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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024:e0000624. [PMID: 38995044 DOI: 10.1128/mmbr.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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2
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Jühlen R, Fahrenkrog B. From the sideline: Tissue-specific nucleoporin function in health and disease, an update. FEBS Lett 2023; 597:2750-2768. [PMID: 37873737 DOI: 10.1002/1873-3468.14761] [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: 08/10/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
The subcellular compartmentalisation of eukaryotic cells requires selective exchange between the cytoplasm and the nucleus. Intact nucleocytoplasmic transport is vital for normal cell function and mutations in the executing machinery have been causally linked to human disease. Central players in nucleocytoplasmic exchange are nuclear pore complexes (NPCs), which are built from ~30 distinct proteins collectively termed nucleoporins. Aberrant nucleoporin expression was detected in human cancers and autoimmune diseases since quite some time, while it was through the increasing use of next generation sequencing that mutations in nucleoporin genes associated with mainly rare hereditary diseases were revealed. The number of newly identified mutations is steadily increasing, as is the number of diseases. Mutational hotspots have emerged: mutations in the scaffold nucleoporins seemingly affect primarily inner organs, such as heart, kidney, and ovaries, whereas genetic alterations in peripheral, cytoplasmic nucleoporins affect primarily the central nervous system and development. In this review, we summarise latest insights on altered nucleoporin function in the context of human hereditary disorders, with a focus on those where mechanistic insights are beginning to emerge.
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Affiliation(s)
- Ramona Jühlen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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3
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Moruzzi N, Leibiger B, Barker CJ, Leibiger IB, Berggren PO. Novel aspects of intra-islet communication: Primary cilia and filopodia. Adv Biol Regul 2023; 87:100919. [PMID: 36266190 DOI: 10.1016/j.jbior.2022.100919] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022]
Abstract
Pancreatic islets are micro-organs composed of a mixture of endocrine and non-endocrine cells, where the former secrete hormones and peptides necessary for metabolic homeostasis. Through vasculature and innervation the cells within the islets are in communication with the rest of the body, while they interact with each other through juxtacrine, paracrine and autocrine signals, resulting in fine-tuned sensing and response to stimuli. In this context, cellular protrusion in islet cells, such as primary cilia and filopodia, have gained attention as potential signaling hubs. During the last decade, several pieces of evidence have shown how the primary cilium is required for islet vascularization, function and homeostasis. These findings have been possible thanks to the development of ciliary/basal body specific knockout models and technological advances in microscopy, which allow longitudinal monitoring of engrafted islets transplanted in the anterior chamber of the eye in living animals. Using this technique in combination with optogenetics, new potential paracrine interactions have been suggested. For example, reshaping and active movement of filopodia-like protrusions of δ-cells were visualized in vivo, suggesting a continuous cell remodeling to increase intercellular contacts. In this review, we discuss these recent discoveries regarding primary cilia and filopodia and their role in islet homeostasis and intercellular islet communication.
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Affiliation(s)
- Noah Moruzzi
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, 171 76, Stockholm, Sweden.
| | - Barbara Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Christopher J Barker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Ingo B Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, 171 76, Stockholm, Sweden.
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Moruzzi N, Valladolid-Acebes I, Kannabiran SA, Bulgaro S, Burtscher I, Leibiger B, Leibiger IB, Berggren PO, Brismar K. Mitochondrial impairment and intracellular reactive oxygen species alter primary cilia morphology. Life Sci Alliance 2022; 5:5/12/e202201505. [PMID: 36104081 PMCID: PMC9475181 DOI: 10.26508/lsa.202201505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
This work shows how altering energetic status and promoting intracellular/mitochondrial ROS induces cell-dependent ciliary impairments, which is relevant in diseases characterized by these features. Primary cilia have recently emerged as cellular signaling organelles. Their homeostasis and function require a high amount of energy. However, how energy depletion and mitochondria impairment affect cilia have barely been addressed. We first studied the spatial relationship between a mitochondria subset in proximity to the cilium in vitro, finding similar mitochondrial activity measured as mitochondrial membrane potential compared with the cellular network. Next, using common primary cilia cell models and inhibitors of mitochondrial energy production, we found alterations in cilia number and/or length due to energy depletion and mitochondrial reactive oxygen species (ROS) overproduction. Finally, by using a mouse model of type 2 diabetes mellitus, we provided in vivo evidence that cilia morphology is impaired in diabetic nephropathy, which is characterized by ROS overproduction and impaired mitochondrial metabolism. In conclusion, we showed that energy imbalance and mitochondrial ROS affect cilia morphology and number, indicating that conditions characterized by mitochondria and radicals imbalances might lead to ciliary impairment.
