICs) 1 and 2 are cargo-binding subunits, though their relative roles are not well understood. Here, we used in utero electroporation of shRNAs or LIC functional domains to determine the relative contributions of the two LICs in the developing rat brain. We find that LIC1, through BicD2, is required for apical nuclear migration in neural progenitors. In newborn neurons, we observe specific roles for LIC1 in the multipolar to bipolar transition and glial-guided neuronal migration. In contrast, LIC2 contributes to a novel dynein role in the little-studied mode of migration, terminal somal translocation. Together, our results provide novel insight into the LICs' unique functions during brain development and dynein regulation overall.
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Affiliation(s)
- João Carlos Gonçalves
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Tiago J Dantas
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
- I3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
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13
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Chen B, Niu J, Kreuzer J, Zheng B, Jarugumilli GK, Haas W, Wu X. Auto-fatty acylation of transcription factor RFX3 regulates ciliogenesis. Proc Natl Acad Sci U S A 2018; 115:E8403-E8412. [PMID: 30127002 PMCID: PMC6130365 DOI: 10.1073/pnas.1800949115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Defects in cilia have been associated with an expanding human disease spectrum known as ciliopathies. Regulatory Factor X 3 (RFX3) is one of the major transcription factors required for ciliogenesis and cilia functions. In addition, RFX3 regulates pancreatic islet cell differentiation and mature β-cell functions. However, how RFX3 protein is regulated at the posttranslational level remains poorly understood. Using chemical reporters of protein fatty acylation and mass spectrometry analysis, here we show that RFX3 transcriptional activity is regulated by S-fatty acylation at a highly conserved cysteine residue in the dimerization domain. Surprisingly, RFX3 undergoes enzyme-independent, "self-catalyzed" auto-fatty acylation and displays preferences for 18-carbon stearic acid and oleic acid. The fatty acylation-deficient mutant of RFX3 shows decreased homodimerization; fails to promote ciliary gene expression, ciliogenesis, and elongation; and impairs Hedgehog signaling. Our findings reveal a regulation of RFX3 transcription factor and link fatty acid metabolism and protein lipidation to the regulation of ciliogenesis.
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Affiliation(s)
- Baoen Chen
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Jixiao Niu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Baohui Zheng
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Gopala K Jarugumilli
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129;
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14
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Roberts AJ. Emerging mechanisms of dynein transport in the cytoplasm versus the cilium. Biochem Soc Trans 2018; 46:967-982. [PMID: 30065109 PMCID: PMC6103457 DOI: 10.1042/bst20170568] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/13/2018] [Accepted: 06/18/2018] [Indexed: 02/08/2023]
Abstract
Two classes of dynein power long-distance cargo transport in different cellular contexts. Cytoplasmic dynein-1 is responsible for the majority of transport toward microtubule minus ends in the cell interior. Dynein-2, also known as intraflagellar transport dynein, moves cargoes along the axoneme of eukaryotic cilia and flagella. Both dyneins operate as large ATP-driven motor complexes, whose dysfunction is associated with a group of human disorders. But how similar are their mechanisms of action and regulation? To examine this question, this review focuses on recent advances in dynein-1 and -2 research, and probes to what extent the emerging principles of dynein-1 transport could apply to or differ from those of the less well-understood dynein-2 mechanoenzyme.
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Affiliation(s)
- Anthony J Roberts
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, U.K.
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15
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Structural atlas of dynein motors at atomic resolution. Biophys Rev 2018; 10:677-686. [PMID: 29478092 DOI: 10.1007/s12551-018-0402-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 12/17/2022] Open
Abstract
Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural studies of every component of dynein and summarize them as a structural atlas that classifies the cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.
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16
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Ishikawa H, Marshall WF. Intraflagellar Transport and Ciliary Dynamics. Cold Spring Harb Perspect Biol 2017; 9:9/3/a021998. [PMID: 28249960 DOI: 10.1101/cshperspect.a021998] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cilia and flagella are microtubule-based organelles whose assembly requires a motile process, known as intraflagellar transport (IFT), to bring tubulin and other components to the distal tip of the growing structure. The IFT system uses a multiprotein complex with components that appear to be specialized for the transport of different sets of cargo proteins. The mechanisms by which cargo is selected for ciliary import and transport by IFT remain an area of active research. The complex dynamics of cilia and flagella are under constant regulation to ensure proper length control, and this regulation appears to involve regulation at the stage of IFT injection into the flagellum, as well as regulation of flagellar disassembly and, possibly, of cargo binding. Cilia and flagella thus represent a convenient model system to study how multiple motile and signaling pathways cooperate to control the assembly and dynamics of a complex cellular structure.
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Affiliation(s)
- Hiroaki Ishikawa
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
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17
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Mijalkovic J, Prevo B, Oswald F, Mangeol P, Peterman EJG. Ensemble and single-molecule dynamics of IFT dynein in Caenorhabditis elegans cilia. Nat Commun 2017; 8:14591. [PMID: 28230057 PMCID: PMC5331336 DOI: 10.1038/ncomms14591] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/13/2017] [Indexed: 12/14/2022] Open
Abstract
Cytoplasmic dyneins drive microtubule-based, minus-end directed transport in eukaryotic cells. Whereas cytoplasmic dynein 1 has been widely studied, IFT dynein has received far less attention. Here, we use fluorescence microscopy of labelled motors in living Caenorhabditis elegans to investigate IFT-dynein motility at the ensemble and single-molecule level. We find that while the kinesin composition of motor ensembles varies along the track, the amount of dynein remains relatively constant. Remarkably, this does not result in directionality changes of cargo along the track, as has been reported for other opposite-polarity, tug-of-war motility systems. At the single-molecule level, IFT-dynein trajectories reveal unexpected dynamics, including diffusion at the base, and pausing and directional switches along the cilium. Stochastic simulations show that the ensemble IFT-dynein distribution depends upon the probability of single-motor directional switches. Our results provide quantitative insight into IFT-dynein dynamics in vivo, shedding light on the complex functioning of dynein motors in general.
