VU Research Portal Synaptic functions of the ubiquitin ligase TRIM3 Schreiber, J. 2016 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Schreiber, J. (2016). Synaptic functions of the ubiquitin ligase TRIM3. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 27. Sep. 2021 VRIJE UNIVERSITEIT Synaptic functions of the ubiquitin ligase TRIM3 ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad Doctor aan de Vrije Universiteit Amsterdam, op gezag van de rector magnificus prof.dr. V. Subramaniam, in het openbaar te verdedigen ten overstaan van de promotiecommissie van de Faculteit der Aard- en Levenswetenschappen op vrijdag 11 maart 2016 om 11.45 uur in de aula van de universiteit, De Boelelaan 1105 door Joerg Schreiber geboren te Zossen, Duitsland promotoren: prof. dr. A. B. Smit copromotoren: dr. R. E. van Kesteren prof. dr. C. I. de Zeeuw All clear, sir. Leescommissie: prof. dr. M. Kneussel prof. dr. J. C. Schwamborn prof. dr. C. C. Hoogenraad dr. R. F. Toonen dr. K. W. Li The research described in this thesis was performed at the department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands. Research was funded by Cerebnet, EU-FP7 Initial Training Network Publication of this thesis was supported by: Sylics (Synaptologics BV) Vrije Universiteit Amsterdam Center for Neurogenomics and Cognitive Research (CNCR) Printed by Ipskamp Drukkers Cover: Curious mice, Joerg Schreiber TABLE OF CONTENTS List of Abbreviations 6 CHAPTER 1 11 General Introduction CHAPTER 2 31 The ubiquitin ligase TRIM3 affects hippocampal synaptic plasticity and learning in mice CHAPTER 3 59 TRIM3 participates in mRNP granules, but is not essential for mRNP granule trafficking CHAPTER 4 73 Identification of TRIM3 ubiquitylation substrates CHAPTER 5 103 TRIM3 ubiquitylates gamma-actin in an activity dependent manner CHAPTER 6 127 General discussion References 140 Summary 155 Acknowledgements 159 List of Abbreviations ABP280 Actin-Binding Protein 280 aCSF Artificial Cerebral Spinal Fluid ACTA Actin, Alpha ACTB Actin, Beta ACTG1 Actin, Gamma 1 ACTG1-cKO Actin, Gamma 1 - Conditional Knockout ACTN4 Actinin, Alpha 4 ADCY1 Adenylate Cyclase 1 AGO2 Argonaute Risc Catalytic Component 2 AMPA Alpha-Amino-3-Hydroxyl-5-Methyl-4-Isoxazole-Propionate ANXA5 Annexin A5 AP2A1 Adaptor-Related Protein Complex 2, Alpha 1 Subunit AP2M1 Adaptor-Related Protein Complex 2, Mu 1 Subunit APC/C Anaphase-Promoting Complex/Cyclosome ARC Activity-Regulated Cytoskeleton-Associated Protein ARF Adp Ribosylation Factor-Like B-BOX B-Box-Type Zinc Finger Domain BBS Bardet-Biedl Syndrome BERP Brain Expressed Ring Finger Protein BN - PAGE Blue Native - Polyacrylamide Gel Electrophoresis BRAT Brain Tumor Protein BSA Bovine Serum Albumin CA1 CA1 Region of Hippocampus CA2 CA2 Region of Hippocampus CA3 CA3 Region of Hippocampus CaCl2 Calcium Chloride CamKII Ca2+/Calmodulin-Dependent Protein Kinase II CART Cytoskeleton-Associated Recycling or Transport CC Coiled-Coil cDNA Complementary Deoxyribonucleic Acid CNQX 6-Cyano-7-Nitroquinoxaline-2,3-Dione DNA Deoxyribonucleic Acid DDM N-Dodecyl β-D-Maltoside DDX3 Dead (Asp-Glu-Ala-Asp) Box Helicase 3, X-Linked DG Dentate Gyrus DMEM Dulbecco's Modified Eagle Culture Medium DMSO Dimethyl Sulfoxide DNM3 Dynamin 3 6 List of Abbreviations DOC Deoxycholic Acid DTT Dithiothreitol DUBs Deubiquitinating Enzymes E1 Ubiquitin-Activating Enzyme E2 Ubiquitin-Conjugating Enzyme E3 Ubiquitin Ligase ECF Enhanced Chemifluorescence ECL Enhanced Chemiluminescent EEF1A2 Eukaryotic Translation Elongation Factor 1 Alpha 2 EGFR Epidermal Growth Factor Receptor EPSC Excitatory Postsynaptic Current F-ACTIN Filamentous-Actin FBX2 F-Box Protein 2 fEPSP Field Excitatory Postsynaptic Potential FIL Filamin-Type Immunoglobulin FMRP Fragile X Mental Retardation Protein 1 FN3 Fibronectin Type 3 GABA Gamma Amino Butyric Acid GABAR GABA Receptor G-ACTIN Globular-Actin GAPDH Glyceraldehyde-3-Phosphate Dehydrogenase GFP Green Fluorescent Protein GIGYF2 Grb10 Interacting Gyf Protein 2 GKAP Guanylate Kinase-Associated Protein GLUK2 Ionotropic Glutamate Receptor Kainate 2 GLUR1 Ionotropic Glutamate Receptor AMPA 1 GLUR2 Ionotropic Glutamate Receptor AMPA 2 HECT Homologous To The E6-Ap Carboxyl Terminus HEK293 Human Embryonic Kidney 293 Cells HEPES N-2-Hydroxyethylpiperazine-N'-2-Ethanesulfonic