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Affiliation(s)
- Noah Moruzzi
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Ismael Valladolid-Acebes
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sukanya A Kannabiran
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sara Bulgaro
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Barbara Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ingo B Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kerstin Brismar
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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5
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Doornbos C, Roepman R. Moonlighting of mitotic regulators in cilium disassembly. Cell Mol Life Sci 2021; 78:4955-4972. [PMID: 33860332 PMCID: PMC8233288 DOI: 10.1007/s00018-021-03827-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/03/2021] [Accepted: 03/27/2021] [Indexed: 02/07/2023]
Abstract
Correct timing of cellular processes is essential during embryological development and to maintain the balance between healthy proliferation and tumour formation. Assembly and disassembly of the primary cilium, the cell’s sensory signalling organelle, are linked to cell cycle timing in the same manner as spindle pole assembly and chromosome segregation. Mitotic processes, ciliary assembly, and ciliary disassembly depend on the centrioles as microtubule-organizing centres (MTOC) to regulate polymerizing and depolymerizing microtubules. Subsequently, other functional protein modules are gathered to potentiate specific protein–protein interactions. In this review, we show that a significant subset of key mitotic regulator proteins is moonlighting at the cilium, among which PLK1, AURKA, CDC20, and their regulators. Although ciliary assembly defects are linked to a variety of ciliopathies, ciliary disassembly defects are more often linked to brain development and tumour formation. Acquiring a better understanding of the overlap in regulators of ciliary disassembly and mitosis is essential in finding therapeutic targets for the different diseases and types of tumours associated with these regulators.
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Affiliation(s)
- Cenna Doornbos
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. .,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Roy K, Marin EP. Lipid Modifications in Cilia Biology. J Clin Med 2019; 8:jcm8070921. [PMID: 31252577 PMCID: PMC6678300 DOI: 10.3390/jcm8070921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/22/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022] Open
Abstract
Cilia are specialized cellular structures with distinctive roles in various signaling cascades. Ciliary proteins need to be trafficked to the cilium to function properly; however, it is not completely understood how these proteins are delivered to their final localization. In this review, we will focus on how different lipid modifications are important in ciliary protein trafficking and, consequently, regulation of signaling pathways. Lipid modifications can play a variety of roles, including tethering proteins to the membrane, aiding trafficking through facilitating interactions with transporter proteins, and regulating protein stability and abundance. Future studies focusing on the role of lipid modifications of ciliary proteins will help our understanding of how cilia maintain specific protein pools strictly connected to their functions.
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Affiliation(s)
- Kasturi Roy
- Department of Internal Medicine, Section of Nephrology, Yale School of Medicine, PO Box 208029, New Haven, CT 06520-8029, USA.
| | - Ethan P Marin
- Department of Internal Medicine, Section of Nephrology, Yale School of Medicine, PO Box 208029, New Haven, CT 06520-8029, USA
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7
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Moonlighting nuclear pore proteins: tissue-specific nucleoporin function in health and disease. Histochem Cell Biol 2018; 150:593-605. [PMID: 30361777 DOI: 10.1007/s00418-018-1748-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2018] [Indexed: 12/14/2022]
Abstract
The nuclear pore complex is the main transportation hub for exchange between the cytoplasm and the nucleus. It is built from nucleoporins that form distinct subcomplexes to establish this huge protein complex in the nuclear envelope. Malfunctioning of nucleoporins is well known in human malignancies, such as gene fusions of NUP214 and NUP98 in hematological neoplasms and overexpression of NUP88 in a variety of human cancers. In the past decade, the incremental utilization of next-generation sequencing has unraveled mutations in nucleoporin genes in the context of an increasing number of hereditary diseases, often in a tissue-specific manner. It emerges that, on one hand, the central nervous system and the heart are particularly sensitive to mutations in nucleoporin genes. On the other hand, nucleoporins forming the scaffold structure of the nuclear pore complex are eminently mutation-prone. These novel and exciting associations between nucleoporins and human diseases emphasize the need to shed light on these unanticipated tissue-specific roles of nucleoporins that may go well beyond their role in nucleocytoplasmic transport. In this review, the current insights into altered nucleoporin function associated with human hereditary disorders will be discussed.
