1
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Chakraborty S, Martinez-Sanchez A, Beck F, Toro-Nahuelpan M, Hwang IY, Noh KM, Baumeister W, Mahamid J. Cryo-ET suggests tubulin chaperones form a subset of microtubule lumenal particles with a role in maintaining neuronal microtubules. Proc Natl Acad Sci U S A 2025; 122:e2404017121. [PMID: 39888918 PMCID: PMC11804619 DOI: 10.1073/pnas.2404017121] [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: 02/27/2024] [Accepted: 11/25/2024] [Indexed: 02/02/2025] Open
Abstract
The functional architecture of the long-lived neuronal microtubule (MT) cytoskeleton is maintained by various MT-associated proteins (MAPs), most of which are known to bind to the MT outer surface. However, electron microscopy (EM) has long ago revealed the presence of particles inside the lumens of neuronal MTs, of yet unknown identity and function. Here, we use cryogenic electron tomography (cryo-ET) to analyze the three-dimensional (3D) organization and structures of MT lumenal particles in primary hippocampal neurons, human induced pluripotent stem cell-derived neurons, and pluripotent and differentiated P19 cells. We obtain in situ density maps of several lumenal particles from the respective cells and detect common structural features underscoring their potential overarching functions. Mass spectrometry-based proteomics combined with structural modeling suggest that a subset of lumenal particles could be tubulin-binding cofactors (TBCs) bound to tubulin monomers. A different subset of smaller particles, which remains unidentified, exhibits densities that bridge across the MT protofilaments. We show that increased lumenal particle concentration within MTs is concomitant with neuronal differentiation and correlates with higher MT curvatures. Enrichment of lumenal particles around MT lattice defects and at freshly polymerized MT open-ends suggests a MT protective role. Together with the identified structural resemblance of a subset of particles to TBCs, these results hint at a role in local tubulin proteostasis for the maintenance of long-lived neuronal MTs.
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Affiliation(s)
- Saikat Chakraborty
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried82152, Germany
| | - Antonio Martinez-Sanchez
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried82152, Germany
- Institute of Neuropathology and Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University Medical Center Göttingen, Göttingen37075, Germany
| | - Florian Beck
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried82152, Germany
- Research group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried82152, Germany
| | - Mauricio Toro-Nahuelpan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - In-Young Hwang
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried82152, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
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2
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Faubert D, Thibault MP, Kmita M, Baskin JM, Gingras AC, Smith MJ, Côté JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. J Cell Sci 2024; 137:jcs262140. [PMID: 38606629 PMCID: PMC11166204 DOI: 10.1242/jcs.262140] [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: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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Affiliation(s)
- Laura Quirion
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Shiying Huang
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gabriela Bernal Astrain
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Regina Strakhova
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Chang Hwa Jo
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yacine Kherdjemil
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | | | - Marie Kmita
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montréal, QC H3G 2M1, Canada
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J. Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
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3
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Thibault MP, Faubert D, Kmita M, Baskin JM, Gingras AC, Smith MJ, Cote JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.01.530598. [PMID: 36909472 PMCID: PMC10002736 DOI: 10.1101/2023.03.01.530598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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4
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Ferreira A, Castanheira P, Escrevente C, Barral DC, Barona T. Membrane trafficking alterations in breast cancer progression. Front Cell Dev Biol 2024; 12:1350097. [PMID: 38533085 PMCID: PMC10963426 DOI: 10.3389/fcell.2024.1350097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/12/2024] [Indexed: 03/28/2024] Open
Abstract
Breast cancer (BC) is the most common type of cancer in women, and remains one of the major causes of death in women worldwide. It is now well established that alterations in membrane trafficking are implicated in BC progression. Indeed, membrane trafficking pathways regulate BC cell proliferation, migration, invasion, and metastasis. The 22 members of the ADP-ribosylation factor (ARF) and the >60 members of the rat sarcoma (RAS)-related in brain (RAB) families of small GTP-binding proteins (GTPases), which belong to the RAS superfamily, are master regulators of membrane trafficking pathways. ARF-like (ARL) subfamily members are involved in various processes, including vesicle budding and cargo selection. Moreover, ARFs regulate cytoskeleton organization and signal transduction. RABs are key regulators of all steps of membrane trafficking. Interestingly, the activity and/or expression of some of these proteins is found dysregulated in BC. Here, we review how the processes regulated by ARFs and RABs are subverted in BC, including secretion/exocytosis, endocytosis/recycling, autophagy/lysosome trafficking, cytoskeleton dynamics, integrin-mediated signaling, among others. Thus, we provide a comprehensive overview of the roles played by ARF and RAB family members, as well as their regulators in BC progression, aiming to lay the foundation for future research in this field. This research should focus on further dissecting the molecular mechanisms regulated by ARFs and RABs that are subverted in BC, and exploring their use as therapeutic targets or prognostic markers.
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Caputo M, Martinelli I, Fini N, Gianferrari G, Simonini C, Trovato R, Santorelli FM, Tessa A, Mandrioli J, Zucchi E. A Variant in TBCD Associated with Motoneuronopathy and Corpus Callosum Hypoplasia: A Case Report. Int J Mol Sci 2023; 24:12386. [PMID: 37569761 PMCID: PMC10418765 DOI: 10.3390/ijms241512386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Mutations in the tubulin-specific chaperon D (TBCD) gene, involved in the assembly and disassembly of the α/β-tubulin heterodimers, have been reported in early-onset progressive neurodevelopment regression, with epilepsy and mental retardation. We describe a rare homozygous variant in TBCD, namely c.881G>A/p.Arg294Gln, in a young woman with a phenotype dominated by distal motorneuronopathy and mild mental retardation, with neuroimaging evidence of corpus callosum hypoplasia. The peculiar phenotype is discussed in light of the molecular interpretation, enriching the literature data on tubulinopathies generated from TBCD mutations.
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Affiliation(s)
- Maria Caputo
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.C.); (G.G.); (C.S.)
| | - Ilaria Martinelli
- Department of Neurosciences, Azienda Ospedaliero-Universitaria Di Modena, Viale Giardini, 1355, 41126 Modena, Italy; (I.M.); (N.F.); (E.Z.)
- Clinical and Experimental PhD Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Nicola Fini
- Department of Neurosciences, Azienda Ospedaliero-Universitaria Di Modena, Viale Giardini, 1355, 41126 Modena, Italy; (I.M.); (N.F.); (E.Z.)
| | - Giulia Gianferrari
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.C.); (G.G.); (C.S.)
| | - Cecilia Simonini
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.C.); (G.G.); (C.S.)
| | - Rosanna Trovato
- Molecular Medicine, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy; (R.T.); (F.M.S.); (A.T.)
| | | | - Alessandra Tessa
- Molecular Medicine, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy; (R.T.); (F.M.S.); (A.T.)
| | - Jessica Mandrioli
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.C.); (G.G.); (C.S.)
- Department of Neurosciences, Azienda Ospedaliero-Universitaria Di Modena, Viale Giardini, 1355, 41126 Modena, Italy; (I.M.); (N.F.); (E.Z.)
| | - Elisabetta Zucchi
- Department of Neurosciences, Azienda Ospedaliero-Universitaria Di Modena, Viale Giardini, 1355, 41126 Modena, Italy; (I.M.); (N.F.); (E.Z.)
- Neuroscience PhD Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
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6
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Li FL, Guan KL. The Arf family GTPases: Regulation of vesicle biogenesis and beyond. Bioessays 2023; 45:e2200214. [PMID: 36998106 PMCID: PMC10282109 DOI: 10.1002/bies.202200214] [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: 11/05/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
The Arf family proteins are best known for their roles in the vesicle biogenesis. However, they also play fundamental roles in a wide range of cellular regulation besides vesicular trafficking, such as modulation of lipid metabolic enzymes, cytoskeleton remodeling, ciliogenesis, lysosomal, and mitochondrial morphology and functions. Growing studies continue to expand the downstream effector landscape of Arf proteins, especially for the less-studied members, revealing new biological functions, such as amino acid sensing. Experiments with cutting-edge technologies and in vivo functional studies in the last decade help to provide a more comprehensive view of Arf family functions. In this review, we summarize the cellular functions that are regulated by at least two different Arf members with an emphasis on those beyond vesicle biogenesis.
