Nidovirus replication structures : hijacking membranes to support viral RNA synthesis
Knoops, K.
Citation
Knoops, K. (2011, May 10). Nidovirus replication structures : hijacking membranes to support viral RNA synthesis. Retrieved from
https://hdl.handle.net/1887/17639
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Nidovirus Replication Structures
Hijacking Membranes to Support Viral RNA Synthesis
Kèvin Knoops
Nidovirus Replication Structures
Hijacking Membranes to Support Viral RNA Synthesis Kèvin Knoops
Ph.D. Thesis Leiden University, 2011
The work presented in this thesis was performed at the Departments of Medical Microbiol- ogy and Molecular Cell Biology of Leiden University Medical Center, the Netherlands.
The printing of this thesis was financially supported by the Stichting tot Bevordering van de Electronenmicroscopie in Nederland (SEN).
ISBN/EAN: 978-94-6169-062-3
Printed by: Optima Grafische Communicatie, Rotterdam, The Netherlands
Cover: Three-dimensional reconstruction of the reticulovesicular network of modified endo- plasmic reticulum derived from a section through a frozen SARS coronavirus-infected Vero E6 cell.
All rights reserved. No part of this thesis may be reproduced or transmitted in any form or by any means without prior written permission of the author.
© Copyright Kèvin Knoops, Grenoble, 2011
Nidovirus Replication Structures
Hijacking Membranes to Support Viral RNA Synthesis
Proefschrift
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden op gezag van de Rector Magnificus Prof. mr. P.F. van der Heijden
volgens het besluit van het College voor Promoties te verdedigen op dinsdag 10 mei 2011
klokke 11:15 uur
door
Kèvin Knoops geboren te Heerlen
in 1980
Promotiecommissie
Promotores: Prof. dr. E.J. Snijder Prof. dr. ir. A.J. Koster
co-promotor: Dr. A.M. Mommaas-Kienhuis
overige leden: Prof. dr. J. Klumperman Universiteit Utrecht
Dr. F. van Kuppeveld
Radboud Universiteit Nijmegen Prof. dr. H.J. Tanke
Table of contents
List of abbreviations 7
chapter 1 General introduction 11
chapter 2 SARS-Coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum
PLoS Biology (2008) 16;6(9):e226
29
chapter 3 Integrity of the early secretory pathway promotes, but is not required for SARS-coronavirus RNA synthesis and virus-induced remodeling of endoplasmic reticulum membranes
Journal of Virology (2010) 84(2):833-46
57
chapter 4 Development and RNA-synthesizing activity of coronavirus replication structures in the absence of protein synthesis
Journal of Virology (in press)
81
chapter 5 Ultrastructural characterization of arterivirus replication structures:
reshaping the endoplasmic reticulum to accommodate viral RNA synthesis
Submitted for publication
89
chapter 6 General discussion 121
References 135
Summary 151
Samenvatting 155
Curriculum vitae 158
Awards 158
List of publications 159
7
List of abbreviations
-RNA Negative-sense RNA +RNA Positive-sense RNA 3-D 3-dimensional
3H Tritium
A Actin
aa Amino acid
ActD Actinomycin D Arf ADP-ribosylation factor Atg Autophagy-related protein BHK Baby hamster kidney BFA Brefeldin A
BIG Brefeldin A-inhibited GEP
BrU Bromouridine
BrUTP Bromouridine triphosphate CCD Charged coupled device
CEACAM Carcinoembryonic antigen-related cell adhesion molecules CF Cryo fixation
CHX Cycloheximide
CM Convoluted membranes COP Coat protein complex
CoV Coronavirus
CPV Cytopathic vacuole CTP Cytidine triphosphate CVB3 Coksackie virus B3 Cy3 Indocarbocyanine 3 DENV Dengue virus
DMV Double-membrane vesicle DNA Deoxyribonucleic acid DNase Deoxyribonuclease
ds Double stranded
dsRNA Double-stranded RNA
E Envelope protein
EAV Equine arteritis virus
EDEM ER degradation enhancing alpha-mannosidase-like protein EFTEM Energy-filtered transmission electron microscopy
EGTA Ethylene glycol tetraacetic acid
8
List of abbreviations
EM Electron microscopy ER Endoplasmic reticulum
ERAD ER-associated protein degradation ERGIC ER-Golgi intermediate compartment ESI Electron spectroscopic imaging ET Electron tomography
eV Electron volt
Exo Exonuclease
FHV Flock house virus
FMDV Footh-and-mouth-disease virus FS Freeze substitution
G Golgi complex
GEF Guanine nucleotide exchange factor GFP Green fluorescent protein
GTP Guanosine-5’-triphosphate HCoV Human coronavirus HCV Hepatitis C virus
HEL Helicase
HeLa Henrietta Lacks
HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
Huh Human hepatoma
IF Immunofluorescence
IEM Immunoelectron microscopy IgG Immunoglobulin G
IM Inner membrane
kb Kilobase
LC3 Light chain 3
M Membrane protein or Mitochondrion Mab Monoclonal antibody
MHV Mouse hepatitis virus MOI Multiplicity of infection
MP Main protease
mRNA Messenger RNA MT Methyl transferase MVB Multivesicular body
N Nucleocapsid protein or Nucleus NaPi Sodium phosphate buffer
NC Nucleocapsid
NS Non-structural protein
9 List of abbreviations
nsp Non-structural protein
OM Outer membrane
ORF Open reading frame P RNA primase or Phosphorus
PALM photo-activated localization microscopy PBS Phosphate buffered saline
PC Paracrystalline arrays PDI Protein disulfide isomerase
PDM Product of the difference from the mean PFA Paraformaldehyde
p.i. Post infection
PI4K Phosphatidylinositol 4-kinase PLP Papain-like protease
pp Polyprotein
PRRSV Porcine reproductive and respiratory syndrome virus
PUR Puromycin
PV Poliovirus
rER Rough endoplasmic reticulum RdRp RNA-dependent RNA polymerase RF Replicative form
RFS Ribosomal frameshift RI Replicative intermediate RNA Ribonucleic acid RNase Ribonuclease
RTC Replication/transcription complex RVN Reticulovesicular network
SARS Severe acute respiratory syndrome
SARS-CoV Severe acute respiratory syndrome coronavirus
SDS-PAGE Sodium dodecyl sulfate polyacrylamide gel electrophoresis siRNA Small interfering RNA
SIRT Simultaneous iterative reconstruction technique SNARE Soluble NSF attachment protein receptor SRP Signal recognition particle
ss Single stranded
STED Stimulated emission depletion
STORM Stochastic optical reconstruction microscopy TEM Transmission electron microscopy
TF Transcriptive form TI Transcriptive intermediate
10
List of abbreviations
TIM Transporter inner membrane
TM Transmembrane domain
TOM Transporter outer membrane TRIS Tris(hydroxymethyl)aminomethane
TUNEL Terminal deoxynucleotidyl transferase dUTP nick end labeling TVC Tubulovesicular cluster
TX-100 Triton-X 100
UTP Uridine-5’-triphosphate V Smooth walled vesicles VP Vesicle packet
WNV West Nile virus
YFP Yellow fluorescent protein