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8
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Leal-Esteban LC, Rothé B, Fortier S, Isenschmid M, Constam DB. Role of Bicaudal C1 in renal gluconeogenesis and its novel interaction with the CTLH complex. PLoS Genet 2018; 14:e1007487. [PMID: 29995892 PMCID: PMC6056059 DOI: 10.1371/journal.pgen.1007487] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/23/2018] [Accepted: 06/13/2018] [Indexed: 01/06/2023] Open
Abstract
Altered glucose and lipid metabolism fuel cystic growth in polycystic kidneys, but the cause of these perturbations is unclear. Renal cysts also associate with mutations in Bicaudal C1 (Bicc1) or in its self-polymerizing sterile alpha motif (SAM). Here, we found that Bicc1 maintains normoglycemia and the expression of the gluconeogenic enzymes FBP1 and PEPCK in kidneys. A proteomic screen revealed that Bicc1 interacts with the C-Terminal to Lis-Homology domain (CTLH) complex. Since the orthologous Gid complex in S. cerevisae targets FBP1 and PEPCK for degradation, we mapped the topology among CTLH subunits and found that SAM-mediated binding controls Bicc1 protein levels, whereas Bicc1 inhibited the accumulation of several CTLH subunits. Under the conditions analyzed, Bicc1 increased FBP1 protein levels independently of the CTLH complex. Besides linking Bicc1 to cell metabolism, our findings reveal new layers of complexity in the regulation of renal gluconeogenesis compared to lower eukaryotes. Polycystic kidney diseases (PKD) are incurable inherited chronic disorders marked by fluid-filled cysts that frequently cause renal failure. A glycolytic metabolism reminiscent of cancerous cells accelerates cystic growth, but the mechanism underlying such metabolic re-wiring is poorly understood. PKD-like cystic kidneys also develop in mice that lack the RNA-binding protein Bicaudal-C (Bicc1), and mutations in a single copy of human BICC1 associate with renal cystic dysplasia. Here, we report that Bicc1 regulates renal gluconeogenesis. A screen for interacting factors revealed that Bicc1 binds the C-Terminal to Lis-Homology domain (CTLH) complex, which in lower eukaryotes mediates degradation of gluconeogenic enzymes. By contrast, Bicc1 and the mammalian CTLH complex regulated each other, and Bicc1 stimulated the accumulation of the rate-limiting gluconeogenic enzyme even in cells depleted of CTLH subunits. Our finding that Bicc1 is required for normoglycemia implies that renal gluconeogenesis may be important to inhibit cyst formation.
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Affiliation(s)
- Lucia Carolina Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Simon Fortier
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Manuela Isenschmid
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Daniel B. Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- * E-mail:
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9
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McClure-Begley TD, Klymkowsky MW. Nuclear roles for cilia-associated proteins. Cilia 2017; 6:8. [PMID: 28560031 PMCID: PMC5445336 DOI: 10.1186/s13630-017-0052-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/02/2017] [Indexed: 01/23/2023] Open
Abstract
Cilia appear to be derived, evolutionarily, from structures present in the ancestral (pre-ciliary) eukaryote, such as microtubule-based vesicle trafficking and chromosome segregation systems. Experimental observations suggest that the ciliary gate, the molecular complex that mediates the selective molecular movement between cytoplasmic and ciliary compartments, shares features with nuclear pores. Our hypothesis is that this shared transport machinery is at least partially responsible for the observation that a number of ciliary and ciliogenesis-associated proteins are found within nuclei where they play roles in the regulation of gene expression, DNA repair, and nuclear import and export. Recognizing the potential for such nuclear roles is critical when considering the phenotypic effects that arise from the mutational modification of ciliary proteins.
