The Effects of ER Morphology on Synaptic Structure and Function in Drosophila Melanogaster James B
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NIH Public Access Author Manuscript Science
NIH Public Access Author Manuscript Science. Author manuscript; available in PMC 2014 September 08. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Science. 2014 January 31; 343(6170): 506–511. doi:10.1126/science.1247363. Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders A full list of authors and affiliations appears at the end of the article. # These authors contributed equally to this work. Abstract Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease. Hereditary spastic paraplegias (HSPs) are a group of genetically heterogeneous neurodegenerative disorders with prevalence between 3 and 10 per 100,000 individuals (1). Hallmark features are axonal degeneration and progressive lower limb spasticity resulting from a loss of corticospinal tract (CST) function. HSP is classified into two broad categories, uncomplicated and complicated, on the basis of the presence of additional clinical features such as intellectual disability, seizures, ataxia, peripheral neuropathy, skin abnormalities, and visual defects. -
Functions of Nogo Proteins and Their Receptors in the Nervous System
REVIEWS Functions of Nogo proteins and their receptors in the nervous system Martin E. Schwab Abstract | The membrane protein Nogo-A was initially characterized as a CNS-specific inhibitor of axonal regeneration. Recent studies have uncovered regulatory roles of Nogo proteins and their receptors — in precursor migration, neurite growth and branching in the developing nervous system — as well as a growth-restricting function during CNS maturation. The function of Nogo in the adult CNS is now understood to be that of a negative regulator of neuronal growth, leading to stabilization of the CNS wiring at the expense of extensive plastic rearrangements and regeneration after injury. In addition, Nogo proteins interact with various intracellular components and may have roles in the regulation of endoplasmic reticulum (ER) structure, processing of amyloid precursor protein and cell survival. Nogo proteins were discovered, and have been exten- The amino-terminal segments of the proteins sively studied, in the context of injury and repair of fibre encoded by the different RTN genes have differing tracts in the CNS1 — a topic of great research interest lengths and there is no homology between them3,5. The and clinical relevance. However, much less in known N termini of the RTN4 products Nogo-A and Nogo-B are about the physiological functions of Nogo proteins in identical, consisting of a 172-amino acid sequence that development and in the intact adult organism, including is encoded by a single exon (exon 1) that is followed by in the brain. Through a number of recent publications, a short exon 2 and, in Nogo-A, by the very long exon Nogo proteins have emerged as important regulators of 3 encoding 800 amino acids2,6 (FIG. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
Hereditary Spastic Paraplegia: from Genes, Cells and Networks to Novel Pathways for Drug Discovery
brain sciences Review Hereditary Spastic Paraplegia: From Genes, Cells and Networks to Novel Pathways for Drug Discovery Alan Mackay-Sim Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia; a.mackay-sim@griffith.edu.au Abstract: Hereditary spastic paraplegia (HSP) is a diverse group of Mendelian genetic disorders affect- ing the upper motor neurons, specifically degeneration of their distal axons in the corticospinal tract. Currently, there are 80 genes or genomic loci (genomic regions for which the causative gene has not been identified) associated with HSP diagnosis. HSP is therefore genetically very heterogeneous. Finding treatments for the HSPs is a daunting task: a rare disease made rarer by so many causative genes and many potential mutations in those genes in individual patients. Personalized medicine through genetic correction may be possible, but impractical as a generalized treatment strategy. The ideal treatments would be small molecules that are effective for people with different causative mutations. This requires identification of disease-associated cell dysfunctions shared across geno- types despite the large number