Acid HOMER1 Homer Scaffolding Protein 1 HSP70 Heat Shock 70kDa Protein HSP90AB1 Heat Shock Protein 90kDa Alpha, Class B Member 1 HSPA2 Heat Shock 70kDa Protein 2 IG-FLMN Immunoglobulin Filamin-Type IGFN1 Immunoglobulin-Like And Fibronectin Type I Domain-Containing Protein 1 IPSC Inhibitory Postsynaptic Current KALRN Kalirin, RhoGEF Kinase KCl Potassium Chloride kDa Kilodalton kg Kilogram 7 KIF21B Kinesin Family Member 21B KO Knockout LGMD2H Limb-Girdle Muscular Dystrophy Type 2H LTD Long-Term Depression LTM Long-Term Memory LTP Long-Term Potentiation MAP2 Microtubule-Associated Protein 2 MATH Meprin and Tumour-Necrosis Factor Receptor- Associated Factor Homology MDM2 Mouse Double Minute 2 Homolog mEPSC Miniature Excitatory Postsynaptic Current MG132 Proteasome Inhibitor MG132 mIPSC Miniature Inhibitory Postsynaptic Current miRNA microRNA ml Milliliter mm Millimeter mM Millimolar mRNA Messenger Ribonucleic Acid mRNP Messenger Ribonucleoprotein mTOR Mechanistic Target of Rapamycin (Serine/Threonine Kinase) mV Millivolt NaCl Sodium Chloride NaH2PO4 Sodium Dihydrogenphosphate NaHCO3 Sodium Bicarbonate NF-L Neurofilament Light Chain NHL Ncl-1, Ht2A And Lin-41 NMDA N-Methyl-D-Aspartic Acid NME1 Nme/Nm23 Nucleoside Diphosphate Kinase 1 NOT4 E3 Liagse Not4 NPTN Neuroplastin NR1 N-Methyl-D-Aspartate Receptor Subunit 1 NR2B N-Methyl-D-Aspartate Receptor Subunit 2B P2 + M Pellet 2 And Microsomes PARK2 Parkin RBR E3 Ubiquitin Protein Ligase P-BODIES Processing Bodies PBS Phosphate Buffered Saline PEI Polyethylenimine PEN - STREP Penicillin-Streptomycin PHD Plant Homeodomain PIASy Protein Inhibitor Of Activated Stat PKA Protein Kinase A PKC Protein Kinase C 8 List of Abbreviations PSD-95 Postsynaptic Density Protein 95 PTMs Post-Translational Modifications PTZ Pentylenetetrazole PURA Purine-Rich Single-Stranded DNA-Binding Protein Alpha PVDF Polyvinylidene Fluoride RBCC Ring Finger, B-Box, Coiled-Coil RIM1 Regulating Synaptic Membrane Exocytosis Protein 1 RING Really Interesting New Gene RNA Ribonucleic Acid RPL3 Ribosomal Protein L3 RT-PCR Reverse Transcription Polymerase Chain Reaction SCF COMPLEX Skp1/Cullin/Fbox Complex SDS-PAGE Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis SEM Standard Error of the Mean SHANK Sh3 And Multiple Ankyrin Repeat Domains SLC1A3 Solute Carrier Family 1, Member 3 SLC25A4 Solute Carrier Family 25, Member 4 SNAP25 Synaptosomal-Associated Protein, 25kDa SPRY Spia Kinase And Ryanodine Receptors Domain STM Short-Term Memory SUMO Small Ubiquitin-Like Modifier TBS Tris Buffered Saline TBS Theta Burst Stimulation TBS-T Tris Buffered Saline - Tween-20 TFA Trifluoroacetic Acid TM Transmembrane TMEM57 Transmembrane Protein 57 TPA 12-O-Tetradecanoylphorbol 13-Acetate TRIM2 Tripartite Motif Containing 2 TRIM3 Tripartite Motif Containing 3 TRIM32 Tripartite Motif Containing 32 TRIM71 Tripartite Motif Containing 71 TRIS 2-Amino-2-(Hydroxymethyl)-1,3-Propanediol TUBB3 Tubulin, Beta 3 TUBEs Tandem Ubiquitin Binding Entities UBE3A Ubiquitin Protein Ligase E3A VIM Vimentin WB Western Blot WT Wildtype XIAP X-Linked Inhibitor Of Apoptosis ZBP1 Z-DNA Binding Protein 1 9 10 General Introduction CHAPTER 1 General Introduction Chapter 1 Prelude – learning and memory There are many different definitions of learning and memory, some extensive and complex and others straightforward and easily comprehensible. In its simplest form, learning is a mechanism by which we acquire new information, and memory is the mechanism by which we retain and possibly retrieve that information. As simple as these definitions may appear, they are the basis for any species to survive, adapt, reproduce and finally succeed in even the harshest environment. When Charles Darwin first proposed his theory of natural selection in 1859 it was controversial and highly debated. Nowadays it is largely accepted by its overwhelming evidence and rather intuitive to most. The ability to learn about the environment, store that information and then retrieve and utilize it, presents an invaluable competitive advantage, which can be appreciated when looking at human evolutionary history. First fossils of the human species (genus: Homo) date back about two to three million years (Schrenk et al., 2007), which is relatively little compared to most other