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Affiliation(s)
- Tristan D McClure-Begley
- Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309 USA
| | - Michael W Klymkowsky
- Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309 USA
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Torrado B, Graña M, Badano JL, Irigoín F. Ciliary Entry of the Hedgehog Transcriptional Activator Gli2 Is Mediated by the Nuclear Import Machinery but Differs from Nuclear Transport in Being Imp-α/β1-Independent. PLoS One 2016; 11:e0162033. [PMID: 27579771 PMCID: PMC5007031 DOI: 10.1371/journal.pone.0162033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 08/16/2016] [Indexed: 01/20/2023] Open
Abstract
Gli2 is the primary transcriptional activator of Hedgehog signalling in mammals. Upon stimulation of the pathway, Gli2 moves into the cilium before reaching the nucleus. However, the mechanisms underlying its entry into the cilium are not completely understood. Since several similarities have been reported between nuclear and ciliary import, we investigated if the nuclear import machinery participates in Gli2 ciliary entry. Here we show that while two conserved classical nuclear localization signals mediate Gli2 nuclear localization via importin (Imp)-α/β1, these sequences are not required for Gli2 ciliary import. However, blocking Imp-mediated transport through overexpression of GTP-locked Ran reduced the percentage of Gli2 positive cilia, an effect that was not explained by increased CRM1-dependent export of Gli2 from the cilium. We explored the participation of Imp-β2 in Gli2 ciliary traffic and observed that this transporter is involved in moving Gli2 into the cilium, as has been described for other ciliary proteins. In addition, our data indicate that Imp-β2 might also collaborate in Gli2 nuclear entry. How does Imp-β2 determine the final destination of a protein that can localize to two distinct subcellular compartments remains an open question. Therefore, our data shows that the nuclear-cytoplasmic shuttling machinery plays a critical role mediating the subcellular distribution of Gli2 and the activation of the pathway, but distinct importins likely play a differential role mediating its ciliary and nuclear translocation.
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Affiliation(s)
- Belén Torrado
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | - Martín Graña
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | - José L. Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | - Florencia Irigoín
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
- Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Gral. Flores 2125, Montevideo CP11800, Uruguay
- * E-mail:
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11
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Dey G, Thattai M, Baum B. On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype. Trends Cell Biol 2016; 26:476-485. [PMID: 27319280 PMCID: PMC4917890 DOI: 10.1016/j.tcb.2016.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 01/16/2023]
Abstract
If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although ‘Loki’ cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon. Eukaryotes are thought to be a product of symbiosis between archaea and bacteria. The recently discovered Lokiarchaeum (‘Loki’) encodes more Eukaryotic Signature Proteins (ESPs) than any other archaeon, making it the closest living relative to the putative ancestor of eukaryotes. Lokiarchaeum is the first prokaryote found to encode small GTPases, gelsolin, BAR domains, and longin domains, leading many to suggest that it might be compartmentalized and be capable of membrane trafficking. Many models for the evolution of eukaryotes invoke an archaeal ancestor that is capable of phagocytosis to explain the entry of the future mitochondrion into the host cell. Understanding the cell biology of Lokiarchaeum will be key to understanding the morphological transitions that characterized the evolution of eukaryotic cellular architecture, but Loki has not yet been cultured or seen.