of HSP genes that suggest a wide diversity of molecular and cellular mechanisms. This review highlights the shared dysfunctional phenotypes in patient-derived cells from patients with different causative mutations and uses bioinformatic analyses of the HSP genes to identify novel cell functions as potential targets for future drug treatments for multiple genotypes. Keywords: neurodegeneration; motor neuron disease; spastic paraplegia; endoplasmic reticulum; Citation: Mackay-Sim, A. Hereditary protein-protein interaction network Spastic Paraplegia: From Genes, Cells and Networks to Novel Pathways for Drug Discovery. Brain Sci. 2021, 11, 403. -
Roles of Reticulons and Reeps in Organisation of Axonal Endoplasmic Reticlum in Drosophila
Roles of reticulons and REEPs in organisation of axonal endoplasmic reticlum in Drosophila Belgin Yalçın1, Niamh C. O’Sullivan1, Martin Stofanko1, Zi Han Kang, Annika Hartwich, Matt Thomas, Cahir J. O’Kane2 (1equal contributions; 2corresponding author) Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK The length of motor axons requires significant engineering for their formation and maintenance. Failures of this maintenance are seen in the Hereditary Spastic Paraplegias (HSPs), characterised by lower limb weakness, and degeneration of longer upper motor axons. To date over 50 causative Spastic Paraplegia Genes (SPGs) have been identified. Several encode endoplasmic reticulum membrane proteins, with intramembrane hairpin structures that curve and model ER membrane. Two of these protein families, reticulons and REEPs, are together required for formation of most tubular ER in yeast. To test whether they are also required for formation or maintenance of axonal ER, we have developed suitable markers in Drosophila, and analyzed mutants that lack members of these protein families. Drosophila has two reticulon genes, one of which, Rtnl1, is widely expressed. YFP-tagged Rtnl1 localises strongly in axons and presynaptic terminals, in contrast to most conventional ER markers. Rtnl1 knockdown reduces levels of smooth ER marker in longer distal motor axons, but not in shorter or proximal ones – analogous to HSP. This effect is also seen in labeled single axons, with no loss of ER continuity. Drosophila has six REEP genes, two of which are widely and highly expressed. ReepA is orthologous to mammalian REEPs 1 to 4, and ReepB to mammalian REEP5 and REEP6. We can detect ReepB::GFP but not ReepA::GFP in axons and presynaptic terminals. -
Expression of a Novel Reticulon-Like Gene in Human Testis
Reproduction (2002) 123, 227–234 Research Expression of a novel reticulon-like gene in human testis Z. M. Zhou1,2, J. H. Sha2, J. M. Li2 , M. Lin2, H. Zhu2, Y. D. Zhou2, L. R. Wang2, H. Zhu2, Y. Q. Wang1 and K. Y. Zhou1 1Institute of Genetic Resources, Nanjing Normal University, Nanjing, Jiangsu Province 210029, People’s Republic of China; and 2Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, 210029, People’s Republic of China Identification of genes that are specifically expressed in the had 968 amino acids. This protein is homologous to the adult testis or the fetal testis is important for the study of six known members of the Rtn family (KIAA0886, Rtn xL, genes related to the development of the testis. In this study, reticulon 4a, Nogo-A, Nogo-A short form, and brain my043) a human testis cDNA microarray was established. PCR but was different at the 5’ end. All homologues originate products of 9216 clones from a human testis cDNA library from one gene, and result from both different promotor were dotted on a nylon membrane; mRNA from adult and regions and different splicing. Rtn-T lacks the first exon and fetal testes were purified and probes were prepared by a contains a second exon that is lacking in the other reverse transcription reaction with testis mRNA as template. homologues. Rtn-T is shorter than KIAA0886, Rtn xL, The microarray was hybridized with probes of adult and reticulon 4a and Nogo-A, but longer than the Nogo-A short fetal testes, and 96.8 and 95.4% of clones were positive, form and brain my043. -
A Single Legionella Effector Catalyzes a Multistep Ubiquitination Pathway to Rearrange Tubular Endoplasmic Reticulum for Replication