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Affiliation(s)
- Jona Mijalkovic
- Department of Physics and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Bram Prevo
- Department of Physics and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Felix Oswald
- Department of Physics and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Pierre Mangeol
- Department of Physics and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Erwin J. G. Peterman
- Department of Physics and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
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18
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Qiao Y, Wen J, Tang F, Martell S, Shomer N, Leung PCK, Stephenson MD, Rajcan-Separovic E. Whole exome sequencing in recurrent early pregnancy loss. Mol Hum Reprod 2016; 22:364-72. [PMID: 26826164 DOI: 10.1093/molehr/gaw008] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/25/2016] [Indexed: 12/20/2022] Open
Abstract
STUDY HYPOTHESIS Exome sequencing can identify genetic causes of idiopathic recurrent pregnancy loss (RPL). STUDY FINDING We identified compound heterozygous deleterious mutations affecting DYNC2H1 and ALOX15 in two out of four families with RPL. Both genes have a role in early development. Bioinformatics analysis of all genes with rare and putatively pathogenic mutations in miscarriages and couples showed enrichment in pathways relevant to pregnancy loss, including the complement and coagulation cascades pathways. WHAT IS KNOWN ALREADY Next generation sequencing (NGS) is increasingly being used to identify known and novel gene mutations in children with developmental delay and in fetuses with ultrasound-detected anomalies. In contrast, NGS is rarely used to study pregnancy loss. Chromosome microarray analysis detects putatively causative DNA copy number variants (CNVs) in ∼2% of miscarriages and CNVs of unknown significance (predominantly parental in origin) in up to 40% of miscarriages. Therefore, a large number of miscarriages still have an unknown cause. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Whole exome sequencing (WES) was performed using Illumina HiSeq 2000 platform on seven euploid miscarriages from four families with RPL. Golden Helix SVS v8.1.5 was used for data assessment and inheritance analysis for deleterious DNA variants predicted to severely disrupt protein-coding genes by introducing a frameshift, loss of the stop codon, gain of the stop codon, changes in splicing or the initial codon. Webgestalt (http://bioinfo.vanderbilt.edu/webgestalt/) was used for pathway and disease association enrichment analysis of a gene pool containing putatively pathogenic variants in miscarriages and couples in comparison to control gene pools. MAIN RESULTS AND THE ROLE OF CHANCE Compound heterozygous mutations in DYNC2H1 and ALOX15 were identified in miscarriages from two families with RPL. DYNC2H1 is involved in cilia biogenesis and has been associated with fetal lethality in humans. ALOX15 is expressed in placenta and its dysregulation has been associated with inflammation, placental, dysfunction, abnormal oxidative stress response and angiogenesis. The pool of putatively pathogenic single nucleotide variants (SNVs) and small insertions and deletions (indels) detected in the miscarriages showed enrichment in 'complement and coagulation cascades pathway', and 'ciliary motility disorders'. We conclude that CNVs, individual SNVs and pool of deleterious gene mutations identified by exome sequencing could contribute to RPL. LIMITATIONS, REASONS FOR CAUTION The size of our sample cohort is small. The functional effect of candidate mutations should be evaluated to determine whether the mutations are causative. WIDER IMPLICATIONS OF THE FINDINGS This is the first study to assess whether SNVs may contribute to the pathogenesis of miscarriage. Furthermore, our findings suggest that collective effect of mutations in relevant biological pathways could be implicated in RPL. STUDY FUNDING AND COMPETING INTERESTS The study was funded by Canadian Institutes of Health Research (grant MOP 106467) and Michael Smith Foundation of Health Research Career Scholar salary award to ERS.
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Affiliation(s)
- Ying Qiao
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Jiadi Wen
- University of Texas, Dallas, TX, USA
| | - Flamingo Tang
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Sally Martell
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Naomi Shomer
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Peter C K Leung
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada V6Z 2 K5
| | - Mary D Stephenson
- University of Chicago and University of Illinois at Chicago, Chicago, IL, USA
| | - Evica Rajcan-Separovic
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
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19
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See SK, Hoogendoorn S, Chung AH, Ye F, Steinman JB, Sakata-Kato T, Miller RM, Cupido T, Zalyte R, Carter AP, Nachury MV, Kapoor TM, Chen JK. Cytoplasmic Dynein Antagonists with Improved Potency and Isoform Selectivity. ACS Chem Biol 2016; 11:53-60. [PMID: 26555042 PMCID: PMC4715766 DOI: 10.1021/acschembio.5b00895] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Cytoplasmic dyneins
1 and 2 are related members of the AAA+ superfamily
(ATPases associated with diverse cellular activities) that function
as the predominant minus-end-directed microtubule motors in eukaryotic
cells. Dynein 1 controls mitotic spindle assembly, organelle movement,
axonal transport, and other cytosolic, microtubule-guided processes,
whereas dynein 2 mediates retrograde trafficking within motile and
primary cilia. Small-molecule inhibitors are important tools for investigating
motor protein-dependent mechanisms, and ciliobrevins were recently
discovered as the first dynein-specific chemical antagonists. Here,
we demonstrate that ciliobrevins directly target the heavy chains
of both dynein isoforms and explore the structure–activity
landscape of these inhibitors in vitro and in cells.
In addition to identifying chemical motifs that are essential for
dynein blockade, we have discovered analogs with increased potency
and dynein 2 selectivity. These antagonists effectively disrupt Hedgehog
signaling, intraflagellar transport, and ciliogenesis, making them
useful probes of these and other cytoplasmic dynein 2-dependent cellular
processes.
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Affiliation(s)
| | | | | | | | - Jonathan B. Steinman
- Laboratory
of Chemistry and Cell Biology, Rockefeller University, New York City, New York 10065, United States
| | | | - Rand M. Miller
- Laboratory
of Chemistry and Cell Biology, Rockefeller University, New York City, New York 10065, United States
| | - Tommaso Cupido
- Laboratory
of Chemistry and Cell Biology, Rockefeller University, New York City, New York 10065, United States
| | - Ruta Zalyte
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge CB2 0QH, United Kingdom
| | - Andrew P. Carter
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge CB2 0QH, United Kingdom
| | | | - Tarun M. Kapoor
- Laboratory
of Chemistry and Cell Biology, Rockefeller University, New York City, New York 10065, United States
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20
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Kessler K, Wunderlich I, Uebe S, Falk NS, Gießl A, Brandstätter JH, Popp B, Klinger P, Ekici AB, Sticht H, Dörr HG, Reis A, Roepman R, Seemanová E, Thiel CT. DYNC2LI1 mutations broaden the clinical spectrum of dynein-2 defects. Sci Rep 2015; 5:11649. [PMID: 26130459 PMCID: PMC4486972 DOI: 10.1038/srep11649] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/27/2015] [Indexed: 12/30/2022] Open
Abstract
Skeletal ciliopathies are a heterogeneous group of autosomal recessive osteochondrodysplasias caused by defects in formation, maintenance and function of the primary cilium. Mutations in the underlying genes affect the molecular motors, intraflagellar transport complexes (IFT), or the basal body. The more severe phenotypes are caused by defects of genes of the dynein-2 complex, where mutations in DYNC2H1, WDR34 and WDR60 have been identified. In a patient with a Jeune-like phenotype we performed exome sequencing and identified compound heterozygous missense and nonsense mutations in DYNC2LI1 segregating with the phenotype. DYNC2LI1 is ubiquitously expressed and interacts with DYNC2H1 to form the dynein-2 complex important for retrograde IFT. Using DYNC2LI1 siRNA knockdown in fibroblasts we identified a significantly reduced cilia length proposed to affect cilia function. In addition, depletion of DYNC2LI1 induced altered cilia morphology with broadened ciliary tips and accumulation of IFT-B complex proteins in accordance with retrograde IFT defects. Our results expand the clinical spectrum of ciliopathies caused by defects of the dynein-2 complex.