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Affiliation(s)
- Gautam Dey
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Mukund Thattai
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bengaluru 560065, India
| | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
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Djuric I, Siebrasse JP, Schulze U, Granado D, Schlüter MA, Kubitscheck U, Pavenstädt H, Weide T. The C-terminal domain controls the mobility of Crumbs 3 isoforms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1208-17. [DOI: 10.1016/j.bbamcr.2016.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 01/12/2023]
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Abstract
Growing lines of evidence implicate the small GTPase RAN, its regulators and effectors--predominantly, nuclear transport receptors--in practically all aspects of centrosome biology in mammalian cells. These include duplication licensing, cohesion, positioning, and microtubule-nucleation capacity. RAN cooperates with the protein nuclear export vector exportin 1/CRM1 to recruit scaffolding proteins containing nuclear export sequences that play roles in the structural organization of centrosomes. Together, they also limit centrosome reduplication by regulating the localization of key "licensing" proteins during the centrosome duplication cycle. In parallel, RAN also regulates the capacity of centrosomes to nucleate and organize functional microtubules, and this predominanlty involves importin vectors: many factors regulating microtubule nucleation or function harbor nuclear localization sequences that interact with importin molecules and such interaction inhibits their activity. Active RANGTP binding to importin molecules removes the inhibition and releases microtubule regulatory factors in the free productive form. A dynamic scenario emerges, in which RAN is pivotal in linking spatiotemporal control of centrosome regulators to the cell cycle machinery.
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Affiliation(s)
- Patrizia Lavia
- Institute of Molecular Biology and Pathology, CNR National Research Council of Italy, c/o Sapienza University of Rome, via degli Apuli 4, Rome, 00185, Italy.
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Jiang X, Zhang D, Zhang H, Huang Y, Teng M. Role of Ran-regulated nuclear-cytoplasmic trafficking of pVHL in the regulation of microtubular stability-mediated HIF-1α in hypoxic cardiomyocytes. Sci Rep 2015; 5:9193. [PMID: 25779090 PMCID: PMC4361876 DOI: 10.1038/srep09193] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/25/2015] [Indexed: 12/30/2022] Open
Abstract
Our previous study suggested that microtubule network alteration affects the process of glycolysis in cardiomyocytes (CMs) via the regulation of hypoxia-inducible factor (HIF)-1α during the early stages of hypoxia. However, little is known regarding the underlying mechanisms of microtubule network alteration-induced changes of HIF-1α. The von Hippel–Lindau tumor suppressor protein (pVHL) has been shown to mediate the ubiquitination of HIF-1α in the nuclear compartment prior to HIF-1α exportation to the cytoplasm, and pVHL dynamic nuclear-cytoplasmic trafficking is indicated to be involved in the process of HIF-1α degradation. In this study, by administering different microtubule-stabilizing and -depolymerizing interventions, we demonstrated that microtubule stabilization promoted pVHL nuclear export and drove the translocation of pVHL to the cytoplasm, while microtubule disruption prevented pVHL nuclear export in hypoxic CMs. Moreover, the ratio between nuclear and cytoplasmic pVHL was associated with HIF-1α regulation. Importantly, microtubule network alteration also affected the subcellular localization of Ran, which was involved in the regulation of pVHL nuclear-cytoplasmic trafficking. The above results suggest that the subcellular translocation of pVHL plays an important role in microtubular structure alteration-induced HIF-1α regulation. Interestingly, Ran is involved in the process of pVHL nuclear-cytoplasmic trafficking following microtubule network alteration in hypoxic CMs.
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Affiliation(s)
- Xupin Jiang
- 1] Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The Third Military Medical University, Chongqing, China [2] Department of Burn and Plastic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dongxia Zhang
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The Third Military Medical University, Chongqing, China
| | - Hengshu Zhang
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuesheng Huang
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The Third Military Medical University, Chongqing, China
| | - Miao Teng
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Diener DR, Lupetti P, Rosenbaum JL. Proteomic analysis of isolated ciliary transition zones reveals the presence of ESCRT proteins. Curr Biol 2015; 25:379-384. [PMID: 25578910 DOI: 10.1016/j.cub.2014.11.066] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/13/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
The transition zone (TZ) is a specialized region of the cilium characterized by Y-shaped connectors between the microtubules of the ciliary axoneme and the ciliary membrane [1]. Located near the base of the cilium, the TZ is in the prime location to act as a gate for proteins into and out of the ciliary compartment, a role supported by experimental evidence [2-6]. The importance of the TZ has been underscored by studies showing that mutations affecting proteins located in the TZ result in cilia-related diseases, or ciliopathies, presenting symptoms including renal cysts, retinal degeneration, and situs inversus [7-9]. Some TZ proteins have been identified and shown to interact with each other through coprecipitation studies in vertebrate cells [4, 10, 11] and genetics studies in C. elegans [3]. As a distinct approach to identify TZ proteins, we have taken advantage of the biology of Chlamydomonas to isolate TZs. Proteomic analysis identified 115 proteins, ten of which were known TZ proteins related to ciliopathies, indicating that the preparation was highly enriched for TZs. Interestingly, six proteins of the endosomal sorting complexes required for transport (ESCRT) were also associated with the TZs. Identification of these and other proteins in the TZ will provide new insights into functions of the TZ, as well as candidate ciliopathy genes.