Article A Single Legionella Effector Catalyzes a Multistep Ubiquitination Pathway to Rearrange Tubular Endoplasmic Reticulum for Replication Graphical Abstract Authors Kristin M. Kotewicz, Vinay Ramabhadran, Nicole Sjoblom, ..., Jessica Behringer, Rebecca A. Scheck, Ralph R. Isberg Correspondence [email protected] In Brief Intracellular pathogens, including Legionella, target host organelles for replication. Kotewicz et al. show that Legionella generates an ER- encompassed replication compartment via Sde protein-mediated ubiquitination of host reticulon 4. Ubiquitination is mediated by sequential action of the ADP-ribosyltransferase and nucleotidase activities of Sde and independent of the host ubiquitination system. Highlights d Legionella Sde proteins remodel tubular ER to initiate intracellular replication d The tubular ER protein reticulon 4 is targeted by Sde proteins d ER remodeling requires ubiquitin transfer by Sde proteins d Ubiquitin transfer involves ADP-ribosyltransferase and nucleotidase activities Kotewicz et al., 2017, Cell Host & Microbe 21, 169–181 February 8, 2017 ª 2016 Elsevier Inc. http://dx.doi.org/10.1016/j.chom.2016.12.007 Cell Host & Microbe Article ASingleLegionella Effector Catalyzes a Multistep Ubiquitination Pathway to Rearrange Tubular Endoplasmic Reticulum for Replication Kristin M. Kotewicz,1,6 Vinay Ramabhadran,1,3,6 Nicole Sjoblom,2 Joseph P. Vogel,4 Eva Haenssler,1,7 Mengyun Zhang,1 Jessica Behringer,5 Rebecca A. Scheck,2 and Ralph R. Isberg1,3,8,* 1Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA 2Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA 02155, USA 3Howard Hughes Medical Institute, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA 4Department of Molecular Microbiology, Washington University School of Medicine, St. -
Leveraging Tissue Specific Gene Expression Regulation to Identify Genes Associated with Complex Diseases
bioRxiv preprint doi: https://doi.org/10.1101/529297; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Leveraging tissue specific gene expression regulation to identify genes associated with complex diseases Wei Liu1,#, Mo Li2,#, Wenfeng Zhang2, Geyu Zhou1, Xing Wu4, Jiawei Wang1, Hongyu Zhao1,2,3* 1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA 06510 2 Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA 06510 3 Department of Genetics, Yale School of Medicine, New Haven, CT, USA 06510 4 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA 06510 # These authors contributed equally to this work * To Whom correspondence should be addressed: Dr. Hongyu Zhao Department of Biostatistics Yale School of Public Health 60 College Street, New Haven, CT, 06520, USA [email protected] Key words: GWAS; gene expression imputation; Alzheimer’s disease; gene-level association test 1 bioRxiv preprint doi: https://doi.org/10.1101/529297; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract To increase statistical power to identify genes associated with complex traits, a number of methods like PrediXcan and FUSION have been developed using gene expression as a mediating trait linking genetic variations and diseases. -
Super-Assembly of ER-Phagy Receptor Atg40 Induces Local ER Remodeling at Contacts with Forming Autophagosomal Membranes
ARTICLE https://doi.org/10.1038/s41467-020-17163-y OPEN Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes ✉ Keisuke Mochida1,4, Akinori Yamasaki 2,3,4, Kazuaki Matoba 2, Hiromi Kirisako1, Nobuo N. Noda 2 & ✉ Hitoshi Nakatogawa 1 1234567890():,; The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rear- ranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super- assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study sig- nificantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles. 1 School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan. 2 Institute of Microbial -
Download Ppis for Each Single Seed, Thus Obtaining Each Seed’S Interactome (Ferrari Et Al., 2018)