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Affiliation(s)
- Fu-Long Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
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7
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Muto V, Benigni F, Magliocca V, Borghi R, Flex E, Pallottini V, Rosa A, Compagnucci C, Tartaglia M. CRISPR/Cas9 and piggyBac Transposon-Based Conversion of a Pathogenic Biallelic TBCD Variant in a Patient-Derived iPSC Line Allows Correction of PEBAT-Related Endophenotypes. Int J Mol Sci 2023; 24:ijms24097988. [PMID: 37175696 PMCID: PMC10178052 DOI: 10.3390/ijms24097988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) have been established as a reliable in vitro disease model system and represent a particularly informative tool when animal models are not available or do not recapitulate the human pathophenotype. The recognized limit in using this technology is linked to some degree of variability in the behavior of the individual patient-derived clones. The development of CRISPR/Cas9-based gene editing solves this drawback by obtaining isogenic iPSCs in which the genetic lesion is corrected, allowing a straightforward comparison with the parental patient-derived iPSC lines. Here, we report the generation of a footprint-free isogenic cell line of patient-derived TBCD-mutated iPSCs edited using the CRISPR/Cas9 and piggyBac technologies. The corrected iPSC line had no genetic footprint after the removal of the selection cassette and maintained its "stemness". The correction of the disease-causing TBCD missense substitution restored proper protein levels of the chaperone and mitotic spindle organization, as well as reduced cellular death, which were used as read-outs of the TBCD KO-related endophenotype. The generated line represents an informative in vitro model to understand the impact of pathogenic TBCD mutations on nervous system development and physiology.
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Affiliation(s)
- Valentina Muto
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Federica Benigni
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
- Department of Science, University Roma Tre, 00146 Rome, Italy
| | - Valentina Magliocca
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Rossella Borghi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Valentina Pallottini
- Department of Science, University Roma Tre, 00146 Rome, Italy
- Neuroendocrinology Metabolism and Neuropharmacology Unit, IRCSS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Alessandro Rosa
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Claudia Compagnucci
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
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8
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Pinho-Correia LM, Prokop A. Maintaining essential microtubule bundles in meter-long axons: a role for local tubulin biogenesis? Brain Res Bull 2023; 193:131-145. [PMID: 36535305 DOI: 10.1016/j.brainresbull.2022.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Axons are the narrow, up-to-meter long cellular processes of neurons that form the biological cables wiring our nervous system. Most axons must survive for an organism's lifetime, i.e. up to a century in humans. Axonal maintenance depends on loose bundles of microtubules that run without interruption all along axons. The continued turn-over and the extension of microtubule bundles during developmental, regenerative or plastic growth requires the availability of α/β-tubulin heterodimers up to a meter away from the cell body. The underlying regulation in axons is poorly understood and hardly features in past and contemporary research. Here we discuss potential mechanisms, particularly focussing on the possibility of local tubulin biogenesis in axons. Current knowledge might suggest that local translation of tubulin takes place in axons, but far less is known about the post-translational machinery of tubulin biogenesis involving three chaperone complexes: prefoldin, CCT and TBC. We discuss functional understanding of these chaperones from a range of model organisms including yeast, plants, flies and mice, and explain what is known from human diseases. Microtubules across species depend on these chaperones, and they are clearly required in the nervous system. However, most chaperones display a high degree of functional pleiotropy, partly through independent functions of individual subunits outside their complexes, thus posing a challenge to experimental studies. Notably, we found hardly any studies that investigate their presence and function particularly in axons, thus highlighting an important gap in our understanding of axon biology and pathology.
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Affiliation(s)
- Liliana Maria Pinho-Correia
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK
| | - Andreas Prokop
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK.
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9
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Gerstner CD, Reed M, Dahl TM, Ying G, Frederick JM, Baehr W. Arf-like Protein 2 (ARL2) Controls Microtubule Neogenesis during Early Postnatal Photoreceptor Development. Cells 2022; 12:147. [PMID: 36611941 PMCID: PMC9818799 DOI: 10.3390/cells12010147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Arf-like protein 2 (ARL2) is a ubiquitously expressed small GTPase with multiple functions. In a cell culture, ARL2 participates with tubulin cofactor D (TBCD) in the neogenesis of tubulin αβ-heterodimers, the building blocks of microtubules. To evaluate this function in the retina, we conditionally deleted ARL2 in mouse retina at two distinct stages, either during the embryonic development (retArl2-/-) or after ciliogenesis specifically in rods (rodArl2-/-). retArl2-/- retina sections displayed distorted nuclear layers and a disrupted microtubule cytoskeleton (MTC) as early as postnatal day 6 (P6). Rod and cone outer segments (OS) did not form. By contrast, the rod ARL2 knockouts were stable at postnatal day 35 and revealed normal ERG responses. Cytoplasmic dynein is reduced in retArl2-/- inner segments (IS), suggesting that dynein may be unstable in the absence of a normal MTC. We investigated the microtubular stability in the absence of either ARL2 (retARL2-/-) or DYNC1H1 (retDync1h1-/-), the dynein heavy chain, and found that both the retArl2-/- and retDync1h1-/- retinas exhibited reduced microtubules and nuclear layer distortion. The results suggest that ARL2 and dynein depend on each other to generate a functional MTC during the early photoreceptor development.
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Affiliation(s)
- Cecilia D. Gerstner
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Michelle Reed
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Tiffanie M. Dahl
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Guoxin Ying
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Jeanne M. Frederick
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Wolfgang Baehr
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
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10
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Yuan H, Chen J, Li N, Miao H, Chen Y, Lyu S, Qiao Y, Yang G, Luo H, Chen L, Mao F, Huang L, He Y, Hu S, Miao C, Qian Y, Feng R. Target-Sequencing of Female Infertility Pathogenic Gene Panel and a Novel TUBB8 Loss-of-Function Mutation. Front Genet 2022; 13:865103. [PMID: 35620457 PMCID: PMC9127544 DOI: 10.3389/fgene.2022.865103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic screening is an important approach for etiology determination and helps to optimize administration protocols in reproductive centers. After the first pathogenic gene of female infertility was reported in 2016, more and more new pathogenic genes were discovered, and we sought to develop an efficient and cost-effective method for genetic screening in patients. In this study, we designed a target-sequencing panel with 22 female infertility-related genes, namely, TUBB8, PATL2, WEE2, and PANX1 and sequenced 68 primary infertility (PI) and recurrent pregnancy loss (RPL) patients. We sequenced 68 samples reaching an average depth of 1559× and detected 3,134 variants. Among them, 62.2% were synonymous single-nucleotide variants (SNVs) and 36.3% were non-synonymous SNVs. The remaining 1.5% are indels (insertions and deletions) and stop-gains. DNAH11 and TUBB8 are the two genes that mutated most frequently. We also found a novel TUBB8 variant (c.898_900del; p.300_300del), proved its loss-of-function mechanism, and profiled the interactome of the wild-type (WT) and mutant TUBB8 proteins. Overall, this target-sequencing method provides an efficient and cost-effective approach for screening in IVF clinics and will support researchers for the discovery of new pathogenic variants.
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Affiliation(s)
- Hongxia Yuan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Jianhua Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Na Li
- The Reproduction Engineer Key Laboratory of Shanxi Health Committee, Department of Reproductive Genetics, Institute of Reproduction and Genetics of Changzhi Medical College, Heping Hospital of Changzhi Medical College, Changzhi, China
| | - Hui Miao
- The Reproduction Engineer Key Laboratory of Shanxi Health Committee, Department of Reproductive Genetics, Institute of Reproduction and Genetics of Changzhi Medical College, Heping Hospital of Changzhi Medical College, Changzhi, China
| | - Yao Chen
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuyan Lyu
- The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Yu Qiao
- The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Guangping Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Hui Luo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Liangliang Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Fei Mao
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lingli Huang
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanni He
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Saifei Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Congxiu Miao
- The Reproduction Engineer Key Laboratory of Shanxi Health Committee, Department of Reproductive Genetics, Institute of Reproduction and Genetics of Changzhi Medical College, Heping Hospital of Changzhi Medical College, Changzhi, China
| | - Yun Qian
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruizhi Feng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Reproductive Medical Center of the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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11
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Complementing the phenotypical spectrum of TUBA1A tubulinopathy and its role in early-onset epilepsies. Eur J Hum Genet 2022; 30:298-306. [PMID: 35017693 PMCID: PMC8904761 DOI: 10.1038/s41431-021-01027-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 12/29/2022] Open
Abstract
TUBA1A tubulinopathy is a rare neurodevelopmental disorder associated with brain malformations as well as early-onset and intractable epilepsy. As pathomechanisms and genotype-phenotype correlations are not completely understood, we aimed to provide further insights into the phenotypic and genetic spectrum. We here present a multicenter case series of ten unrelated individuals from four European countries using systematic MRI re-evaluation, protein structure analysis, and prediction score modeling. In two cases, pregnancy was terminated due to brain malformations. Amongst the eight living individuals, the phenotypic range showed various severity. Global developmental delay and severe motor impairment with tetraparesis was present in 63% and 50% of the subjects, respectively. Epilepsy was observed in 75% of the cases, which showed infantile onset in 83% and a refractory course in 50%. One individual presented a novel TUBA1A-associated electroclinical phenotype with evolvement from early myoclonic encephalopathy to continuous spike-and-wave during sleep. Neuroradiological features comprised a heterogeneous spectrum of cortical and extracortical malformations including rare findings such as cobblestone lissencephaly and subcortical band heterotopia. Two individuals developed hydrocephalus with subsequent posterior infarction. We report four novel and five previously published TUBA1A missense variants whose resulting amino acid substitutions likely affect longitudinal, lateral, and motor protein interactions as well as GTP binding. Assessment of pathogenic and benign variant distributions in synopsis with prediction scores revealed sections of variant enrichment and intolerance to missense variation. We here extend the clinical, neuroradiological, and genetic spectrum of TUBA1A tubulinopathy and provide insights into residue-specific pathomechanisms and genotype-phenotype correlations.