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Affiliation(s)
- Dennis R Diener
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
| | - Pietro Lupetti
- Department of Life Sciences, University of Siena, Siena 53100, Italy
| | - Joel L Rosenbaum
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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Baum DA, Baum B. An inside-out origin for the eukaryotic cell. BMC Biol 2014; 12:76. [PMID: 25350791 PMCID: PMC4210606 DOI: 10.1186/s12915-014-0076-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 09/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the origin of the eukaryotic cell has long been recognized as the single most profound change in cellular organization during the evolution of life on earth, this transition remains poorly understood. Models have always assumed that the nucleus and endomembrane system evolved within the cytoplasm of a prokaryotic cell. RESULTS Drawing on diverse aspects of cell biology and phylogenetic data, we invert the traditional interpretation of eukaryotic cell evolution. We propose that an ancestral prokaryotic cell, homologous to the modern-day nucleus, extruded membrane-bound blebs beyond its cell wall. These blebs functioned to facilitate material exchange with ectosymbiotic proto-mitochondria. The cytoplasm was then formed through the expansion of blebs around proto-mitochondria, with continuous spaces between the blebs giving rise to the endoplasmic reticulum, which later evolved into the eukaryotic secretory system. Further bleb-fusion steps yielded a continuous plasma membrane, which served to isolate the endoplasmic reticulum from the environment. CONCLUSIONS The inside-out theory is consistent with diverse kinds of data and provides an alternative framework by which to explore and understand the dynamic organization of modern eukaryotic cells. It also helps to explain a number of previously enigmatic features of cell biology, including the autonomy of nuclei in syncytia and the subcellular localization of protein N-glycosylation, and makes many predictions, including a novel mechanism of interphase nuclear pore insertion.
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17
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Brasseur A, Bayat S, Chua XL, Zhang Y, Zhou Q, Low BC, He CY. The bi-lobe-associated LRRP1 regulates Ran activity in Trypanosoma brucei. J Cell Sci 2014; 127:4846-56. [PMID: 25217630 DOI: 10.1242/jcs.148015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cilia and flagella are conserved eukaryotic organelles important for motility and sensory. The RanGTPase, best known for nucleocytoplasmic transport functions, may also play a role in protein trafficking into the specialized flagellar/ciliary compartments, although the regulatory mechanisms controlling Ran activity at the flagellum remain unclear. The unicellular parasite Trypanosoma brucei contains a single flagellum necessary for cell movement, division and morphogenesis. Correct flagellum functions require flagellar attachment to the cell body, which is mediated by a specialized flagellum attachment zone (FAZ) complex that is assembled together with the flagellum during the cell cycle. We have previously identified the leucine-rich-repeat protein 1 LRRP1 on a bi-lobe structure at the proximal base of flagellum and FAZ. LRRP1 is essential for bi-lobe and FAZ biogenesis, consequently affecting flagellum-driven cell motility and division. Here, we show that LRRP1 forms a complex with Ran and a Ran-binding protein, and regulates Ran-GTP hydrolysis in T. brucei. In addition to mitotic inhibition, depletion of Ran inhibits FAZ assembly in T. brucei, supporting the presence of a conserved mechanism that involves Ran in the regulation of flagellum functions in an early divergent eukaryote.