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Affiliation(s)
- Kristin Kessler
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ina Wunderlich
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nathalie S Falk
- Animal Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Gießl
- Animal Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Bernt Popp
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Patricia Klinger
- Department of Orthopaedic Rheumatology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Helmuth-Günther Dörr
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Eva Seemanová
- Department of Clinical Genetics, Institute of Biology and Medical Genetics, 2nd Medical School, Charles University, Prague, Czech Republic
| | - Christian T Thiel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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21
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Alonso A, Greenlee M, Matts J, Kline J, Davis KJ, Miller RK. Emerging roles of sumoylation in the regulation of actin, microtubules, intermediate filaments, and septins. Cytoskeleton (Hoboken) 2015; 72:305-39. [PMID: 26033929 PMCID: PMC5049490 DOI: 10.1002/cm.21226] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/25/2015] [Accepted: 05/27/2015] [Indexed: 12/29/2022]
Abstract
Sumoylation is a powerful regulatory system that controls many of the critical processes in the cell, including DNA repair, transcriptional regulation, nuclear transport, and DNA replication. Recently, new functions for SUMO have begun to emerge. SUMO is covalently attached to components of each of the four major cytoskeletal networks, including microtubule-associated proteins, septins, and intermediate filaments, in addition to nuclear actin and actin-regulatory proteins. However, knowledge of the mechanisms by which this signal transduction system controls the cytoskeleton is still in its infancy. One story that is beginning to unfold is that SUMO may regulate the microtubule motor protein dynein by modification of its adaptor Lis1. In other instances, cytoskeletal elements can both bind to SUMO non-covalently and also be conjugated by it. The molecular mechanisms for many of these new functions are not yet clear, but are under active investigation. One emerging model links the function of MAP sumoylation to protein degradation through SUMO-targeted ubiquitin ligases, also known as STUbL enzymes. Other possible functions for cytoskeletal sumoylation are also discussed.
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Affiliation(s)
- Annabel Alonso
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Matt Greenlee
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Jessica Matts
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Jake Kline
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Kayla J. Davis
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Rita K. Miller
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
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22
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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: 61] [Impact Index Per Article: 6.8] [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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23
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TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport. Nat Commun 2015; 6:7074. [PMID: 26044572 PMCID: PMC4468853 DOI: 10.1038/ncomms8074] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/31/2015] [Indexed: 02/06/2023] Open
Abstract
The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. Severe congenital development defects such as Jeune syndrome can result from the malfunction of primary cilia and dynein. Here Schmidts et al. report unique biallelic null mutations in a gene encoding a dynein light chain, helping to explain the nature of ciliopathies in human patients.
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24
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Affiliation(s)
- Yuqing Hou
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, United States
| | - George B Witman
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, United States.
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25
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Abstract
Primary cilia are essential cellular organelles projecting from the cell surface to sense and transduce developmental signaling. They are tiny but have complicated structures containing microtubule (MT)-based internal structures (the axoneme) and mother centriole formed basal body. Intraflagellar transport (Ift) operated by Ift proteins and motors are indispensable for cilia formation and function. Mutations in Ift proteins or Ift motors cause various human diseases, some of which have severe bone defects. Over the last few decades, major advances have occurred in understanding the roles of these proteins and cilia in bone development and remodeling by examining cilia/Ift protein-related human diseases and establishing mouse transgenic models. In this review, we describe current advances in the understanding of the cilia/Ift structure and function. We further summarize cilia/Ift-related human diseases and current mouse models with an emphasis on bone-related phenotypes, cilia morphology, and signaling pathways.
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Affiliation(s)
- Xue Yuan
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, 3435 Main Street, Buffalo, NY, 14214, USA
| | - Shuying Yang
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, 3435 Main Street, Buffalo, NY, 14214, USA
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, 701 Ellicott St, Buffalo, NY, 14203, USA
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26
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Ranjan P, Kashyap RS, Goel M, Veetil SK, Kateriya S. Cellular organelles facilitate dimerization of a newly identified Arf from Chlamydomonas reinhardtii. JOURNAL OF PHYCOLOGY 2014; 50:1137-1145. [PMID: 26988793 DOI: 10.1111/jpy.12245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 08/22/2014] [Indexed: 06/05/2023]
Abstract
GTPases of the Ras superfamily regulate a wide variety of cellular processes including vesicular transport and various secretory pathways of the cell. ADP - ribosylation factor (ARF) belongs to one of the five major families of the Ras superfamily and serves as an important component of vesicle formation and transport machinery of the cells. The binding of GTP to these Arfs and its subsequent hydrolysis, induces conformational changes in these proteins leading to their enzymatic activities. The dimeric form of Arf is associated with membrane pinch-off during vesicle formation. In this report, we have identified an arf gene from the unicellular green alga Chlamydomonas reinhardtii, CrArf, and showed that the oligomeric state of the protein in C. renhardtii is modulated by the cellular membrane environment of the organism. Protein cross-linking experiments showed that the purified recombinant CrArf has the ability to form a dimer. Both the 20-kDa monomeric and 40-kDa dimeric forms of CrArf were recognized from Chlamydomonas total cell lysate (CrTLC) and purified recombinant CrArf by the CrArf specific antibody. The membranous environment of the cell appeared to facilitate dimerization of the CrArf, as dimeric form was found exclusively associated with the membrane bound organelles. The subcellular localization studies in Chlamydomonas suggested that CrArf mainly localized in the cytosol and was mislocalized in vesicle transport machinery inhibitor treated cells. This research sheds light on the importance of the cellular membrane environment for regulating the oligomeric state of CrArf protein in this organism and associated functional role.
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Affiliation(s)
- Peeyush Ranjan
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Rudra Shankar Kashyap
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Manisha Goel
- Department of Biophysics, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Sindhu Kandoth Veetil
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Suneel Kateriya
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
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Schroeder CM, Ostrem JML, Hertz NT, Vale RD. A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region. eLife 2014; 3:e03351. [PMID: 25272277 PMCID: PMC4359372 DOI: 10.7554/elife.03351] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/27/2014] [Indexed: 11/18/2022] Open
Abstract
Cytoplasmic dynein, a microtubule-based motor protein, transports many intracellular cargos by means of its light intermediate chain (LIC). In this study, we have determined the crystal structure of the conserved LIC domain, which binds the motor heavy chain, from a thermophilic fungus. We show that the LIC has a Ras-like fold with insertions that distinguish it from Ras and other previously described G proteins. Despite having a G protein fold, the fungal LIC has lost its ability to bind nucleotide, while the human LIC1 binds GDP preferentially over GTP. We show that the LIC G domain binds the dynein heavy chain using a conserved patch of aromatic residues, whereas the less conserved C-terminal domain binds several Rab effectors involved in membrane transport. These studies provide the first structural information and insight into the evolutionary origin of the LIC as well as revealing how this critical subunit connects the dynein motor to cargo. DOI:http://dx.doi.org/10.7554/eLife.03351.001 Living cells are constantly bustling with activity. They take in nutrients, carefully split their genetic information between new cells when they divide, and move their internal components into the right positions. To move these cargos around, the cell uses proteins—such as dynein—that essentially walks along the cell's internal scaffolding by making step-like movements. However, how a dynein motor protein is tethered to its cargo is not known in detail. One part of the dynein structure thought to play an important role in binding the motor to its cargo is called the light intermediate chain (LIC). Schroeder et al. used X-ray crystallography to solve the structure of the light intermediate chain of dynein motors from a fungus. This information with other experimental techniques reveals that the LIC subunit has two distinct regions: one that binds to three different proteins that serve as adapters for cargo attachment, and one that binds to the rest of the dynein motor. The structure of the LIC includes a fold that is also found in many proteins belonging to a family of enzymes called GTPases, suggesting that the LIC evolved from this family. GTPases use a molecule called GTP to release energy and often act as on–off switches for various processes inside cells. However, the fungal LIC subunit cannot bind to molecules called nucleotides—which can act as energy sources—the way GTPases do. This prevents the LIC subunit from acting as a molecular switch. In contrast, the human version of the LIC is able to bind to some nucleotides, in particular one called GDP. However, since the LIC cannot bind to the high-energy nucleotide GTP, the human LICs most likely also do not act as on–off switches: Schroeder et al. instead propose that the LIC may use GDP only to stabilize the protein. It remains to be seen how cargo attachment to the LIC is regulated. Further structural work and biochemistry with the LIC bound to the dynein motor and cargo will provide more insight into the mechanism of intracellular cargo transport. DOI:http://dx.doi.org/10.7554/eLife.03351.002
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Affiliation(s)
- Courtney M Schroeder
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Jonathan M L Ostrem
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Nicholas T Hertz
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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Asante D, Stevenson NL, Stephens DJ. Subunit composition of the human cytoplasmic dynein-2 complex. J Cell Sci 2014; 127:4774-87. [PMID: 25205765 PMCID: PMC4215718 DOI: 10.1242/jcs.159038] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cytoplasmic dynein-2 is the motor for retrograde intraflagellar transport (IFT), and mutations in dynein-2 are known to cause skeletal ciliopathies. Here, we define for the first time the composition of the human cytoplasmic dynein-2 complex. We show that the proteins encoded by the ciliopathy genes WDR34 and WDR60 are bona fide dynein-2 intermediate chains and are both required for dynein-2 function. In addition, we identify TCTEX1D2 as a unique dynein-2 light chain that is itself required for cilia function. We define several subunits common to both dynein-1 and dynein-2, including TCTEX-1 (also known as DYNLT1) and TCTEX-3 (also known as DYNLT3), roadblock-1 (also known as DYNLRB1) and roadblock-2 (also known as DYNLRB2), and LC8-1 and LC8-2 light chains (DYNLL1 and DYNLL2, respectively). We also find that NudCD3 associates with dynein-2 as it does with dynein-1. By contrast, the common dynein-1 regulators dynactin, LIS1 (also known as PAFAH1B1) and BICD2 are not found in association with dynein-2. These data explain why mutations in either WDR34 or WDR60 cause disease, as well as identifying TCTEX1D2 as a candidate ciliopathy gene.