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12
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Bieniussa L, Jain I, Bosch Grau M, Juergens L, Hagen R, Janke C, Rak K. Microtubule and auditory function - an underestimated connection. Semin Cell Dev Biol 2022; 137:74-86. [PMID: 35144861 DOI: 10.1016/j.semcdb.2022.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
Abstract
The organ of Corti, located in the cochlea within the inner ear is the receptor organ for hearing. It converts auditory signals into neuronal action potentials that are transmitted to the brain for further processing. The mature organ of Corti consists of a variety of highly differentiated sensory cells that fulfil unique tasks in the processing of auditory signals. The actin and microtubule cytoskeleton play essential function in hearing, however so far, more attention has been paid to the role of actin. Microtubules play important roles in maintaining cellular structure and intracellular transport in virtually all eukaryotic cells. Their functions are controlled by interactions with a large variety of microtubule-associated proteins (MAPs) and molecular motors. Current advances show that tubulin posttranslational modifications, as well as tubulin isotypes could play key roles in modulating microtubule properties and functions in cells. These mechanisms could have various effects on the stability and functions of microtubules in the highly specialised cells of the cochlea. Here, we review the current understanding of the role of microtubule-regulating mechanisms in the function of the cochlea and their implications for hearing, which highlights the importance of microtubules in the field of hearing research.
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Affiliation(s)
- Linda Bieniussa
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery and the Comprehensive Hearing Center, University of Würzburg, Germany
| | - Ipsa Jain
- Institute of Stem cell Biology and Regenerative Medicine, Bangalore, India
| | - Montserrat Bosch Grau
- Genetics and Physiology of Hearing Laboratory, Institute Pasteur, 75015 Paris, France
| | - Lukas Juergens
- Department of Ophthalmology, University of Duesseldorf, Germany
| | - Rudolf Hagen
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery and the Comprehensive Hearing Center, University of Würzburg, Germany
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Kristen Rak
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery and the Comprehensive Hearing Center, University of Würzburg, Germany.
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13
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Turn RE, Hu Y, Dewees SI, Devi N, East MP, Hardin KR, Khatib T, Linnert J, Wolfrum U, Lim MJ, Casanova JE, Caspary T, Kahn RA. The ARF GAPs ELMOD1 and ELMOD3 act at the Golgi and cilia to regulate ciliogenesis and ciliary protein traffic. Mol Biol Cell 2022; 33:ar13. [PMID: 34818063 PMCID: PMC9236152 DOI: 10.1091/mbc.e21-09-0443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/11/2022] Open
Abstract
ELMODs are a family of three mammalian paralogues that display GTPase-activating protein (GAP) activity toward a uniquely broad array of ADP-ribosylation factor (ARF) family GTPases that includes ARF-like (ARL) proteins. ELMODs are ubiquitously expressed in mammalian tissues, highly conserved across eukaryotes, and ancient in origin, being present in the last eukaryotic common ancestor. We described functions of ELMOD2 in immortalized mouse embryonic fibroblasts (MEFs) in the regulation of cell division, microtubules, ciliogenesis, and mitochondrial fusion. Here, using similar strategies with the paralogues ELMOD1 and ELMOD3, we identify novel functions and locations of these cell regulators and compare them to those of ELMOD2, allowing the determination of functional redundancy among the family members. We found strong similarities in phenotypes resulting from deletion of either Elmod1 or Elmod3 and marked differences from those arising in Elmod2 deletion lines. Deletion of either Elmod1 or Elmod3 results in the decreased ability of cells to form primary cilia, loss of a subset of proteins from cilia, and accumulation of some ciliary proteins at the Golgi, predicted to result from compromised traffic from the Golgi to cilia. These phenotypes are reversed upon activating mutant expression of either ARL3 or ARL16, linking their roles to ELMOD1/3 actions.
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Affiliation(s)
- Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305
| | - Yihan Hu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China
| | - Skylar I. Dewees
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Narra Devi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Michael P. East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Katherine R. Hardin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Tala Khatib
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Joshua Linnert
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Michael J. Lim
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - James E. Casanova
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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14
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Systematic Analysis of Clemastine, a Candidate Apicomplexan Parasite-Selective Tubulin-Targeting Agent. Int J Mol Sci 2021; 23:ijms23010068. [PMID: 35008492 PMCID: PMC8744746 DOI: 10.3390/ijms23010068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Apicomplexan parasites, such as Toxoplasma gondii, Plasmodium spp., Babesia spp., and Cryptosporidium spp., cause significant morbidity and mortality. Existing treatments are problematic due to toxicity and the emergence of drug-resistant parasites. Because protozoan tubulin can be selectively disrupted by small molecules to inhibit parasite growth, we assembled an in vitro testing cascade to fully delineate effects of candidate tubulin-targeting drugs on Toxoplasma gondii and vertebrate host cells. Using this analysis, we evaluated clemastine, an antihistamine that has been previously shown to inhibit Plasmodium growth by competitively binding to the CCT/TRiC tubulin chaperone as a proof-of-concept. We concurrently analyzed astemizole, a distinct antihistamine that blocks heme detoxification in Plasmodium. Both drugs have EC50 values of ~2 µM and do not demonstrate cytotoxicity or vertebrate microtubule disruption at this concentration. Parasite subpellicular microtubules are shortened by treatment with either clemastine or astemizole but not after treatment with pyrimethamine, indicating that this effect is not a general response to antiparasitic drugs. Immunoblot quantification indicates that the total α-tubulin concentration of 0.02 pg/tachyzoite does not change with clemastine treatment. In conclusion, the testing cascade allows profiling of small-molecule effects on both parasite and vertebrate cell viability and microtubule integrity.
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15
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Jaimon E, Tripathi A, Khurana A, Ghosh D, Sugatha J, Datta S. Binding with heat shock cognate protein HSC70 fine-tunes the Golgi association of the small GTPase ARL5B. J Biol Chem 2021; 297:101422. [PMID: 34798070 PMCID: PMC8661063 DOI: 10.1016/j.jbc.2021.101422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022] Open
Abstract
ARL5B, an ARF-like small GTPase localized to the trans-Golgi, is known for regulating endosome-Golgi trafficking and promoting the migration and invasion of breast cancer cells. Although a few interacting partners have been identified, the mechanism of the shuttling of ARL5B between the Golgi membrane and the cytosol is still obscure. Here, using GFP-binding protein (GBP) pull-down followed by mass spectrometry, we identified heat shock cognate protein (HSC70) as an additional interacting partner of ARL5B. Our pull-down and isothermal titration calorimetry (ITC)-based studies suggested that HSC70 binds to ARL5B in an ADP-dependent manner. Additionally, we showed that the N-terminal helix and the nucleotide status of ARL5B contribute to its recognition by HSC70. The confocal microscopy and cell fractionation studies in MDA-MB-231 breast cancer cells revealed that the depletion of HSC70 reduces the localization of ARL5B to the Golgi. Using in vitro reconstitution approach, we provide evidence that HSC70 fine-tunes the association of ARL5B with Golgi membrane. Finally, we demonstrated that the interaction between ARL5B and HSC70 is important for the localization of cation independent mannose-6-phosphate receptor (CIMPR) at Golgi. Collectively, we propose a mechanism by which HSC70, a constitutively expressed chaperone, modulates the Golgi association of ARL5B, which in turn has implications for the Golgi-associated functions of this GTPase.
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Affiliation(s)
- Ebsy Jaimon
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Aashutosh Tripathi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Arohi Khurana
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Dipanjana Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Jini Sugatha
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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16
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Quitmann CM, Rust S, Reunert J, Biskup S, Fiedler B, Marquardt T. Tubulin Folding Cofactor D Deficiency: Missing the Diagnosis With Whole Exome Sequencing. Child Neurol Open 2021; 8:2329048X211034969. [PMID: 34423067 PMCID: PMC8370890 DOI: 10.1177/2329048x211034969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Two siblings with an early onset of a neurodegenerative disease were presented
with muscular hypotonia, secondary microcephaly, and severe developmental delay.
