Virus-Host Interactions: Methods and Protocols

371 Pages·2013·7.206 MB·English

by  Hannah Striebinger, Manfred Koegl, Susanne M. Bailer (auth.), Susanne M. Bailer, Diana Lieber (eds.)

Methods in
Molecular Biology 1064
Susanne M. Bailer
Diana Lieber Editors
Virus-Host
Interactions
Methods and Protocols
M M B ™
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Virus-Host Interactions
Methods and Protocols
Edited by
Susanne M. Bailer
Institute for Interfacial Engineering and Plasma Technology, University of Stuttgart, Stuttgart, Germany
Diana Lieber

Institute of Virology, Ulm University Medical Center, Ulm, Germany
Editors
Susanne M. Bailer Diana Lieber
Institute for Interfacial Engineering Institute of Virology
and Plasma Technology Ulm University Medical Center
University of Stuttgart Ulm , Germany
Stuttgart, G ermany
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-62703-600-9 ISBN 978-1-62703-601-6 (eBook)
DOI 10.1007/978-1-62703-601-6
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Pref ace
Viruses represent a reduced form of life that depends on host cells for propagation. To this
end, viruses approach and penetrate cells and usurp cellular machineries for their own ben-
efi t. In the course of infection, cellular processes may be attacked, hijacked, or silenced by
the invader. Naturally, interactions formed between a virus and its host are very complex.
Many viruses exploit the DNA replication machinery for their own genomic amplifi cation.
Synthesis of viral proteins takes advantage of transcriptional and translational functions
available in the host. Moreover, enveloped viruses remodel cellular membranes to wrap
their capsids. Thus, during formation of infectious progeny, all components of a virus
including its envelope, structural, and regulatory proteins as well as the genomic material
contact host structures.
Usually, a virus aims at maximally exploiting the host functions while maintaining its
integrity and vitality. Hosts in turn are equipped with mechanisms for defence involving
immunological as well as cell-based means. While the intricate interplay between viral rep-
lication and immunological defense has been subject of intensive research for a long time,
more recently, virus- and host-encoded small RNAs have emerged as tug-of-war for coex-
istence of virus and host.
Classical virology in particular of viruses with complex genomes focused on the charac-
terization of individual genes and their function during viral replication with the aim to
defi ne their disease-causing potential and to develop antiviral strategies. At the same time,
viruses have been used as models to understand cellular processes, e.g., the development of
cancer. In addition, viruses allowed insights into basic principles of cell and molecular biol-
ogy, demonstrated by the identifi cation of protein-embedded signals for nucleocytoplasmic
transport. Recent technological improvements have enabled the systematic analysis of the
virus–host interplay be it on the genomic, the transcriptomic, or proteomic level. In paral-
lel, bioinformatic tools have emerged in support of the large datasets generated by these
high-throughput approaches.
This comprehensive volume consists of 25 chapters and covers various aspects of viro-
logical research. Current protocols are provided in great detail where small-scale analyses are
equally considered as state-of-the-art systematic approaches. The main intention is to equip
researchers with protocols of widely used techniques and to further broaden the repertoire
of experienced virologists by adding most recently developed systematic technologies.
Chapters 1 – 8 on biochemical approaches include molecular interactions and regulatory
mechanisms on the protein as well as the RNA level with a strong focus on the manifold
possibilities to study protein–protein interactions. As small regulatory RNAs have progres-
sively drawn attention of the fi eld, there are chapters on RNAi screens and functional analy-
ses of miRNAs. Since large-scale analysis has lately become more and more important,
bioinformatic methods have been given special consideration in a separate review.
v
vi Preface
Chapters 9 – 18 detail cell biological methodologies. These include a number of
visualizing and imaging techniques ranging from traditional electron microscopy to
advanced high-resolution and live-imaging microscopy, allowing elucidation of protein and
infection dynamics. Moreover, tools and methods to monitor characteristic parameters of
infectivity and to trace viral genomes or live viruses in vitro and i n vivo such as in 3D tissue
or animal models have been included. Finally, this volume concludes with immunological
aspects in Chapters 1 9 – 25 , highlighting viral interactions with immune cells and the usabil-
ity of immunological assays and mouse genetic models as powerful tools in virology.