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Affiliation(s)
- David Asante
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Nicola L Stevenson
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - David J Stephens
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
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Asante D, Maccarthy-Morrogh L, Townley AK, Weiss MA, Katayama K, Palmer KJ, Suzuki H, Westlake CJ, Stephens DJ. A role for the Golgi matrix protein giantin in ciliogenesis through control of the localization of dynein-2. J Cell Sci 2013; 126:5189-97. [PMID: 24046448 DOI: 10.1242/jcs.131664] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The correct formation of primary cilia is central to the development and function of nearly all cells and tissues. Cilia grow from the mother centriole by extension of a microtubule core, the axoneme, which is then surrounded with a specialized ciliary membrane that is continuous with the plasma membrane. Intraflagellar transport moves particles along the length of the axoneme to direct assembly of the cilium and is also required for proper cilia function. The microtubule motor, cytoplasmic dynein-2 mediates retrograde transport along the axoneme from the tip to the base; dynein-2 is also required for some aspects of cilia formation. In most cells, the Golgi lies adjacent to the centrioles and key components of the cilia machinery localize to this organelle. Golgi-localized proteins have also been implicated in ciliogenesis and in intraflagellar transport. Here, we show that the transmembrane Golgi matrix protein giantin (GOLGB1) is required for ciliogenesis. We show that giantin is not required for the Rab11-Rabin8-Rab8 pathway that has been implicated in the early stages of ciliary membrane formation. Instead we find that suppression of giantin results in mis-localization of WDR34, the intermediate chain of dynein-2. Highly effective depletion of giantin or WDR34 leads to an inability of cells to form primary cilia. Partial depletion of giantin or of WDR34 leads to an increase in cilia length consistent with the concept that giantin acts through dynein-2. Our data implicate giantin in ciliogenesis through control of dynein-2 localization.
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Affiliation(s)
- David Asante
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
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Schmidts M, Arts HH, Bongers EMHF, Yap Z, Oud MM, Antony D, Duijkers L, Emes RD, Stalker J, Yntema JBL, Plagnol V, Hoischen A, Gilissen C, Forsythe E, Lausch E, Veltman JA, Roeleveld N, Superti-Furga A, Kutkowska-Kazmierczak A, Kamsteeg EJ, Elçioğlu N, van Maarle MC, Graul-Neumann LM, Devriendt K, Smithson SF, Wellesley D, Verbeek NE, Hennekam RCM, Kayserili H, Scambler PJ, Beales PL, Knoers NVAM, Roepman R, Mitchison HM. Exome sequencing identifies DYNC2H1 mutations as a common cause of asphyxiating thoracic dystrophy (Jeune syndrome) without major polydactyly, renal or retinal involvement. J Med Genet 2013; 50:309-23. [PMID: 23456818 PMCID: PMC3627132 DOI: 10.1136/jmedgenet-2012-101284] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/21/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Jeune asphyxiating thoracic dystrophy (JATD) is a rare, often lethal, recessively inherited chondrodysplasia characterised by shortened ribs and long bones, sometimes accompanied by polydactyly, and renal, liver and retinal disease. Mutations in intraflagellar transport (IFT) genes cause JATD, including the IFT dynein-2 motor subunit gene DYNC2H1. Genetic heterogeneity and the large DYNC2H1 gene size have hindered JATD genetic diagnosis. AIMS AND METHODS To determine the contribution to JATD we screened DYNC2H1 in 71 JATD patients JATD patients combining SNP mapping, Sanger sequencing and exome sequencing. RESULTS AND CONCLUSIONS We detected 34 DYNC2H1 mutations in 29/71 (41%) patients from 19/57 families (33%), showing it as a major cause of JATD especially in Northern European patients. This included 13 early protein termination mutations (nonsense/frameshift, deletion, splice site) but no patients carried these in combination, suggesting the human phenotype is at least partly hypomorphic. In addition, 21 missense mutations were distributed across DYNC2H1 and these showed some clustering to functional domains, especially the ATP motor domain. DYNC2H1 patients largely lacked significant extra-skeletal involvement, demonstrating an important genotype-phenotype correlation in JATD. Significant variability exists in the course and severity of the thoracic phenotype, both between affected siblings with identical DYNC2H1 alleles and among individuals with different alleles, which suggests the DYNC2H1 phenotype might be subject to modifier alleles, non-genetic or epigenetic factors. Assessment of fibroblasts from patients showed accumulation of anterograde IFT proteins in the ciliary tips, confirming defects similar to patients with other retrograde IFT machinery mutations, which may be of undervalued potential for diagnostic purposes.