Seizures were refractory to treatment but could be controlled with a ketogenic
diet. Over the course of 5 years, whole exome sequencing (WES) was performed
twice in both children. The first time the diagnosis was missed. The next one
revealed compound heterozygous mutations in the gene coding for the tubulin
folding cofactor D. Technical improvements in WES mandated a new investigation
after a few years in children where the diagnosis has not been found.
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Affiliation(s)
| | - Stephan Rust
- University Children's Hospital Muenster, Muenster, Germany
| | - Janine Reunert
- University Children's Hospital Muenster, Muenster, Germany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics, Tübingen, Germany
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17
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Vargová R, Wideman JG, Derelle R, Klimeš V, Kahn RA, Dacks JB, Eliáš M. A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family. Genome Biol Evol 2021; 13:6319025. [PMID: 34247240 PMCID: PMC8358228 DOI: 10.1093/gbe/evab157] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.
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Affiliation(s)
- Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Romain Derelle
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, United Kingdom
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
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18
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Turn RE, Linnert J, Gigante ED, Wolfrum U, Caspary T, Kahn RA. Roles for ELMOD2 and Rootletin in ciliogenesis. Mol Biol Cell 2021; 32:800-822. [PMID: 33596093 PMCID: PMC8108518 DOI: 10.1091/mbc.e20-10-0635] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ELMOD2 is a GTPase-activating protein with uniquely broad specificity for ARF family GTPases. We previously showed that it acts with ARL2 in mitochondrial fusion and microtubule stability and with ARF6 during cytokinesis. Mouse embryonic fibroblasts deleted for ELMOD2 also displayed changes in cilia-related processes including increased ciliation, multiciliation, ciliary morphology, ciliary signaling, centrin accumulation inside cilia, and loss of rootlets at centrosomes with loss of centrosome cohesion. Increasing ARL2 activity or overexpressing Rootletin reversed these defects, revealing close functional links between the three proteins. This was further supported by the findings that deletion of Rootletin yielded similar phenotypes, which were rescued upon increasing ARL2 activity but not ELMOD2 overexpression. Thus, we propose that ARL2, ELMOD2, and Rootletin all act in a common pathway that suppresses spurious ciliation and maintains centrosome cohesion. Screening a number of markers of steps in the ciliation pathway supports a model in which ELMOD2, Rootletin, and ARL2 act downstream of TTBK2 and upstream of CP110 to prevent spurious release of CP110 and to regulate ciliary vesicle docking. These data thus provide evidence supporting roles for ELMOD2, Rootletin, and ARL2 in the regulation of ciliary licensing.
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Affiliation(s)
- Rachel E Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322.,Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Joshua Linnert
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, Mainz 655099, Germany
| | - Eduardo D Gigante
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.,Neuroscience Graduate Program, Emory University, Atlanta, GA 30322
| | - Uwe Wolfrum
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, Mainz 655099, Germany
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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19
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Juergens L, Bieniussa L, Voelker J, Hagen R, Rak K. Spatio-temporal distribution of tubulin-binding cofactors and posttranslational modifications of tubulin in the cochlea of mice. Histochem Cell Biol 2020; 154:671-681. [PMID: 32712744 PMCID: PMC7723944 DOI: 10.1007/s00418-020-01905-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The five tubulin-binding cofactors (TBC) are involved in tubulin synthesis and the formation of microtubules. Their importance is highlighted by various diseases and syndromes caused by dysfunction or mutation of these proteins. Posttranslational modifications (PTMs) of tubulin promote different characteristics, including stability-creating subpopulations of tubulin. Cell- and time-specific distribution of PTMs has only been investigated in the organ of Corti in gerbils. The aim of the presented study was to investigate the cell type-specific and time-specific expression patterns of TBC proteins and PTMs for the first time in murine cochleae over several developmental stages. For this, murine cochleae were investigated at the postnatal (P) age P1, P7 and P14 by immunofluorescence analysis. The investigations revealed several profound interspecies differences in the distribution of PTMs between gerbil and mouse. Furthermore, this is the first study to describe the spatio-temporal distribution of TBCs in any tissue ever showing a volatile pattern of expression. The expression analysis of TBC proteins and PTMs of tubulin reveals that these proteins play a role in the physiological development of the cochlea and might be essential for hearing.
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Affiliation(s)
- Lukas Juergens
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, The Comprehensive Hearing Center, University of Wuerzburg, Josef-Schneider-Strasse 11, 97080, Wuerzburg, Germany
- Department of Ophthalmology, University of Duesseldorf, Duesseldorf, Germany
| | - Linda Bieniussa
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, The Comprehensive Hearing Center, University of Wuerzburg, Josef-Schneider-Strasse 11, 97080, Wuerzburg, Germany
| | - Johannes Voelker
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, The Comprehensive Hearing Center, University of Wuerzburg, Josef-Schneider-Strasse 11, 97080, Wuerzburg, Germany
| | - Rudolf Hagen
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, The Comprehensive Hearing Center, University of Wuerzburg, Josef-Schneider-Strasse 11, 97080, Wuerzburg, Germany
| | - Kristen Rak
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, The Comprehensive Hearing Center, University of Wuerzburg, Josef-Schneider-Strasse 11, 97080, Wuerzburg, Germany.
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20
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Neurobiology of environmental enrichment in pigs: hanges in monoaminergic neurotransmitters in several brain areas and in the hippocampal proteome. J Proteomics 2020; 229:103943. [DOI: 10.1016/j.jprot.2020.103943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/18/2020] [Accepted: 08/09/2020] [Indexed: 02/08/2023]
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21
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Fisher S, Kuna D, Caspary T, Kahn RA, Sztul E. ARF family GTPases with links to cilia. Am J Physiol Cell Physiol 2020; 319:C404-C418. [PMID: 32520609 PMCID: PMC7500214 DOI: 10.1152/ajpcell.00188.2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The ADP-ribosylation factor (ARF) superfamily of regulatory GTPases, including both the ARF and ARF-like (ARL) proteins, control a multitude of cellular functions, including aspects of vesicular traffic, lipid metabolism, mitochondrial architecture, the assembly and dynamics of the microtubule and actin cytoskeletons, and other pathways in cell biology. Considering their general utility, it is perhaps not surprising that increasingly ARF/ARLs have been found in connection to primary cilia. Here, we critically evaluate the current knowledge of the roles four ARF/ARLs (ARF4, ARL3, ARL6, ARL13B) play in cilia and highlight key missing information that would help move our understanding forward. Importantly, these GTPases are themselves regulated by guanine nucleotide exchange factors (GEFs) that activate them and by GTPase-activating proteins (GAPs) that act as both effectors and terminators of signaling. We believe that the identification of the GEFs and GAPs and better models of the actions of these GTPases and their regulators will provide a much deeper understanding and appreciation of the mechanisms that underly ciliary functions and the causes of a number of human ciliopathies.
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Affiliation(s)
- Skylar Fisher
- 1Department of Biochemistry, Emory University
School of Medicine, Atlanta,
Georgia
| | - Damian Kuna
- 2Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham,
Birmingham, Alabama
| | - Tamara Caspary
- 3Department of Human Genetics, Emory
University School of Medicine, Atlanta,
Georgia
| | - Richard A. Kahn
- 1Department of Biochemistry, Emory University
School of Medicine, Atlanta,
Georgia
| | - Elizabeth Sztul
- 2Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham,
Birmingham, Alabama
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22
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Turn RE, East MP, Prekeris R, Kahn RA. The ARF GAP ELMOD2 acts with different GTPases to regulate centrosomal microtubule nucleation and cytokinesis. Mol Biol Cell 2020; 31:2070-2091. [PMID: 32614697 PMCID: PMC7543072 DOI: 10.1091/mbc.e20-01-0012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
ELMOD2 is a ∼32 kDa protein first purified by its GTPase-activating protein (GAP) activity toward ARL2 and later shown to have uniquely broad specificity toward ARF family GTPases in in vitro assays. To begin the task of defining its functions in cells, we deleted ELMOD2 in immortalized mouse embryonic fibroblasts and discovered a number of cellular defects, which are reversed upon expression of ELMOD2-myc. We show that these defects, resulting from the loss of ELMOD2, are linked to two different pathways and two different GTPases: with ARL2 and TBCD to support microtubule nucleation from centrosomes and with ARF6 in cytokinesis. These data highlight key aspects of signaling by ARF family GAPs that contribute to previously underappreciated sources of complexity, including GAPs acting from multiple sites in cells, working with multiple GTPases, and contributing to the spatial and temporal control of regulatory GTPases by serving as both GAPs and effectors.
