Adenovirus Methods and Protocols 2nd Edition Vol 2: Ad Proteins and RNA, Lifecycle and Host Interactions, and Phyologenetics (Methods in Molecular Medicine)

378 Pages·2007·3.217 MB·English

by  William S.M. Wold, Ann E. Tollefson

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Adenovirus Methods and Protocols, Second Edition
V 2
OLUME
M E T H O D S I N M O L E C U L A R M E D I C I N E™
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M E T H O D S I N M O L E C U L A R M E D I C I N E™
Adenovirus Methods
and Protocols
S E
ECOND DITION
Volume 2: Ad Proteins, RNA, Lifecycle,
Host Interactions, and Phylogenetics
Edited by
William S. M. Wold
Ann E. Tollefson
Department of Molecular Microbiology and Immunology
Saint Louis University School of Medicine
St. Louis, Missouri
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Library of Congress Cataloging-in-Publication Data
Adenovirus methods and protocols / edited by William S.M. Wold, Ann E. Tollefson. -- 2nd ed.
v. ; cm. -- (Methods in molecular medicine, ISSN 1543-1894 ; 130-131)
Includes bibliographical references and indexes.
Contents: v. 1. Adenoviruses, ad vectors, quantitation, and animal models -- v. 2. Ad proteins, RNA,
lifecycle, host interactions, and phylogenetics.
ISBN 1-58829-598-2 (v. 1 : alk. paper) -- ISBN 1-58829-901-5 (v. 2 : alk. paper)
1. Adenoviruses--Laboratory manuals. 2. Molecular biology--Laboratory manuals. I. Wold, William S. M.
II. Tollefson, Ann E. III. Series.
[DNLM: 1. Adenoviridae--Laboratory Manuals. W1 ME9616JM v.130-131 2007 / QW 25 A232 2007]
QR396.A336 2007
579.2'443--dc22
2006012284
Preface
Since their discovery in 1954, adenoviruses (Ads) have become a model for
studying virology, as well as molecular and cellular biology. Ads are easily
grown and manipulated, stable, and versatile. Ads replicate reproducibly, can
transform rodent cells to an oncogenic state, can induce tumors in certain ani-
mals, and have been instrumental in defining key cellular proteins and mecha-
nisms such as splicing, transcriptional regulation through transcription adaptor
proteins, and regulation of cell division and apoptosis. About half of the
approximately 35 Ad proteins physically interact with cellular proteins and
subvert them for use by the virus. In recent years, Ads have become premier
tools in vector technology and in experimental gene therapy research.
The Adenovirus Methods and Protocols volumes are designed to help new
researchers to conduct studies involving Ads and to help established researchers
to branch into new areas. The chapters, which are written by prominent investi-
gators, provide a brief general introduction to a topic, followed by tried and
true step-by-step methods pertinent to the subject. We thank returning con-
tributors for their updated and new chapters, and thank new contributors who
have expanded the content of this book.
Adenovirus Methods and Protocols, Second Edition, Volume 2: Ad Proteins,
RNA, Lifecycle, Host Interactions, and Phylogenetics, focuses on methods that
elucidate and quantitate the interactions of Ad with the host. This volume pro-
vides methods for analysis of transcription, splicing, RNA interference, sub-
cellular localization of proteins during infection, and cell cycle effects. Four
chapters are devoted to definition of interactions of viral and cellular proteins
(by co-immunoprecipitation or tandem mass spectrometry) or protein interac-
tions with viral DNA (by chromatin immunoprecipitation and electrophoretic
mobility shift assays). Other chapters provide thorough descriptions of the use
of microinjection procedures, transformation assays, and NK cell-mediated
cytolysis. Several chapters describe characterization of specific Ad proteins
(hexon, fiber, or protease/proteinase). Two chapters are devoted to defining
the phylogenetic relationships of Ads.
We thank contributors for sharing their secrets, John Walker for his patience,
and especially Dawn Schwartz, without whose expert assistance this work
would not have been possible.
William S. M. Wold
Ann E. Tollefson
v