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Affiliation(s)
- Miriam Schmidts
- Molecular Medicine Unit, Birth Defects Research Centre, University College London (UCL) Institute of Child Health, London, UK
| | - Heleen H Arts
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Zhimin Yap
- Molecular Medicine Unit, Birth Defects Research Centre, University College London (UCL) Institute of Child Health, London, UK
| | - Machteld M Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Dinu Antony
- Molecular Medicine Unit, Birth Defects Research Centre, University College London (UCL) Institute of Child Health, London, UK
| | - Lonneke Duijkers
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Department of Physiology, Radboud University Medical Centre Nijmegen, Nijmegen, The Netherlands
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, Leicestershire, UK
| | - Jim Stalker
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jan-Bart L Yntema
- Department of Paediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Vincent Plagnol
- Department of Genetics, Environment and Evolution, UCL Genetics Institute (UGI), University College London, London, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Elisabeth Forsythe
- Molecular Medicine Unit, Birth Defects Research Centre, University College London (UCL) Institute of Child Health, London, UK
| | - Ekkehart Lausch
- Division of Pediatric Genetics, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Nel Roeleveld
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
- Department of Epidemiology, Biostatistics and HTA, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Evidence Based Practice, Radboud University, Nijmegen, The Netherlands
| | - Andrea Superti-Furga
- Department of Pediatrics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Nursel Elçioğlu
- Department of Pediatric Genetics, Marmara University Hospital, Istanbul, Turkey
| | - Merel C van Maarle
- Department of Clinical Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Koenraad Devriendt
- Laboratory for Genetics of Human Development, Department of Human Genetics, KU Leuven University, Leuven, Belgium
| | - Sarah F Smithson
- Department of Clinical Genetics, St. Michael's Hospital, Bristol, UK
| | - Diana Wellesley
- Faculty of Medicine, University of Southampton and Essex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Nienke E Verbeek
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Raoul C M Hennekam
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hulya Kayserili
- Istanbul Medical Faculty, Medical Genetics Department, Istanbul University, Istanbul, Turkey
| | - Peter J Scambler
- Molecular Medicine Unit, Birth Defects Research Centre, University College London (UCL) Institute of Child Health, London, UK
| | - Philip L Beales
- Molecular Medicine Unit, Birth Defects Research Centre, University College London (UCL) Institute of Child Health, London, UK
| | - Nine VAM Knoers
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University, Nijmegen, The Netherlands
| | - Hannah M Mitchison
- Molecular Medicine Unit, Birth Defects Research Centre, University College London (UCL) Institute of Child Health, London, UK
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Arborization of dendrites by developing neocortical neurons is dependent on primary cilia and type 3 adenylyl cyclase. J Neurosci 2013; 33:2626-38. [PMID: 23392690 DOI: 10.1523/jneurosci.2906-12.2013] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The formation of primary cilia is a highly choreographed process that can be disrupted in developing neurons by overexpressing neuromodulatory G-protein-coupled receptors GPCRs or by blocking intraflagellar transport. Here, we examined the effects of overexpressing the ciliary GPCRs, 5HT6 and SSTR3, on cilia structure and the differentiation of neocortical neurons. Neuronal overexpression of 5HT6 and SSTR3 was achieved by electroporating mouse embryo cortex in utero with vectors encoding these receptors. We found that overexpression of ciliary GPCRs in cortical neurons, especially 5HT6, induced the formation of long (>30 μm) and often forked cilia. These changes were associated with increased levels of intraflagellar transport proteins and accelerated ciliogenesis in neonatal neocortex, the induction of which required Kif3a, an anterograde motor critical for cilia protein trafficking and growth. GPCR overexpression also altered the complement of signaling molecules within the cilia. We found that SSTR3 and type III adenylyl cyclase (ACIII), proteins normally enriched in neuronal cilia, were rarely detected in 5HT6-elongated cilia. Intriguingly, the changes in cilia structure were accompanied by changes in neuronal morphology. Specifically, disruption of normal ciliogenesis in developing neocortical neurons, either by overexpressing cilia GPCRs or a dominant-negative form of Kif3a, significantly impaired dendrite outgrowth. Remarkably, coexpression of ACIII with 5HT6 restored ACIII to cilia, normalized cilia structure, and restored dendrite outgrowth, effects that were not observed in neurons coexpressing ACIII and dominant-negative form of Kif3a. Collectively, our data suggest the formation of neuronal dendrites in developing neocortex requires structurally normal cilia enriched with ACIII.
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Yu X, Wallqvist A, Reifman J. Inferring high-confidence human protein-protein interactions. BMC Bioinformatics 2012; 13:79. [PMID: 22558947 PMCID: PMC3416704 DOI: 10.1186/1471-2105-13-79] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 05/04/2012] [Indexed: 01/09/2023] Open
Abstract
Background As numerous experimental factors drive the acquisition, identification, and interpretation of protein-protein interactions (PPIs), aggregated assemblies of human PPI data invariably contain experiment-dependent noise. Ascertaining the reliability of PPIs collected from these diverse studies and scoring them to infer high-confidence networks is a non-trivial task. Moreover, a large number of PPIs share the same number of reported occurrences, making it impossible to distinguish the reliability of these PPIs and rank-order them. For example, for the data analyzed here, we found that the majority (>83%) of currently available human PPIs have been reported only once. Results In this work, we proposed an unsupervised statistical approach to score a set of diverse, experimentally identified PPIs from nine primary databases to create subsets of high-confidence human PPI networks. We evaluated this ranking method by comparing it with other methods and assessing their ability to retrieve protein associations from a number of diverse and independent reference sets. These reference sets contain known biological data that are either directly or indirectly linked to interactions between proteins. We quantified the average effect of using ranked protein interaction data to retrieve this information and showed that, when compared to randomly ranked interaction data sets, the proposed method created a larger enrichment (~134%) than either ranking based on the hypergeometric test (~109%) or occurrence ranking (~46%). Conclusions From our evaluations, it was clear that ranked interactions were always of value because higher-ranked PPIs had a higher likelihood of retrieving high-confidence experimental data. Reducing the noise inherent in aggregated experimental PPIs via our ranking scheme further increased the accuracy and enrichment of PPIs derived from a number of biologically relevant data sets. These results suggest that using our high-confidence protein interactions at different levels of confidence will help clarify the topological and biological properties associated with human protein networks.
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Affiliation(s)
- Xueping Yu
- Biotechnology High-Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, USA
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Palmer KJ, MacCarthy-Morrogh L, Smyllie N, Stephens DJ. A role for Tctex-1 (DYNLT1) in controlling primary cilium length. Eur J Cell Biol 2011; 90:865-71. [PMID: 21700358 DOI: 10.1016/j.ejcb.2011.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 05/03/2011] [Accepted: 05/03/2011] [Indexed: 11/18/2022] Open
Abstract
The microtubule motor complex cytoplasmic dynein is known to be involved in multiple processes including endomembrane organization and trafficking, mitosis, and microtubule organization. The majority of studies of cytoplasmic dynein have focused on the form of the motor that is built around the dynein-1 heavy chain. A second isoform, dynein heavy chain-2, and its specifically associated light intermediate chain, LIC3 (D2LIC), are known to be involved in the formation and function of primary cilia. We have used RNAi in human epithelial cells to define the cytoplasmic dynein subunits that function with dynein heavy chain 2 in primary cilia. We identify the dynein light chain Tctex-1 as a key modulator of cilia length control; depletion of Tctex-1 results in longer cilia as defined by both acetylated tubulin labeling of the axoneme and Rab8a labeling of the cilia membrane. Suppression of dynein heavy chain-2 causes concomitant loss of Tctex-1 and this correlates with an increase in cilia length. Compared to individual depletions, double siRNA depletion of DHC2 and Tctex-1 causes an even greater increase in cilia length. Our data show that Tctex-1 is a key regulator of cilia length and most likely functions as part of dynein-2.