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Affiliation(s)
- Anaïs Brasseur
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | - Shima Bayat
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | - Xiu Ling Chua
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | - Yu Zhang
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | | | - Boon Chuan Low
- Singapore Mechanobiology Institute, National University of Singapore, T-Lab, #10-01, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Cynthia Y He
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
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Picariello T, Valentine MS, Yano J, Van Houten J. Reduction of meckelin leads to general loss of cilia, ciliary microtubule misalignment and distorted cell surface organization. Cilia 2014; 3:2. [PMID: 24484742 PMCID: PMC4124839 DOI: 10.1186/2046-2530-3-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meckelin (MKS3), a conserved protein linked to Meckel Syndrome, assists in the migration of centrioles to the cell surface for ciliogenesis. We explored for additional functions of MKS3p using RNA interference (RNAi) and expression of FLAG epitope tagged protein in the ciliated protozoan Paramecium tetraurelia. This cell has a highly organized cell surface with thousands of cilia and basal bodies that are grouped into one or two basal body units delineated by ridges. The highly systematized nature of the P. tetraurelia cell surface provides a research model of MKS and other ciliopathies where changes in ciliary structure, subcellular organization and overall arrangement of the cell surface can be easily observed. We used cells reduced in IFT88 for comparison, as the involvement of this gene's product with cilia maintenance and growth is well understood. RESULTS FLAG-MKS3p was found above the plane of the distal basal body in the transition zone. Approximately 95% of those basal bodies observed had staining for FLAG-MKS3. The RNAi phenotype for MKS3 depleted cells included global shortening and loss of cilia. Basal body structure appeared unaffected. On the dorsal surface, the basal bodies and their associated rootlets appeared rotated out of alignment from the normal anterior-posterior rows. Likewise, cortical units were abnormal in shape and out of alignment from normal rows. A GST pull down using the MKS3 coiled-coil domain suggests previously unidentified interacting partners. CONCLUSIONS Reduction of MKS3p shows that this protein affects development and maintenance of cilia over the entire cell surface. Reduction of MKS3p is most visible on the dorsal surface. The anterior basal body is attached to and moves along the striated rootlet of the posterior basal body in preparation for duplication. We propose that with reduced MKS3p, this attachment and guidance of the basal body is lost. The basal body veers off course, causing basal body rows to be misaligned and units to be misshapen. Rootlets form normally on these misaligned basal bodies but are rotated out of their correct orientation. Our hypothesis is further supported by the identification of novel interacting partners of MKS3p including a kinetodesmal fiber protein, KdB2.
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Affiliation(s)
- Tyler Picariello
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
| | - Megan Smith Valentine
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
| | - Junji Yano
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
| | - Judith Van Houten
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
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Ounjai P, Kim KD, Liu H, Dong M, Tauscher AN, Witkowska HE, Downing KH. Architectural insights into a ciliary partition. Curr Biol 2013; 23:339-44. [PMID: 23375896 DOI: 10.1016/j.cub.2013.01.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 12/12/2012] [Accepted: 01/11/2013] [Indexed: 11/16/2022]
Abstract
Ciliary compartmentalization plays pivotal roles in ciliogenesis and in various signaling pathways. Here we describe a structure at the ciliary base that appears to have all the features required for compartmentalization and which we thus call the "ciliary partitioning system" (CPS). This complex consists of the terminal plate, which serves as a cytosolic "ciliary pore complex" (CPC), and a membrane region well suited to serve as a diffusion barrier. The CPC is a plate-shaped structure containing nine pores through which the microtubule doublets of the basal body pass. Each pore expands from the doublet B-tubule into an opening well suited for the passage of intraflagellar transport particles. The membrane diffusion barrier encompasses an extended region of detergent-resistant periciliary membrane (ciliary pocket) and a ring complex that connects the CPC to the membrane. Proteomics analysis shows involvement of the ciliary pocket in vesicle trafficking, suggesting that this region plays an active role in membrane transport. The CPC and the ring together form a complete partition defining the ciliary boundary.
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Affiliation(s)
- Puey Ounjai
- Donner Laboratory, Life Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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