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Affiliation(s)
- Rachel E Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322.,Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
| | - Michael P East
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado, Aurora, CO 80045
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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23
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Sheikh SA, Sisk RA, Schiavon CR, Waryah YM, Usmani MA, Steel DH, Sayer JA, Narsani AK, Hufnagel RB, Riazuddin S, Kahn RA, Waryah AM, Ahmed ZM. Homozygous Variant in ARL3 Causes Autosomal Recessive Cone Rod Dystrophy. Invest Ophthalmol Vis Sci 2020; 60:4811-4819. [PMID: 31743939 PMCID: PMC6944245 DOI: 10.1167/iovs.19-27263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Purpose Cone rod dystrophy (CRD) is a group of inherited retinopathies characterized by the loss of cone and rod photoreceptor cells, which results in poor vision. This study aims to clinically and genetically characterize the segregating CRD phenotype in two large, consanguineous Pakistani families. Methods Funduscopy, optical coherence tomography (OCT), electroretinography (ERG), color vision, and visual acuity assessments were performed to evaluate the retinal structure and function of the affected individuals. Exome sequencing was performed to identify the genetic cause of CRD. Furthermore, the mutation's effect was evaluated using purified, bacterially expressed ADP-ribosylation factor-like protein 3 (ARL3) and mammalian cells. Results Fundus photography and OCT imaging demonstrated features that were consistent with CRD, including bull's eye macular lesions, macular atrophy, and central photoreceptor thinning. ERG analysis demonstrated moderate to severe reduction primarily of photopic responses in all affected individuals, and scotopic responses show reduction in two affected individuals. The exome sequencing revealed a novel homozygous variant (c.296G>T) in ARL3, which is predicted to substitute an evolutionarily conserved arginine with isoleucine within the encoded protein GTP-binding domain (R99I). The functional studies on the bacterial and heterologous mammalian cells revealed that the arginine at position 99 is essential for the stability of ARL3. Conclusions Our study uncovers an additional CRD gene and assigns the CRD phenotype to a variant of ARL3. The results imply that cargo transportation in photoreceptors as mediated by the ARL3 pathway is essential for cone and rod cell survival and vision in humans.
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Affiliation(s)
- Shakeel A Sheikh
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States.,Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Robert A Sisk
- Abrahamson Pediatric Eye Institute, Cincinnati Children's Hospital, Cincinnati, Ohio, United States.,Cincinnati Eye Institute, Cincinnati, Ohio, United States
| | - Cara R Schiavon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Yar M Waryah
- Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Muhammad A Usmani
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States
| | - David H Steel
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Robert B Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Ali M Waryah
- Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Zubair M Ahmed
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States
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Li W, Feng Y, Chen A, Li T, Huang S, Liu J, Liu X, Liu Y, Gao J, Yan D, Sun J, Mei L, Liu X, Ling J. Elmod3 knockout leads to progressive hearing loss and abnormalities in cochlear hair cell stereocilia. Hum Mol Genet 2019; 28:4103-4112. [PMID: 31628468 PMCID: PMC7305813 DOI: 10.1093/hmg/ddz240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 01/28/2023] Open
Abstract
ELMOD3, an ARL2 GTPase-activating protein, is implicated in causing hearing impairment in humans. However, the specific role of ELMOD3 in auditory function is still far from being elucidated. In the present study, we used the CRISPR/Cas9 technology to establish an Elmod3 knockout mice line in the C57BL/6 background (hereinafter referred to as Elmod3-/- mice) and investigated the role of Elmod3 in the cochlea and auditory function. Elmod3-/- mice started to exhibit hearing loss from 2 months of age, and the deafness progressed with aging, while the vestibular function of Elmod3-/- mice was normal. We also observed that Elmod3-/- mice showed thinning and receding hair cells in the organ of Corti and much lower expression of F-actin cytoskeleton in the cochlea compared with wild-type mice. The deafness associated with the mutation may be caused by cochlear hair cells dysfunction, which manifests with shortening and fusion of inner hair cells stereocilia and progressive degeneration of outer hair cells stereocilia. Our finding associates Elmod3 deficiencies with stereocilia dysmorphologies and reveals that they might play roles in the actin cytoskeleton dynamics in cochlear hair cells, and thus relate to hearing impairment.
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Affiliation(s)
- Wu Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Head and Neck Surgery, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
- Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Anhai Chen
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Taoxi Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
- Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Sida Huang
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Jing Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Xianlin Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Yalan Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Jiangang Gao
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, Shandong, China
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jie Sun
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Lingyun Mei
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Xuezhong Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jie Ling
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University and Hunan Key Laboratory of Molecular Precision Medicine, Changsha, Hunan, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China
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25
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Wenta T, Jarzab M, Rychlowski M, Borysiak M, Latala A, Zurawa-Janicka D, Filipek A, Lipinska B. Cellular substrates and pro-apoptotic function of the human HtrA4 protease. J Proteomics 2019; 209:103505. [PMID: 31470122 DOI: 10.1016/j.jprot.2019.103505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/25/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022]
Abstract
The human HtrA4 protein, belonging to the HtrA family of proteases/chaperones, participates in oncogenesis and placentation, and plays a role in preeclampsia. As the knowledge concerning the biochemical features of this protein and its role at the molecular level is limited, in this work we characterized the HtrA4 molecule and searched for its cellular function. We found that recombinant HtrA4 composed of the protease and PDZ domains is a trimeric protein of intermediate thermal stability whose activity is considerably lower compared to other human HtrA proteases. By pull-down combined with mass spectrometry we identified a large array of potential HtrA4 partners. Using other experimental approaches, including immunoprecipitation, enzyme-linked immunosorbent assay and fluorescence microscopy we confirmed that HtrA4 formed complexes in vitro and in cellulo with proteins such as XIAP (inhibitor of apoptosis protein), caspases 7 and 9, β-tubulin, actin, TCP1α and S100A6. The recombinant HtrA4 degraded XIAP, the caspases, β-tubulin and actin but not TCP1α or S100A6. Together, these results suggest that HtrA4 may influence various cellular functions, including apoptosis. Furthermore, the panel of potential HtrA4 partners may serve as a basis for future studies of HtrA4 function.
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Affiliation(s)
- Tomasz Wenta
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Poland
| | - Miroslaw Jarzab
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Poland
| | - Michal Rychlowski
- Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Monika Borysiak
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Poland
| | - Anna Latala
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Poland
| | - Dorota Zurawa-Janicka
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Poland
| | - Anna Filipek
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Barbara Lipinska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Poland.
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Sztul E, Chen PW, Casanova JE, Cherfils J, Dacks JB, Lambright DG, Lee FJS, Randazzo PA, Santy LC, Schürmann A, Wilhelmi I, Yohe ME, Kahn RA. ARF GTPases and their GEFs and GAPs: concepts and challenges. Mol Biol Cell 2019; 30:1249-1271. [PMID: 31084567 PMCID: PMC6724607 DOI: 10.1091/mbc.e18-12-0820] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
Detailed structural, biochemical, cell biological, and genetic studies of any gene/protein are required to develop models of its actions in cells. Studying a protein family in the aggregate yields additional information, as one can include analyses of their coevolution, acquisition or loss of functionalities, structural pliability, and the emergence of shared or variations in molecular mechanisms. An even richer understanding of cell biology can be achieved through evaluating functionally linked protein families. In this review, we summarize current knowledge of three protein families: the ARF GTPases, the guanine nucleotide exchange factors (ARF GEFs) that activate them, and the GTPase-activating proteins (ARF GAPs) that have the ability to both propagate and terminate signaling. However, despite decades of scrutiny, our understanding of how these essential proteins function in cells remains fragmentary. We believe that the inherent complexity of ARF signaling and its regulation by GEFs and GAPs will require the concerted effort of many laboratories working together, ideally within a consortium to optimally pool information and resources. The collaborative study of these three functionally connected families (≥70 mammalian genes) will yield transformative insights into regulation of cell signaling.
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Affiliation(s)
- Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, MA 01267
| | - James E. Casanova
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS and Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France
| | - Joel B. Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - David G. Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Amherst, MA 01605
| | - Fang-Jen S. Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | | | - Lorraine C. Santy
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Annette Schürmann
- German Institute of Human Nutrition, 85764 Potsdam-Rehbrücke, Germany
| | - Ilka Wilhelmi
- German Institute of Human Nutrition, 85764 Potsdam-Rehbrücke, Germany
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322-3050
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27
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Schiavon CR, Turn RE, Newman LE, Kahn RA. ELMOD2 regulates mitochondrial fusion in a mitofusin-dependent manner, downstream of ARL2. Mol Biol Cell 2019; 30:1198-1213. [PMID: 30865555 PMCID: PMC6724520 DOI: 10.1091/mbc.e18-12-0804] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are essential and dynamic organelles undergoing constant fission and fusion. The primary players in mitochondrial morphology (MFN1/2, OPA1, DRP1) have been identified, but their mechanism(s) of regulation are still being elucidated. ARL2 is a regulatory GTPase that has previously been shown to play a role in the regulation of mitochondrial morphology. Here we demonstrate that ELMOD2, an ARL2 GTPase-activating protein (GAP), is necessary for ARL2 to promote mitochondrial elongation. We show that loss of ELMOD2 causes mitochondrial fragmentation and a lower rate of mitochondrial fusion, while ELMOD2 overexpression promotes mitochondrial tubulation and increases the rate of fusion in a mitofusin-dependent manner. We also show that a mutant of ELMOD2 lacking GAP activity is capable of promoting fusion, suggesting that ELMOD2 does not need GAP activity to influence mitochondrial morphology. Finally, we show that ELMOD2, ARL2, Mitofusins 1 and 2, Miros 1 and 2, and mitochondrial phospholipase D (mitoPLD) all localize to discrete, regularly spaced puncta along mitochondria. These results suggest that ELMOD2 is functioning as an effector downstream of ARL2 and upstream of the mitofusins to promote mitochondrial fusion. Our data provide insights into the pathway by which mitochondrial fusion is regulated in the cell.