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Affiliation(s)
- Krysten J Palmer
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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Dynein LIC1 localizes to the mitotic spindle and midbody and LIC2 localizes to spindle poles during cell division. Cell Biol Int 2011; 35:171-8. [DOI: 10.1042/cbi20100284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tan SC, Scherer J, Vallee RB. Recruitment of dynein to late endosomes and lysosomes through light intermediate chains. Mol Biol Cell 2010; 22:467-77. [PMID: 21169557 PMCID: PMC3038645 DOI: 10.1091/mbc.e10-02-0129] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cytoplasmic dynein is involved in a wide range of cellular processes, but how it is regulated and how it recognizes an extremely wide range of cargo are incompletely understood. The dynein light intermediate chains, LIC1 and LIC2 (DYNC1LI1 and DYNC1LI2, respectively), have been implicated in cargo binding, but their full range of functions is unknown. Using LIC isoform-specific antibodies, we report the first characterization of their subcellular distribution and identify a specific association with elements of the late endocytic pathway, but not other vesicular compartments. LIC1 and LIC2 RNA interference (RNAi) each specifically disrupts the distribution of lysosomes and late endosomes. Stimulation of dynein-mediated late-endosomal transport by the Rab7-interacting lysosomal protein (RILP) is reversed by LIC1 RNAi, which displaces dynein, but not dynactin, from these structures. Conversely, expression of ΔN-RILP or the dynactin subunit dynamitin each fails to displace dynein, but not dynactin. Thus, using a variety of complementary approaches, our results indicate a novel specific role for the LICs in dynein recruitment to components of the late endocytic pathway.
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Affiliation(s)
- Serena C Tan
- Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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Rumpf C, Cipak L, Novatchkova M, Li Z, Polakova S, Dudas A, Kovacikova I, Miadokova E, Ammerer G, Gregan J. High-throughput knockout screen in Schizosaccharomyces pombe identifies a novel gene required for efficient homolog disjunction during meiosis I. Cell Cycle 2010; 9:1802-8. [PMID: 20404563 DOI: 10.4161/cc.9.9.11526] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Meiosis is the process which produces haploid gametes from diploid precursor cells. This reduction of chromosome number is achieved by two successive divisions. Whereas homologs segregate during meiosis I, sister chromatids segregate during meiosis II. To identify novel proteins required for proper segregation of chromosomes during meiosis, we applied a high-throughput knockout technique to delete 87 S. pombe genes whose expression is upregulated during meiosis and analyzed the mutant phenotypes. Using this approach, we identified a new protein, Dil1, which is required to prevent meiosis I homolog non-disjunction. We show that Dil1 acts in the dynein pathway to promote oscillatory nuclear movement during meiosis.
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Affiliation(s)
- Cornelia Rumpf
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna, Vienna, Austria
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Rashid S, Grzmil P, Drenckhahn JD, Meinhardt A, Adham I, Engel W, Neesen J. Disruption of the murine dynein light chain gene Tcte3-3 results in asthenozoospermia. Reproduction 2010; 139:99-111. [PMID: 19778998 DOI: 10.1530/rep-09-0243] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To elucidate the role of the mouse gene Tcte3 (Tctex2), which encodes a putative light chain of the outer dynein arm of cilia and sperm flagella, we have inactivated this gene in mice using targeted disruption. Breeding of heterozygous males and females resulted in normal litter size; however, we were not able to detect homozygous Tcte3-deficent mice using standard genotype techniques. In fact, our results indicate the presence of at least three highly similar copies of the Tcte3 gene (Tcte3-1, Tcte3-2, and Tcte3-3) in the murine genome. Therefore, quantitative real-time PCR was established to differentiate between mice having one or two targeted Tcte3-3 alleles. By this approach, Tcte3-3(-/-) animals were identified, which were viable and revealed no obvious malformation. Interestingly, some homozygous Tcte3-3-deficient male mice bred with wild-type female produced no offspring while other Tcte3-3-deficient males revealed decreased sperm motility but were fertile. In infertile Tcte3-3(-/-) males, spermatogenesis was affected and sperm motility was reduced, too, resulting in decreased ability of Tcte3-3-deficient spermatozoa to move from the uterus into the oviduct. Impaired flagellar motility is not correlated with any gross defects in the axonemal structure, since outer dynein arms are detectable in sperm of Tcte3-3(-/-) males. However, in infertile males, deficient Tcte3-3 function is correlated with increased apoptosis during male germ cell development, resulting in a reduction of sperm number. Moreover, multiple malformations in developing haploid germ cells are present. Our results support a role of Tcte3-3 in generation of sperm motility as well as in male germ cell differentiation.
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Affiliation(s)
- Sajid Rashid
- Institute of Human Genetics, University of Goettingen, 37073 Goettingen, Germany
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Palmer KJ, Hughes H, Stephens DJ. Specificity of cytoplasmic dynein subunits in discrete membrane-trafficking steps. Mol Biol Cell 2009; 20:2885-99. [PMID: 19386764 DOI: 10.1091/mbc.e08-12-1160] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The cytoplasmic dynein motor complex is known to exist in multiple forms, but few specific functions have been assigned to individual subunits. A key limitation in the analysis of dynein in intact mammalian cells has been the reliance on gross perturbation of dynein function, e.g., inhibitory antibodies, depolymerization of the entire microtubule network, or the use of expression of dominant negative proteins that inhibit dynein indirectly. Here, we have used RNAi and automated image analysis to define roles for dynein subunits in distinct membrane-trafficking processes. Depletion of a specific subset of dynein subunits, notably LIC1 (DYNC1LI1) but not LIC2 (DYNC1LI2), recapitulates a direct block of ER export, revealing that dynein is required to maintain the steady-state composition of the Golgi, through ongoing ER-to-Golgi transport. Suppression of LIC2 but not of LIC1 results in a defect in recycling endosome distribution and cytokinesis. Biochemical analyses also define the role of each subunit in stabilization of the dynein complex; notably, suppression of DHC1 or IC2 results in concomitant loss of Tctex1. Our data demonstrate that LIC1 and LIC2 define distinct dynein complexes that function at the Golgi versus recycling endosomes, respectively, suggesting that functional populations of dynein mediate discrete intracellular trafficking pathways.
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Affiliation(s)
- Krysten J Palmer
- Cell Biology Laboratories, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS81TD, United Kingdom
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Rajagopalan V, Subramanian A, Wilkes DE, Pennock DG, Asai DJ. Dynein-2 affects the regulation of ciliary length but is not required for ciliogenesis in Tetrahymena thermophila. Mol Biol Cell 2009; 20:708-20. [PMID: 19019986 PMCID: PMC2626569 DOI: 10.1091/mbc.e08-07-0746] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 10/28/2008] [Accepted: 11/07/2008] [Indexed: 11/11/2022] Open
Abstract
Eukaryotic cilia and flagella are assembled and maintained by the bidirectional intraflagellar transport (IFT). Studies in alga, nematode, and mouse have shown that the heavy chain (Dyh2) and the light intermediate chain (D2LIC) of the cytoplasmic dynein-2 complex are essential for retrograde intraflagellar transport. In these organisms, disruption of either dynein-2 component results in short cilia/flagella with bulbous tips in which excess IFT particles have accumulated. In Tetrahymena, the expression of the DYH2 and D2LIC genes increases during reciliation, consistent with their roles in IFT. However, the targeted elimination of either DYH2 or D2LIC gene resulted in only a mild phenotype. Both knockout cell lines assembled motile cilia, but the cilia were of more variable lengths and less numerous than wild-type controls. Electron microscopy revealed normally shaped cilia with no swelling and no obvious accumulations of material in the distal ciliary tip. These results demonstrate that dynein-2 contributes to the regulation of ciliary length but is not required for ciliogenesis in Tetrahymena.