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.14.425874; this version posted January 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias Nikoleta Vavouraki1,2, James E. Tomkins1, Eleanna Kara3, Henry Houlden3, John Hardy4, Marcus J. Tindall2,5, Patrick A. Lewis1,4,6, Claudia Manzoni1,7* Author Affiliations 1: Department of Pharmacy, University of Reading, Reading, RG6 6AH, United Kingdom 2: Department of Mathematics and Statistics, University of Reading, Reading, RG6 6AH, United Kingdom 3: Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom 4: Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom 5: Institute of Cardiovascular and Metabolic Research, University of Reading, Reading, RG6 6AS, United Kingdom 6: Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, United Kingdom 7: School of Pharmacy, University College London, London, WC1N 1AX, United Kingdom *Corresponding author: [email protected] Abstract The Hereditary Spastic Paraplegias are a group of neurodegenerative diseases characterized by spasticity and weakness in the lower body. Despite the identification of causative mutations in over 70 genes, the molecular aetiology remains unclear. Due to the combination of genetic diversity and variable clinical presentation, the Hereditary Spastic Paraplegias are a strong candidate for protein- protein interaction network analysis as a tool to understand disease mechanism(s) and to aid functional stratification of phenotypes. -
A Conserved Amphipathic Helix Is Required for Membrane Tubule Formation by Yop1p
A conserved amphipathic helix is required for PNAS PLUS membrane tubule formation by Yop1p Jacob P. Brady, Jolyon K. Claridge, Peter G. Smith, and Jason R. Schnell1 Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom Edited by William F. DeGrado, School of Pharmacy, University of California, San Francisco, CA, and approved December 31, 2014 (received for review August 18, 2014) The integral membrane proteins of the DP1 (deleted in polyposis) C-terminal tubulin binding domains providing a link between ER and reticulon families are responsible for maintaining the high morphology and the cytoskeleton (19). membrane curvature required for both smooth endoplasmic retic- The RHDs are proposed to form hydrophobic hairpins too ulum (ER) tubules and the edges of ER sheets, and mutations in short to traverse the membrane fully, leading to greater dis- these proteins lead to motor neuron diseases, such as hereditary placement of lipids from the outer leaflet than from the in- spastic paraplegia. Reticulon/DP1 proteins contain reticulon ho- ner leaflet. By this mechanism, a combination of hydrophobic mology domains (RHDs) that have unusually long hydrophobic wedging and oligomeric scaffolding could lead to the stabiliza- segments and are proposed to adopt intramembrane helical hair- tion of the tubular ER membrane. However, there is currently pins that stabilize membrane curvature. We have characterized no structural information available for these intramembrane the secondary structure and dynamics of the DP1 family protein domains, and the exact mechanism of curvature generation and produced from the YOP1 gene (Yop1p) and identified a C-termi- stabilization remains unknown. The mechanism for exclusive nal conserved amphipathic helix (APH) that, on its own, interacts localization of RHD proteins to highly curved membranes also strongly with negatively charged membranes and is necessary remains unclear; however, the transmembrane domains have for membrane tubule formation. -
Update on the Genetics of Spastic Paraplegias Maxime Boutry, Sara Morais, Giovanni Stevanin
Update on the genetics of spastic paraplegias Maxime Boutry, Sara Morais, Giovanni Stevanin To cite this version: Maxime Boutry, Sara Morais, Giovanni Stevanin. Update on the genetics of spastic paraple- gias. Current Neurology and Neuroscience Reports, Current Medicine Group, 2019, 19 (4), pp.18. 10.1007/s11910-019-0930-2. hal-02272013 HAL Id: hal-02272013 https://hal.sorbonne-universite.fr/hal-02272013 Submitted on 27 Aug 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Update on the genetics of spastic paraplegias Maxime Boutry1,2*, Sara Morais1,2,3, Giovanni Stevanin1,2 1 Institut du Cerveau et de la Moelle épinière, Sorbonne Université UMR_S1127, INSERM Unit 1127, CNRS UMR7225, 75013, Paris, France 2 Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres (PSL) Research University, Neurogenetics team, 75013, Paris, France 3 UnIGENe, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal *Current affiliation: Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada Corresponding author: Giovanni Stevanin [email protected] ORCID 0000-0001-9368-8657 Abstract Purpose of review Hereditary spastic paraplegias are a genetically heterogeneous group of neurological disorders.