Stuttgart , Germany Susanne M. Bailer
Ulm , Germany Diana L ieber
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 A High-Throughput Yeast Two-Hybrid Protocol to Determine
Virus–Host Protein Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Hannah Striebinger, Manfred Koegl, and Susanne M. Bailer
2 Analysis of Protein–Protein Interactions Using LUMIER Assays . . . . . . . . . . . 17
Sonja Blasche and Manfred Koegl
3 Detection of Protein Interactions During Virus Infection
by Bimolecular Fluorescence Complementation . . . . . . . . . . . . . . . . . . . . . . . 29
Stefan Becker and Jens von Einem
4 Discovery of Host–Viral Protein Complexes During Infection. . . . . . . . . . . . . 43
Daniell L. Rowles, Scott S. Terhune, and Ileana M. Cristea
5 Screening for Host Proteins with Pro- and Antiviral Activity
Using High-Throughput RNAi. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Samantha J. Griffiths
6 High Resolution Gene Expression Profiling of RNA Synthesis,
Processing, and Decay by Metabolic Labeling of Newly Transcribed RNA
Using 4-Thiouridine. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Lars Dölken
7 Isolation and Characterization of Pathogen-Bearing Endosomes Enable
Analysis of Endosomal Escape and Identification of New Cellular Cofactors
of Infection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Konstanze D. Scheffer, Ruth Popa-Wagner, and Luise Florin
8 Computational Analysis of Virus–Host Interactomes. . . . . . . . . . . . . . . . . . . . 115
Caroline C. Friedel
9 Interspecies Heterokaryon Assay to Characterize the Nucleocytoplasmic
Shuttling of Herpesviral Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Shuai Wang, Kezheng Wang, and Chunfu Zheng
10 Detection of Integrated Herpesvirus Genomes by Fluorescence
In Situ Hybridization (FISH) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Benedikt B. Kaufer
11 Fast Generation of Stable Cell Lines Expressing Fluorescent Marker
Molecules to Study Pathogen Induced Processes. . . . . . . . . . . . . . . . . . . . . . . 153
Jens Bernhard Bosse, Jessica Ragues, and Harald Wodrich
12 Determination of HSV-1 Infectivity by Plaque Assay and a Luciferase
Reporter Cell Line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Diana Lieber and Susanne M. Bailer
vii
viii Contents
13 Generation of a Stable Cell Line for Constitutive miRNA Expression . . . . . . . 183
Diana Lieber
14 Applications for a Dual Fluorescent Human Cytomegalovirus in the Analysis
of Viral Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Kerstin Laib Sampaio, Gerhard Jahn, and Christian Sinzger
15 High Temporal Resolution Imaging Reveals Endosomal Membrane
Penetration and Escape of Adenoviruses in Real Time. . . . . . . . . . . . . . . . . . . 211
Ruben Martinez, Andrew M. Burrage, Christopher M. Wiethoff,
and Harald Wodrich
16 Three-Dimensional Visualization of Virus-Infected Cells by Serial Sectioning:
An Electron Microscopic Study Using Resin Embedded Cells. . . . . . . . . . . . . 227
Martin Schauflinger, Clarissa Villinger, and Paul Walther
17 3D-Tissue Model for Herpes Simplex Virus-1 Infections. . . . . . . . . . . . . . . . . 239
Ina Hogk, Steffen Rupp, and Anke Burger-Kentischer
18 In Vivo Visualization of Encephalitic Lesions in Herpes Simplex Virus
Type 1 (HSV-1) Infected Mice by Magnetic Resonance Imaging (MRI) . . . . . 253
Wali Hafezi and Verena Hoerr
19 Detection of Antigen-Specific T Cells Based on Intracellular Cytokine
Staining Using Flow-Cytometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
Tina Schmidt and Martina Sester