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Affiliation(s)
| | | | - David E. Wilkes
- *Department of Biology, Harvey Mudd College, Claremont, CA 91711
| | | | - David J. Asai
- *Department of Biology, Harvey Mudd College, Claremont, CA 91711
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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Pedersen LB, Veland IR, Schrøder JM, Christensen ST. Assembly of primary cilia. Dev Dyn 2008; 237:1993-2006. [PMID: 18393310 DOI: 10.1002/dvdy.21521] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Primary cilia are microtubule-based, hair-like sensory organelles present on the surface of most growth-arrested cells in our body. Recent research has demonstrated a crucial role for primary cilia in regulating vertebrate developmental pathways and tissue homeostasis, and defects in genes involved in primary cilia assembly or function have been associated with a panoply of disorders and diseases, including polycystic kidney disease, left-right asymmetry defects, hydrocephalus, and Bardet Biedl Syndrome. Here we provide an up-to-date review focused on the molecular mechanisms involved in the assembly of primary cilia in vertebrate cells. We present an overview of the early stages of the cilia assembly process, as well as a description of the intraflagellar transport (IFT) system. IFT is a highly conserved process required for assembly of almost all eukaryotic cilia and flagella, and much of our current knowledge about IFT is based on studies performed in Chlamydomonas and Caenorhabditis elegans. Therefore, our review of the IFT literature includes studies performed in these two model organisms. The role of several non-IFT proteins (e.g., centrosomal proteins) in the ciliary assembly process is also discussed.
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Affiliation(s)
- Lotte B Pedersen
- Department of Biology, Section of Cell and Molecular Biology, University of Copenhagen, Copenhagen, Denmark.
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42
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Mische S, He Y, Ma L, Li M, Serr M, Hays TS. Dynein light intermediate chain: an essential subunit that contributes to spindle checkpoint inactivation. Mol Biol Cell 2008; 19:4918-29. [PMID: 18799620 DOI: 10.1091/mbc.e08-05-0483] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The dynein light intermediate chain (LIC) is a subunit unique to the cytoplasmic form of dynein, but how it contributes to dynein function is not fully understood. Previous work has established that the LIC homodimer binds directly to the dynein heavy chain and may mediate the attachment of dynein to centrosomes and other cargoes. Here, we report our characterization of the LIC in Drosophila. Unlike vertebrates, in which two Lic genes encode multiple subunit isoforms, the Drosophila LIC is encoded by a single gene. We determined that the single LIC polypeptide is phosphorylated, and that different phosphoisoforms can assemble into the dynein motor complex. Our mutational analyses demonstrate that, similar to other dynein subunits, the Drosophila LIC is required for zygotic development, germline specification of the oocyte, and mitotic cell division. We show that RNA interference depletion of LIC in Drosophila S2 cells does not block the recruitment of a dynein complex to kinetochores, but it does delay inactivation of Mad2 signaling and mitotic progression. Our observations suggest the LIC contributes to a broad range of dynein functions.
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Affiliation(s)
- Sarah Mische
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
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Yang Z, Wu J. Mouse dynein axonemal intermediate chain 2: cloning and expression. DNA Cell Biol 2008; 27:479-88. [PMID: 18547164 DOI: 10.1089/dna.2008.0752] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ovarian follicular development is a complex process. Investigation of the mechanisms regulating the initiation of follicular growth, and the growth and differentiation of preantral follicles is of great interest. In an effort to clone follicular development-related genes, we selected a partial cDNA fragment by differential display reverse-transcription PCR using total RNA extracted from 5-day-old and 10-day-old mouse ovaries, and its open reading frame was obtained by rapid amplification of cDNA ends. Sequencing showed that the fragment is the mouse dynein axonemal intermediate chain 2 gene (Dnaic2), which has an 87% homology with human DNAI2, a candidate gene for primary ciliary dyskinesia. Northern and western analyses indicate that Dnaic2 produces an approximate 3 kb mRNA that is translated into an approximate 70 kDa protein. The mRNA is predominantly expressed in mouse ovary, testis, and lung. In mouse ovaries, Dnaic2 mRNA was detected at high levels in vivo on day 10, with a subsequent decrease on days 15 and 20, in adult and old ovaries. However, Dnaic2 expression was weak on day 5. Dnaic2 protein was localized on the surface of the oocyte. No obvious fluorescence signal was detected in primordial and primary follicles, while strong signals were detected on the oocyte surface of secondary and antral follicles, in particular for secondary follicles in day 10. These data suggest that Dnaic2 plays a role in ovarian follicular development.
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Affiliation(s)
- Zhaojuan Yang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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45
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Rompolas P, Pedersen LB, Patel-King RS, King SM. Chlamydomonas FAP133 is a dynein intermediate chain associated with the retrograde intraflagellar transport motor. J Cell Sci 2007; 120:3653-65. [PMID: 17895364 DOI: 10.1242/jcs.012773] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intraflagellar transport (IFT) is the bi-directional movement of particles along the length of axonemal outer doublet microtubules and is needed for the assembly and maintenance of eukaryotic cilia and flagella. Retrograde IFT requires cytoplasmic dynein 1b, a motor complex whose organization, structural composition and regulation is poorly understood. We have characterized the product of the Chlamydomonas FAP133 gene that encodes a new WD-repeat protein similar to dynein intermediate chains and homologous to the uncharacterized vertebrate protein WD34. FAP133 is located at the peri-basal body region as well as in punctate structures along the flagella. This protein is associated with the IFT machinery because it is specifically depleted from the flagella of cells with defects in anterograde IFT. Fractionation of flagellar matrix proteins indicates that FAP133 associates with both the LC8 dynein light chain and the IFT dynein heavy chain and light intermediate chain (DHC1b-D1bLIC) motor complex. In the absence of DHC1b or D1bLIC, FAP133 fails to localize at the peri-basal body region but, rather, is concentrated in a region of the cytoplasm near the cell center. Furthermore, we found that FAP133, LC8, DHC1b, D1bLIC, the FLA10 kinesin-2 necessary for anterograde IFT and other IFT scaffold components associate to form a large macromolecular assembly.