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Affiliation(s)
- Cara R Schiavon
- Cancer Biology and bBiochemistry, Cell, and Developmental Biology Graduate Programs, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322
| | - Rachel E Turn
- Cancer Biology and bBiochemistry, Cell, and Developmental Biology Graduate Programs, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322
| | - Laura E Newman
- Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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28
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Hillert EK, Brnjic S, Zhang X, Mazurkiewicz M, Saei AA, Mofers A, Selvaraju K, Zubarev R, Linder S, D'Arcy P. Proteasome inhibitor b-AP15 induces enhanced proteotoxicity by inhibiting cytoprotective aggresome formation. Cancer Lett 2019; 448:70-83. [PMID: 30768956 DOI: 10.1016/j.canlet.2019.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/28/2018] [Accepted: 02/01/2019] [Indexed: 01/26/2023]
Abstract
Proteasome inhibitors have been shown to induce cell death in cancer cells by triggering an acute proteotoxic stress response characterized by accumulation of poly-ubiquitinated proteins, ER stress and the production of reactive oxygen species. The aggresome pathway has been described as an escape mechanism from proteotoxicity by sequestering toxic cellular aggregates. Here we show that b-AP15, a small-molecule inhibitor of proteasomal deubiquitinase activity, induces poly-ubiquitin accumulation in absence of aggresome formation. b-AP15 was found to affect organelle transport in treated cells, raising the possibility that microtubule-transport of toxic protein aggregates is inhibited, leading to enhanced cytotoxicity. In contrast to the antiproliferative effects of the clinically used proteasome inhibitor bortezomib, the effects of b-AP15 are not further enhanced by the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA). Our results suggest an inhibitory effect of b-AP15 on the transport of misfolded proteins, resulting in a lack of aggresome formation, and a strong proteotoxic stress response.
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Affiliation(s)
| | - Slavica Brnjic
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Xiaonan Zhang
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | | | - Amir Ata Saei
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Arjan Mofers
- Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Karthik Selvaraju
- Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Roman Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Stig Linder
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden; Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Padraig D'Arcy
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden; Department of Medical and Health Sciences, Linköping University, Linköping, Sweden.
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29
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Scharf C, Eymann C, Emicke P, Bernhardt J, Wilhelm M, Görries F, Winter J, von Woedtke T, Darm K, Daeschlein G, Steil L, Hosemann W, Beule A. Improved Wound Healing of Airway Epithelial Cells Is Mediated by Cold Atmospheric Plasma: A Time Course-Related Proteome Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:7071536. [PMID: 31223425 PMCID: PMC6541959 DOI: 10.1155/2019/7071536] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/28/2019] [Indexed: 01/08/2023]
Abstract
The promising potential of cold atmospheric plasma (CAP) treatment as a new therapeutic option in the field of medicine, particularly in Otorhinolaryngology and Respiratory medicine, demands primarily the assessment of potential risks and the prevention of any direct and future cell damages. Consequently, the application of a special intensity of CAP that is well tolerated by cells and tissues is of particular interest. Although improvement of wound healing by CAP treatment has been described, the underlying mechanisms and the molecular influences on human tissues are so far only partially characterized. In this study, human S9 bronchial epithelial cells were treated with cold plasma of atmospheric pressure plasma jet that was previously proven to accelerate the wound healing in a clinically relevant extent. We studied the detailed cellular adaptation reactions for a specified plasma intensity by time-resolved comparative proteome analyses of plasma treated vs. nontreated cells to elucidate the mechanisms of the observed improved wound healing and to define potential biomarkers and networks for the evaluation of plasma effects on human epithelial cells. K-means cluster analysis and time-related analysis of fold-change factors indicated concordantly clear differences between the short-term (up to 1 h) and long-term (24-72 h) adaptation reactions. Thus, the induction of Nrf2-mediated oxidative and endoplasmic reticulum stress response, PPAR-alpha/RXR activation as well as production of peroxisomes, and prevention of apoptosis already during the first hour after CAP treatment are important cell strategies to overcome oxidative stress and to protect and maintain cell integrity and especially microtubule dynamics. After resolving of stress, when stress adaptation was accomplished, the cells seem to start again with proliferation and cellular assembly and organization. The observed strategies and identification of marker proteins might explain the accelerated wound healing induced by CAP, and these indicators might be subsequently used for risk assessment and quality management of application of nonthermal plasma sources in clinical settings.
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Affiliation(s)
- Christian Scharf
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Christine Eymann
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Philipp Emicke
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Jörg Bernhardt
- 2Institute for Microbiology, University of Greifswald, Germany
| | - Martin Wilhelm
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Fabian Görries
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Jörn Winter
- 3Leibniz Institute for Plasma Science and Technology (INP), Greifswald, Germany
| | - Thomas von Woedtke
- 3Leibniz Institute for Plasma Science and Technology (INP), Greifswald, Germany
- 4Department of Hygiene and Environmental Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Katrin Darm
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Georg Daeschlein
- 5Department of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- 6Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Germany
| | - Werner Hosemann
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Achim Beule
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
- 7Department of Otorhinolaryngology, University Hospital Münster, Münster, Germany
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iTRAQ-based proteome profiling of hyposaline responses in zygotes of the Pacific oyster Crassostrea gigas. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 30:14-24. [PMID: 30771561 DOI: 10.1016/j.cbd.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/22/2022]
Abstract
Low salinity treatment is proven to be the practical polyploidy inducing method for shellfish with advantages of lower cost, higher operability and reliable food security. However, little is known about the possible molecular mechanism of hypotonic induction. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) based proteomic profiling was pursued to investigate the responses of zygotes of the Pacific oyster Crassostrea gigas to low salinity. A total of 2235 proteins were identified and 87 proteins were considered differentially expressed, of which 14 were up-regulated and 69 were down-regulated. Numerous functional proteins including ADP ribosylation factor 2, DNA repair protein Rad50, splicing factor 3B, tubulin-specific Chaperone D were significantly changed in abundance, and were involved in various biology processes including energy generation, vesicle trafficking, DNA/RNA/protein metabolism and cytoskeleton modification, indicating the prominent modulation of cell division and embryonic development. Parallel reaction monitoring (PRM) analyses were carried out for validation of the expression levels of differentially expressed proteins (DEPs), which indicated high reliability of the proteomic results. Our study not only demonstrated the proteomic alterations in oyster zygotes under low salinity, but also provided, in part, clues to the relatively lower hatching rate and higher mortality of induced larvae. Above all, this study presents a valuable foundation for further studies on mechanisms of hypotonic induction.
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31
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Wright ZC, Loskutov Y, Murphy D, Stoilov P, Pugacheva E, Goldberg AFX, Ramamurthy V. ADP-Ribosylation Factor-Like 2 (ARL2) regulates cilia stability and development of outer segments in rod photoreceptor neurons. Sci Rep 2018; 8:16967. [PMID: 30446707 PMCID: PMC6240099 DOI: 10.1038/s41598-018-35395-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/28/2018] [Indexed: 01/31/2023] Open
Abstract
Photoreceptor cells are specialized neurons with a sensory cilium carrying an elaborate membrane structure, the outer segment (OS). Inherited mutations in genes involved in ciliogenesis frequently result in OS malformation and blindness. ADP-ribosylation factor-like 2 (ARL2) has recently been implicated in OS formation through its association with Binder of ARL2 (BART or ARL2BP), a protein linked to inherited blinding disease. To test the role of ARL2 in vision we created a transgenic mouse model expressing a tagged-dominant active form of human ARL2 (ARL2-Q70L) under a rod-specific promoter. Transgenic ARL2-Q70L animals exhibit reduced photoreceptor cell function as early as post-natal day 16 and progressive rod degeneration. We attribute loss of photoreceptor function to the defective OS morphogenesis in the ARL2-Q70L transgenic model. ARL2-Q70L expression results in shortened inner and outer segments, shortened and mislocalized axonemes and cytoplasmic accumulation of rhodopsin. In conclusion, we show that ARL2-Q70L is crucial for photoreceptor neuron sensory cilium development. Future research will expand upon our hypothesis that ARL2-Q70L mutant interferes with microtubule maintenance and tubulin regulation resulting in impaired growth of the axoneme and elaboration of the photoreceptor outer segment.