20 Functional NK Cell Cytotoxicity Assays Against Virus Infected Cells. . . . . . . . 275
Rebecca J. Aicheler and Richard J. Stanton
21 Assessment of Natural Killer Cell Responses to Human
Cytomegalovirus-Infected Macrophages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Zeguang Wu, Giada Frascaroli, and Thomas Mertens
22 Analysis of Cell Migration During Human Cytomegalovirus (HCMV) Infection . . . 299
Stefania Varani and Giada Frascaroli
23 Gene Targeting in Mice: A Review . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
Hicham Bouabe and Klaus Okkenhaug
24 A Protocol for Construction of Gene Targeting Vectors
and Generation of Homologous Recombinant Embryonic Stem Cells. . . . . . . 337
Hicham Bouabe and Klaus Okkenhaug
25 Measurement of Mouse Cytomegalovirus-Induced Interferon-β
with Immortalized Luciferase Reporter Cells. . . . . . . . . . . . . . . . . . . . . . . . . . 355
Evgenia Scheibe, Stefan Lienenklaus, Tobias May,
Vladimir Gonçalves Magalhães, Siegfried Weiss, and Melanie M. Brinkmann
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
Contributors
REBECCA J. AICHELER • Institute of Infection and Immunity, School of Medicine, Cardiff
University , Cardiff, UK
SUSANNE M. BAILER • Institute for Interfacial Engineering and Plasma Technology IGVP,
University of Stuttgart , Stuttgart, Germany
STEFAN BECKER • Institute of Virology, Ulm University Medical Center , Ulm , Germany
SONJA BLASCHE • Genomics and Proteomics Core Facility, German Cancer Research
Center , Heidelberg, Germany
JENS B ERNHARD B OSSE • Department of Molecular Biology , P rinceton University , Princeton,
NJ , USA
HICHAM BOUABE • Laboratory of Lymphocyte Signalling and Development, Babraham
Institute , Cambridge, UK
MELANIE M. BRINKMANN • Helmholtz Centre for Infection Research , Braunschweig,
Germany
ANKE BURGER-KENTISCHER • Molecular Biotechnology , Fraunhofer Institute for Interfacial
Engineering and Biotechnology IGB , Stuttgart, Germany
ANDREW M. BURRAGE • Department of Microbiology and Immunology, Loyola University
Medical Center , Maywood , IL , USA
ILEANA M. CRISTEA • Department of Molecular Biology , Princeton University , Princeton,
NJ , USA
LARS DÖLKEN • Department of Medicine, Addenbrooke’s Hospital, University of
Cambridge , Cambridge, UK
LUISE FLORIN • Department of Medical Microbiology and Hygiene , Johannes Gutenberg
University Mainz, Mainz, Germany
GIADA FRASCAROLI • Institute of Virology, Ulm University Medical Center , Ulm , Germany
CAROLINE C. FRIEDEL • Institute for Informatics, Ludwig-Maximilians-Universität ,
München, Germany
SAMANTHA J. GRIFFITHS • Division of Pathway Medicine, University of Edinburgh ,
Edinburgh, UK
WALI HAFEZI • Institute of Medical Microbiology Clinical Virology, University Hospital
Münster , Münster , Germany
VERENA HOERR • Institute of Clinical Radiology, University Hospital Münster , Münster ,
Germany
INA HOGK • Institute for Interfacial Engineering and Plasma Technology IGVP,
University of Stuttgart , Stuttgart, Germany
GERHARD JAHN • Institute of Medical Virology and Epidemiology of Virus Diseases,
University Hospital Tuebingen , Tuebingen, Germany
BENEDIKT B. KAUFER • Institute of Virology, Freie Universität Berlin , Berlin , Germany
MANFRED KOEGL • Boehringer Ingelheim Oncology , Vienna, Austria
KERSTIN LAIB SAMPAIO • Institute of Medical Virology and Epidemiology of Virus Diseases,
University Hospital Tuebingen , Tuebingen, Germany
DIANA LIEBER • Institute of Virology, Ulm University Medical Center , Ulm , Germany
STEFAN LIENENKLAUS • Helmholtz Centre for Infection Research , Braunschweig, Germany
ix