Contents
Preface ..............................................................................................................v
Contents of the Companion Volume................................................................ix
Contributors .....................................................................................................xi
1 Analysis of the Efficiency of Adenovirus Transcription.........................1
Cristina Iftode and S. J. Flint
2 The Use of In Vitro Transcription to Probe Regulatory Functions
of Viral Protein Domains ................................................................15
Paul M. Loewenstein, Chao-Zhong Song, and Maurice Green
3 Preparation of Soluble Extracts From Adenovirus-Infected Cells
for Studies of RNA Splicing.............................................................33
Oliver Mühlemann and Göran Akusjärvi
4 In Vitro Methods to Study RNA Interference During
an Adenovirus Infection..................................................................47
Gunnar Andersson, Ning Xu, and Göran Akusjärvi
5 Simultaneous Detection of Adenovirus RNA and Cellular Proteins
by Fluorescent Labeling In Situ.......................................................63
Eileen Bridge
6 Study of Nucleolar Localization of Adenovirus Core Proteins............73
David A. Matthews
7 Analysis of Adenovirus Infections in Synchronized Cells ...................83
David A. Ornelles, Robin N. Broughton-Shepard,
and Felicia D. Goodrum
8 Co-Immunoprecipitation of Protein Complexes................................103
Peter Yaciuk
9 Chromatin Immunoprecipitation to Study the Binding of Proteins
to the Adenovirus Genome In Vivo ..............................................113
Jihong Yang and Patrick Hearing
10 Assaying Protein–DNA Interactions In Vivo and In Vitro Using
Chromatin Immunoprecipitation and Electrophoretic Mobility
Shift Assays ...................................................................................123
Pilar Perez-Romero and Michael J. Imperiale
11 Identifying Functional Adenovirus–Host Interactions Using
Tandem Mass Spectrometry..........................................................141
Anuj Gaggar, Dmitry Shayakhmetov, and André Lieber
vii
viii Contents
12 The Use of Cell Microinjection for the In Vivo Analysis of Viral
Transcriptional Regulatory Protein Domains................................157
Maurice Green, Andrew Thorburn, Robert Kern,
and Paul M. Loewenstein
13 Determination of the Transforming Activities
of Adenovirus Oncogenes.............................................................187
Michael Nevels and Thomas Dobner
14 Human Adenovirus Type 12: Crossing Species Barriers
to Immortalize the Viral Genome.................................................197
Walter Doerfler
15 Measurement of Natural-Killer Cell Lytic Activity of Adenovirus-
Infected or Adenovirus-Transformed Cells....................................213
John M. Routes
16 A Flow Cytometric Assay for Analysis of Natural-Killer
Cell-Mediated Cytolysis of Adenovirus-Transformed Cells...........221
Graham Bottley, Graham P. Cook, and G. Eric Blair
17 Large-Scale Purification and Crystallization of Adenovirus Hexon......231
John J. Rux and Roger M. Burnett
18 Synthesis and Assay of Recombinant Adenovirus Protease.............. 251
Joseph M. Weber
19 Assay for the Adenovirus Proteinase: Purification of the Enzyme
and Synthesis of a Fluorogenic Substrate......................................257
Walter F. Mangel and William J. McGrath
20 Cofactors of the Adenovirus Proteinase: Measuring Equilibrium
Dissociation Constants and Stoichiometries of Binding................269
Walter F. Mangel and William J. McGrath
21 Characterization of the Adenovirus Fiber Protein.............................281
Jeffrey A. Engler and Jeong Shin Hong
22 Phylogenetic Analysis of Adenovirus Sequences ..............................299
Balázs Harrach and Mária Benko"
23 Assessment of Genetic Variability Among Subspecies B1 Human
Adenoviruses for Molecular Epidemiology Studies.......................335
Adriana E. Kajon and Dean D. Erdman
Index ............................................................................................................357
C C V
ONTENTS OF THE OMPANION OLUME
Volume 1: Adenoviruses, Ad Vectors, Quantitation,
and Animal Models
1 Manipulation of Early Region 4
Julie Boyer and Gary Ketner
2 Isolation, Growth, and Purification of Defective Adenovirus
Deletion Mutants
Gary Ketner and Julie Boyer
3 Construction of Adenovirus Type 5 Early Region 1 (E1) and 4 (E4)
Virus Mutants
Peter Groitl and Thomas Dobner
4 Construction of Mouse Adenovirus Type 1 Mutants
Angela N. Cauthen, Amanda R. Welton, and Katherine R. Spindler
5 Generation of Recombinant Adenovirus Using Escherichia coli BJ5183
Recombination System
P. Seshidhar Reddy, Shanthi Ganesh, Lynda Hawkins,
and Neeraja Idamakanti
6 Production and Release Testing of Ovine Atadenovirus Vectors
Gerald W. Both, Fiona Cameron, Anne Collins, Linda J. Lockett,
and Jan Shaw
7 Construction of Capsid-Modified Recombinant Bovine Adenovirus
Type 3
Alexander N. Zakhartchouk, Qiaohua Wu, and Suresh K. Tikoo
8 Adenovirus Capsid Chimeras: Fiber Terminal Exon Insertions/Gene
Replacements in the MLTU
Jason Gall, John Schoggins, and Erik Falck-Pedersen
9 Temperature-Sensitive Replication-Competent Adenovirus shRNA
Vectors to Study Cellular Genes in Virus-Induced Apoptosis
Thirugnana Subramanian and Govindaswamy Chinnadurai
10 Evaluating Apoptosis in Tumor Cells Infected With Adenovirus
Expressing p53 Tumor Suppressor Gene
Elizabeth Perron, M. Behzad Zafar, Amanda Pister, Zhen-Guo Wang,
Jun Tian, and Prem Seth
11 Growth and Purification of Enteric Adenovirus Type 40
Vivien Mautner
ix