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Affiliation(s)
- Zachary C Wright
- Departments of Ophthalmology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Yuriy Loskutov
- Departments of Biochemistry, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Daniel Murphy
- Departments of Biochemistry, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Peter Stoilov
- Departments of Biochemistry, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Elena Pugacheva
- Departments of Biochemistry, West Virginia University, Morgantown, West Virginia, 26506, USA
| | | | - Visvanathan Ramamurthy
- Departments of Ophthalmology, West Virginia University, Morgantown, West Virginia, 26506, USA. .,Departments of Biochemistry, West Virginia University, Morgantown, West Virginia, 26506, USA. .,Center for Neuroscience, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, 26506, USA.
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32
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Schiavon CR, Griffin ME, Pirozzi M, Parashuraman R, Zhou W, Jinnah HA, Reines D, Kahn RA. Compositional complexity of rods and rings. Mol Biol Cell 2018; 29:2303-2316. [PMID: 30024290 PMCID: PMC6249804 DOI: 10.1091/mbc.e18-05-0274] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rods and rings (RRs) are large linear- or circular-shaped structures typically described as polymers of IMPDH (inosine monophosphate dehydrogenase). They have been observed across a wide variety of cell types and species and can be induced to form by inhibitors of IMPDH. RRs are thought to play a role in the regulation of de novo guanine nucleotide synthesis; however, the function and regulation of RRs is poorly understood. Here we show that the regulatory GTPase, ARL2, a subset of its binding partners, and several resident proteins at the endoplasmic reticulum (ER) also localize to RRs. We also have identified two new inducers of RR formation: AICAR and glucose deprivation. We demonstrate that RRs can be disassembled if guanine nucleotides can be generated by salvage synthesis regardless of the inducer. Finally, we show that there is an ordered addition of components as RRs mature, with IMPDH first forming aggregates, followed by ARL2, and only later calnexin, a marker of the ER. These findings suggest that RRs are considerably more complex than previously thought and that the function(s) of RRs may include involvement of a regulatory GTPase, its effectors, and potentially contacts with intracellular membranes.
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Affiliation(s)
- Cara R Schiavon
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Maxwell E Griffin
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Marinella Pirozzi
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Raman Parashuraman
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - H A Jinnah
- Department of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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Sar D, Srivastava I, Misra SK, Ostadhossein F, Fathi P, Pan D. Copper-Catalyzed Syntheses of Pyrene-Pyrazole Pharmacophores and Structure Activity Studies for Tubulin Polymerization. ACS OMEGA 2018; 3:6378-6387. [PMID: 30221233 PMCID: PMC6130796 DOI: 10.1021/acsomega.8b00320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/05/2018] [Indexed: 05/04/2023]
Abstract
Tubulin polymerization is critical in mitosis process, which regulates uncontrolled cell divisions. Here, we report a new class of pyrene-pyrazole pharmacophore (PPP) for targeting microtubules. Syntheses of seven pyrenyl-substituted pyrazoles with side-chain modification at N-1 and C-3 positions of the pyrazole ring were accomplished from alkenyl hydrazones via C-N dehydrogenative cross-coupling using copper catalyst under aerobic condition. Tubulin polymerization with PPPs was investigated using docking and biological tools to reveal that these ligands are capable of influencing microtubule polymerization and their interaction with α-, β-tubulin active binding sites, which are substituent specific. Furthermore, cytotoxicity response of these PPPs was tested on cancer cells of different origin, such as MCF-7, MDA-MB231, and C32, and also noncancerous normal cells, such as MCF-10A. All newly synthesized PPPs showed excellent anticancer activities. The anticancer activities and half-maximal inhibitory concentration (IC50) values of all PPPs across different cancer cell lines (MCF-7, MDA-MB231, and C32) have been demonstrated. 1,3-Diphenyl-5-(pyren-1-yl)-1H-pyrazole was found to be best among all other PPPs in killing significant population of all of the cancerous cell with IC50 values 1 ± 0.5, 0.5 ± 0.2, and 5.0 ± 2.0 μM in MCF-7, MDA-MB231, and C32 cells, respectively.
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Affiliation(s)
- Dinabandhu Sar
- Department
of Bioengineering, Department of Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Mills
Breast Cancer Institute and Carle Foundation Hospital, 502 North Busey, Urbana, Illinois 61801, United States
| | - Indrajit Srivastava
- Department
of Bioengineering, Department of Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Mills
Breast Cancer Institute and Carle Foundation Hospital, 502 North Busey, Urbana, Illinois 61801, United States
| | - Santosh K. Misra
- Department
of Bioengineering, Department of Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Mills
Breast Cancer Institute and Carle Foundation Hospital, 502 North Busey, Urbana, Illinois 61801, United States
| | - Fatemeh Ostadhossein
- Department
of Bioengineering, Department of Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Mills
Breast Cancer Institute and Carle Foundation Hospital, 502 North Busey, Urbana, Illinois 61801, United States
| | - Parinaz Fathi
- Department
of Bioengineering, Department of Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Mills
Breast Cancer Institute and Carle Foundation Hospital, 502 North Busey, Urbana, Illinois 61801, United States
| | - Dipanjan Pan
- Department
of Bioengineering, Department of Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Mills
Breast Cancer Institute and Carle Foundation Hospital, 502 North Busey, Urbana, Illinois 61801, United States
- E-mail:
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Wang Y, Guan G, Cheng W, Jiang Y, Shan F, Wu A, Cheng P, Guo Z. ARL2 overexpression inhibits glioma proliferation and tumorigenicity via down-regulating AXL. BMC Cancer 2018; 18:599. [PMID: 29843637 PMCID: PMC5975491 DOI: 10.1186/s12885-018-4517-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/18/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Glioma is the most common primary brain tumor in adults with a poor prognosis. As a member of ARF subfamily GTPase, ARL2 plays a key role in regulating the dynamics of microtubules and mitochondrial functions. Recently, ARL2 has been identified as a prognostic and therapeutic target in a variety range of malignant tumors. However, the biological functional role of ARL2 in glioma still remains unknown. The aim of this study was to explore the expression and functional role of ARL2 in glioma. METHODS In this study, we investigated the expression of ARL2 in glioma samples by using RT-PCR, immunohistochemistry and western blot. The correlation between ARL2 expression and the outcomes of glioma patients was evaluated with survival data from TCGA, CGGA and Rembrandt dataset. Lentiviral technique was used for ARL2 overexpression in U87 and U251 cells. CCK8 assay, colony formation assay, wound healing test, transwell invasion assay and in vivo subcutaneous xenograft model were performed to investigated the biological functions of ARL2. RESULTS ARL2 expression was down-regulated in glioma, and was inversely associated with poor prognosis in glioma patients. Furthermore, exogenous ARL2 overexpression attenuated the growth and colony-formation abilities of glioma cells, as well as their migration and invasive capabilities. Moreover, elevated expression of ARL2 inhibited in vivo tumorigenicity of glioma cells. Mechanistically, ARL2 regulated AXL expression, which was known as an important functional regulator of proliferation and tumorigenicity in glioma cells. CONCLUSION Our study suggests that ARL2 inhibits the proliferation, migration and tumorigenicity of glioma cells by regulating the expression of AXL and may conduct as a new prognostic and therapeutic target for glioma.
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Affiliation(s)
- Yulin Wang
- Department of Neurosurgery, The First Hospital of China Medical University, 155 Nanjingbei Street, Heping, Shenyang, Liaoning, 110001, People's Republic of China
| | - Gefei Guan
- Department of Neurosurgery, The First Hospital of China Medical University, 155 Nanjingbei Street, Heping, Shenyang, Liaoning, 110001, People's Republic of China
| | - Wen Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, 155 Nanjingbei Street, Heping, Shenyang, Liaoning, 110001, People's Republic of China
| | - Yang Jiang
- Department of Neurosurgery, The First Hospital of China Medical University, 155 Nanjingbei Street, Heping, Shenyang, Liaoning, 110001, People's Republic of China
| | - Fengping Shan
- Department of Immunology, School of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Anhua Wu
- Department of Neurosurgery, The First Hospital of China Medical University, 155 Nanjingbei Street, Heping, Shenyang, Liaoning, 110001, People's Republic of China
| | - Peng Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, 155 Nanjingbei Street, Heping, Shenyang, Liaoning, 110001, People's Republic of China.
| | - Zongze Guo
- Department of Neurosurgery, The First Hospital of China Medical University, 155 Nanjingbei Street, Heping, Shenyang, Liaoning, 110001, People's Republic of China.