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Affiliation(s)
- Panteleimon Rompolas
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030, USA
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46
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Houde C, Dickinson RJ, Houtzager VM, Cullum R, Montpetit R, Metzler M, Simpson EM, Roy S, Hayden MR, Hoodless PA, Nicholson DW. Hippi is essential for node cilia assembly and Sonic hedgehog signaling. Dev Biol 2006; 300:523-33. [PMID: 17027958 PMCID: PMC5053816 DOI: 10.1016/j.ydbio.2006.09.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 08/30/2006] [Accepted: 09/05/2006] [Indexed: 11/28/2022]
Abstract
Hippi functions as an adapter protein that mediates pro-apoptotic signaling from poly-glutamine-expanded huntingtin, an established cause of Huntington disease, to the extrinsic cell death pathway. To explore other functions of Hippi we generated Hippi knock-out mice. This deletion causes randomization of the embryo turning process and heart looping, which are hallmarks of defective left-right (LR) axis patterning. We report that motile monocilia normally present at the surface of the embryonic node, and proposed to initiate the break in LR symmetry, are absent on Hippi-/- embryos. Furthermore, defects in central nervous system development are observed. The Sonic hedgehog (Shh) pathway is downregulated in the neural tube in the absence of Hippi, which results in failure to establish ventral neural cell fate. Together, these findings demonstrate a dual role for Hippi in cilia assembly and Shh signaling during development, in addition to its proposed role in apoptosis signal transduction in the adult brain under pathogenically stressful conditions.
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Affiliation(s)
- Caroline Houde
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
| | - Robin J. Dickinson
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | | | - Rebecca Cullum
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Rachel Montpetit
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Martina Metzler
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Sophie Roy
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
- Merck Research Laboratories, Rahway, New Jersey 07065, USA
| | - Michael R. Hayden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Pamela A. Hoodless
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Donald W. Nicholson
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
- Merck Research Laboratories, Rahway, New Jersey 07065, USA
- Corresponding author. D.N. Merck Research Laboratories, Merck and Co. Inc., RY80Y-370, 126 East Lincoln Avenue, P.O. Box 2000, Rahway, NJ 07065-0900, USA. Fax: +1 732 594 3910. (D.W. Nicholson)
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47
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Follit JA, Tuft RA, Fogarty KE, Pazour GJ. The intraflagellar transport protein IFT20 is associated with the Golgi complex and is required for cilia assembly. Mol Biol Cell 2006; 17:3781-92. [PMID: 16775004 PMCID: PMC1593158 DOI: 10.1091/mbc.e06-02-0133] [Citation(s) in RCA: 387] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 05/09/2006] [Accepted: 06/05/2006] [Indexed: 11/11/2022] Open
Abstract
Eukaryotic cilia are assembled via intraflagellar transport (IFT) in which large protein particles are motored along ciliary microtubules. The IFT particles are composed of at least 17 polypeptides that are thought to contain binding sites for various cargos that need to be transported from their site of synthesis in the cell body to the site of assembly in the cilium. We show here that the IFT20 subunit of the particle is localized to the Golgi complex in addition to the basal body and cilia where all previous IFT particle proteins had been found. In living cells, fluorescently tagged IFT20 is highly dynamic and moves between the Golgi complex and the cilium as well as along ciliary microtubules. Strong knock down of IFT20 in mammalian cells blocks ciliary assembly but does not affect Golgi structure. Moderate knockdown does not block cilia assembly but reduces the amount of polycystin-2 that is localized to the cilia. This work suggests that IFT20 functions in the delivery of ciliary membrane proteins from the Golgi complex to the cilium.
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Affiliation(s)
| | - Richard A. Tuft
- Biomedical Imaging Group, Department of Physiology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Kevin E. Fogarty
- Biomedical Imaging Group, Department of Physiology, University of Massachusetts Medical School, Worcester, MA 01605
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48
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Pfister KK, Shah PR, Hummerich H, Russ A, Cotton J, Annuar AA, King SM, Fisher EMC. Genetic analysis of the cytoplasmic dynein subunit families. PLoS Genet 2006; 2:e1. [PMID: 16440056 PMCID: PMC1331979 DOI: 10.1371/journal.pgen.0020001] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cytoplasmic dyneins, the principal microtubule minus-end-directed motor proteins of the cell, are involved in many essential cellular processes. The major form of this enzyme is a complex of at least six protein subunits, and in mammals all but one of the subunits are encoded by at least two genes. Here we review current knowledge concerning the subunits, their interactions, and their functional roles as derived from biochemical and genetic analyses. We also carried out extensive database searches to look for new genes and to clarify anomalies in the databases. Our analysis documents evolutionary relationships among the dynein subunits of mammals and other model organisms, and sheds new light on the role of this diverse group of proteins, highlighting the existence of two cytoplasmic dynein complexes with distinct cellular roles.
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Affiliation(s)
- K Kevin Pfister
- Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA.
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49
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Vallee RB, Höök P. Autoinhibitory and other autoregulatory elements within the dynein motor domain. J Struct Biol 2006; 156:175-81. [PMID: 16647270 DOI: 10.1016/j.jsb.2006.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 02/02/2006] [Accepted: 02/17/2006] [Indexed: 11/17/2022]
Abstract
The dyneins are a family of microtubule motor proteins. The motor domain, which represents the C-terminal 2/3 of the dynein heavy chain, exhibits homology to the AAA family of ATPases. It consists of a ring of six related but divergent AAA+ units, with two substantial sized protruding projections, the stem, or tail, which anchors the protein to diverse subcellular sites, and the stalk, which binds microtubules. This article reviews recent efforts to probe the mechanism by which the dyneins produce force, and work from the authors' lab regarding long-range conformational regulation of dynein enzymatic activity.
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Affiliation(s)
- Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, P and S 15-410, 630 W. 168th St., New York, NY 10032, USA.
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50
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Colantonio JR, Bekker JM, Kim SJ, Morrissey KM, Crosbie RH, Hill KL. Expanding the Role of the Dynein Regulatory Complex to Non-Axonemal Functions: Association of GAS11 with the Golgi Apparatus. Traffic 2006; 7:538-48. [PMID: 16643277 DOI: 10.1111/j.1600-0854.2006.00411.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The mammalian GAS11 gene is a candidate tumor suppressor of unknown function that was previously identified as one of several genes upregulated upon growth arrest. Interestingly, although GAS11 homologs in Trypanosoma brucei (trypanin) and Chlamydomonas reinhardtii (PF2) are integral components of the flagellar axoneme and are necessary for regulating flagellar beat, the GAS11 gene was discovered based on its expression in cells that do not assemble a motile cilium. This suggests that GAS11 function might not be restricted to the cilium. To investigate this possibility, we generated GAS11-specific antibodies and demonstrate here that GAS11 is expressed in a variety of mammalian cells that lack a motile cilium. In COS7 cells, GAS11 is associated with the detergent-insoluble cytoskeleton and exhibits a juxtanuclear localization that overlaps with the pericentrosomal Golgi apparatus. This localization is dependent upon intact microtubules and is cell-cycle regulated, such that GAS11 is dispersed throughout the cytoplasm as cells progress through mitosis. GAS11 remains associated with Golgi fragments following depolymerization of cytoplasmic microtubules but is dispersed upon disruption of the Golgi with brefeldin A. These data suggest that GAS11 is associated with the Golgi apparatus. In support of this, recombinant GAS11 binds Golgi membranes in vitro. In growth-arrested mIMCD3 cells, GAS11 co-localizes with gamma-tubulin at the base of the primary cilium. The pericentrosomal Golgi apparatus and base of the cilium both represent convergence points for microtubule minus ends and correspond to sites where dynein regulation is required. The algal GAS11 homolog functions as part of a dynein regulatory complex (DRC) in the axoneme (Rupp and Porter. J Cell Biol 2003;162:47-57) and our findings suggest that components of this axonemal dynein regulatory system have been adapted in mammalian cells to participate in non-axonemal functions.
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Affiliation(s)
- Jessica R Colantonio
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
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