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HtrA3 is a cellular partner of cytoskeleton proteins and TCP1α chaperonin. J Proteomics 2018; 177:88-111. [PMID: 29477555 DOI: 10.1016/j.jprot.2018.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 02/13/2018] [Accepted: 02/19/2018] [Indexed: 01/09/2023]
Abstract
The human HtrA3 protease is involved in placentation, mitochondrial homeostasis, stimulation of apoptosis and proposed to be a tumor suppressor. Molecular mechanisms of the HtrA3 functions are poorly understood and knowledge concerning its cellular targets is very limited. There are two HtrA3 isoforms, the long (HtrA3L) and short (HtrA3S). Upon stress, their N-terminal domains are removed, resulting in the more active ΔN-HtrA3. By pull down and mass spectrometry techniques, we identified a panel of putative ΔN-HtrA3L/S substrates. We confirmed that ΔN-HtrA3L/S formed complexes with actin, β-tubulin, vimentin and TCP1α in vitro and in a cell and partially co-localized with the actin and vimentin filaments, microtubules and TCP1α in a cell. In vitro, both isoforms cleaved the cytoskeleton proteins, promoted tubulin polymerization and displayed chaperone-like activity, with ΔN-HtrA3S being more efficient in proteolysis and ΔN-HtrA3L - in polymerization. TCP1α, essential for the actin and tubulin folding, was directly bound by the ΔN-HtrA3L/S but not cleaved. These results indicate that actin, β-tubulin, vimentin, and TCP1α are HtrA3 cellular partners and suggest that HtrA3 may influence cytoskeleton dynamics. They also suggest different roles of the HtrA3 isoforms and a possibility that HtrA3 protease may also function as a co-chaperone. SIGNIFICANCE The HtrA3 protease stimulates apoptosis and is proposed to be a tumor suppressor and a therapeutic target, however little is known about its function at the molecular level and very few HtrA3 physiological substrates have been identified so far. Furthermore, HtrA3 is the only member of the HtrA family of proteins which, apart from the long isoform possessing the PD and PDZ domains (HtrA3L), has a short isoform (HtrA3S) lacking the PDZ domain. In this work we identified a large panel (about 150) of the tentative HtrA3L/S cellular partners which provides a good basis for further research concerning the HtrA3 function. We have shown that the cytoskeleton proteins actin, β-tubulin and vimentin, and the TCP1α chaperonin are cellular partners of both HtrA3 isoforms. Our findings indicate that HtrA3 may promote destabilization of the actin and vimentin cytoskeleton and suggest that it may influence the dynamics of the microtubule network, with the HtrA3S being more efficient in cytoskeleton protein cleavage and HtrA3L - in tubulin polymerization. Also, we have shown for the first time that HtrA3 has a chaperone-like, holdase activity in vitro - activity typical for co-chaperone proteins. The proposed HtrA3 influence on the cytoskeleton dynamics may be one of the ways in which HtrA3 promotes cell death and affects cancerogenesis. We believe that the results of this study provide a new insight into the role of HtrA3 in a cell and further confirm the notion that HtrA3 should be considered as a target of new anti-cancer therapies.
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Francis JW, Goswami D, Novick SJ, Pascal BD, Weikum ER, Ortlund EA, Griffin PR, Kahn RA. Nucleotide Binding to ARL2 in the TBCD∙ARL2∙β-Tubulin Complex Drives Conformational Changes in β-Tubulin. J Mol Biol 2017; 429:3696-3716. [PMID: 28970104 DOI: 10.1016/j.jmb.2017.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/31/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022]
Abstract
Microtubules are highly dynamic tubulin polymers that are required for a variety of cellular functions. Despite the importance of a cellular population of tubulin dimers, we have incomplete information about the mechanisms involved in the biogenesis of αβ-tubulin heterodimers. In addition to prefoldin and the TCP-1 Ring Complex, five tubulin-specific chaperones, termed cofactors A-E (TBCA-E), and GTP are required for the folding of α- and β-tubulin subunits and assembly into heterodimers. We recently described the purification of a novel trimer, TBCD•ARL2•β-tubulin. Here, we employed hydrogen/deuterium exchange coupled with mass spectrometry to explore the dynamics of each of the proteins in the trimer. Addition of guanine nucleotides resulted in changes in the solvent accessibility of regions of each protein that led to predictions about each's role in tubulin folding. Initial testing of that model confirmed that it is ARL2, and not β-tubulin, that exchanges GTP in the trimer. Comparisons of the dynamics of ARL2 monomer to ARL2 in the trimer suggested that its protein interactions were comparable to those of a canonical GTPase with an effector. This was supported by the use of nucleotide-binding assays that revealed an increase in the affinity for GTP by ARL2 in the trimer. We conclude that the TBCD•ARL2•β-tubulin complex represents a functional intermediate in the β-tubulin folding pathway whose activity is regulated by the cycling of nucleotides on ARL2. The co-purification of guanine nucleotide on the β-tubulin in the trimer is also shown, with implications to modeling the pathway.
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Affiliation(s)
- Joshua W Francis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Devrishi Goswami
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States.
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37
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Ivanova AA, Caspary T, Seyfried NT, Duong DM, West AB, Liu Z, Kahn RA. Biochemical characterization of purified mammalian ARL13B protein indicates that it is an atypical GTPase and ARL3 guanine nucleotide exchange factor (GEF). J Biol Chem 2017; 292:11091-11108. [PMID: 28487361 PMCID: PMC5491791 DOI: 10.1074/jbc.m117.784025] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/02/2017] [Indexed: 12/11/2022] Open
Abstract
Primary cilia play central roles in signaling during metazoan development. Several key regulators of ciliogenesis and ciliary signaling are mutated in humans, resulting in a number of ciliopathies, including Joubert syndrome (JS). ARL13B is a ciliary GTPase with at least three missense mutations identified in JS patients. ARL13B is a member of the ADP ribosylation factor family of regulatory GTPases, but is atypical in having a non-homologous, C-terminal domain of ∼20 kDa and at least one key residue difference in the consensus GTP-binding motifs. For these reasons, and to establish a solid biochemical basis on which to begin to model its actions in cells and animals, we developed preparations of purified, recombinant, murine Arl13b protein. We report results from assays for solution-based nucleotide binding, intrinsic and GTPase-activating protein-stimulated GTPase, and ARL3 guanine nucleotide exchange factor activities. Biochemical analyses of three human missense mutations found in JS and of two consensus GTPase motifs reinforce the atypical properties of this regulatory GTPase. We also discovered that murine Arl13b is a substrate for casein kinase 2, a contaminant in our preparation from human embryonic kidney cells. This activity, and the ability of casein kinase 2 to use GTP as a phosphate donor, may be a source of differences between our data and previously published results. These results provide a solid framework for further research into ARL13B on which to develop models for the actions of this clinically important cell regulator.
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Affiliation(s)
| | - Tamara Caspary
- Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | | | | | - Andrew B West
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Zhiyong Liu
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
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Newman LE, Schiavon CR, Turn RE, Kahn RA. The ARL2 GTPase regulates mitochondrial fusion from the intermembrane space. CELLULAR LOGISTICS 2017; 7:e1340104. [PMID: 28944094 PMCID: PMC5602422 DOI: 10.1080/21592799.2017.1340104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/05/2017] [Indexed: 01/11/2023]
Abstract
Mitochondria are essential, dynamic organelles that regularly undergo both fusion and fission in response to cellular conditions, though mechanisms of the regulation of their dynamics are incompletely understood. We provide evidence that increased activity of the small GTPase ARL2 is strongly correlated with an increase in fusion, while loss of ARL2 activity results in a decreased rate of mitochondrial fusion. Strikingly, expression of activated ARL2 can partially restore the loss of fusion resulting from deletion of either mitofusin 1 (MFN1) or mitofusin 2 (MFN2), but not deletion of both. We only observe the full effects of ARL2 on mitochondrial fusion when it is present in the intermembrane space (IMS), as constructs driven to the matrix or prevented from entering mitochondria are essentially inactive in promoting fusion. Thus, ARL2 is the first regulatory (small) GTPase shown to act inside mitochondria or in the fusion pathway. Finally, using high-resolution, structured illumination microscopy (SIM), we find that ARL2 and mitofusin immunoreactivities present as punctate staining along mitochondria that share a spatial convergence in fluorescence signals. Thus, we propose that ARL2 plays a regulatory role in mitochondrial fusion, acting from the IMS and requiring at least one of the mitofusins in their canonical role in fusion of the outer membranes.
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Affiliation(s)
- Laura E. Newman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Cara R. Schiavon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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