Handbook of Transcription Factor NF kappaB - 1st Edition

Visit the link below to download the full version of this book:

https://medidownload.com/product/handbook-of-transcription-factor-nf-kappab-1st-
edition/

Click Download Now

2794_book.fm Page iii Sunday, September 24, 2006 9:17 AM

Title Page
HANDBOOK OF

Transcription
Factor
NF-kappaB
Edited by
Sankar Ghosh

Boca Raton London New York

CRC Press is an imprint of the

Taylor & Francis Group, an informa business
 2794_book.fm Page iv Sunday, September 24, 2006 9:17 AM

CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2007 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business

No claim to original U.S. Government works

Printed in the United States of America on acid-free paper
10 9 8 7 6 5 4 3 2 1

International Standard Book Number-10: 0-8493-2794-6 (Hardcover)

International Standard Book Number-13: 978-0-8493-2794-0 (Hardcover)

This book contains information obtained from authentic and highly regarded sources. Reprinted
material is quoted with permission, and sources are indicated. A wide variety of references are
listed. Reasonable efforts have been made to publish reliable data and information, but the author
and the publisher cannot assume responsibility for the validity of all materials or for the conse-
quences of their use.

No part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any
electronic, mechanical, or other means, now known or hereafter invented, including photocopying,
microfilming, and recording, or in any information storage or retrieval system, without written
permission from the publishers.

For permission to photocopy or use material electronically from this work, please access www.
copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC)
222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that
provides licenses and registration for a variety of users. For organizations that have been granted a
photocopy license by the CCC, a separate system of payment has been arranged.

Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and
are used only for identification and explanation without intent to infringe.

Library of Congress Cataloging-in-Publication Data

Handbook of transcription factor NF-kappaB / [edited by] Sankar Ghosh.

p. ; cm.
Includes bibliographical references and index.
ISBN-13: 978-0-8493-2794-0 (alk. paper)
1. NF-kappa B (DNA-binding protein)--Handbooks, manuals, etc. 2. Tran-
scription factors--Handbooks, manuals, etc. 3. Gene expression--Handbooks,
manuals, etc. I. Ghosh, Sankar, 1959-
[DNLM: 1. NF-kappa B. QU 58.5 H2368 2006]

QP552.N46H36 2006
611’.018166--dc22 2006013488

Visit the Taylor & Francis Web site at

http://www.taylorandfrancis.com
and the CRC Press Web site at
http://www.crcpress.com

T&F_LOC_A_Master.indd 1 6/1/06 12:02:39 PM

2794_book.fm Page v Sunday, September 24, 2006 9:17 AM

Preface
In 1986, my laboratory was searching for transcription factors that might control
the activation of the kappa immunoglobulin light chain when we came across NF-κB.
We thought it was specific to B-lymphocytes and never imagined that it would turn
out to be among the most protean of transcription factors ever discovered. But that
realization came during the next few years as we first found that it could be induced
in many cells and then found that it was stored in the cytoplasm, ready to be activated
by a wide range of inducing stimuli. When its sequence was first determined, we
realized that it had a history before 1986; Howard Temin’s laboratory had discovered
the Rel oncogene years before and it is a slightly altered member of the NF-κB
family of proteins.
This book contains much that is known about the basic biology of NF-κB or at
least references to it. Its clearest function is as a transcription factor orchestrating
the activation and repression of many genes involved in inflammation, but it also
helps activate genes of innate and adaptive immunity in response to pathogens,
maintains liver integrity in the developing mouse, plays multiple roles in the nervous
system, and is implicated in skin, hair, and tooth formation and much more in the
vertebrate body. In insects, homologues of the mammalian proteins are involved in
defense against pathogens but also play key roles in development (for example,
dorsal in Drosophila establishes dorsal/ventral polarity in the developing embryo).
Any system in the body that plays so many important roles is likely to also cause
pathology when it goes awry, and NF-κB is no exception. Its role as an oncogene
showed early on that it could be a cause of cancer, and the linkage of cancer and
inflammation, which is so widely discussed today, is another reason for linking
NF-κB to cancer induction. NF-κB is implicated in a wide range of other pathologies,
including heart disease, muscular dystrophy, and many other conditions involving
chronic inflammation.
In 1986, we knew only a few transcription factors and only a few of the
intracellular proteins that transduce signals from cell surface receptors. Today, we
stare at myriads of components whose interactions make urban subway systems look
simple. A remarkable fraction of these intracellular mediators are parts of pathways
that lead to or through NF-κB. Thus, what was supposed to be a simple regulator
of a particular step in differentiation has turned out to be linked by transduction
pathways to many of the cellular signaling pathways. This book then is one of many
that should be read together if the full richness of the cell’s transduction machinery
is to be understood. No one person can today absorb this body of knowledge and
no one can keep pace with its continued growth. But each member of the community
of interested scientists must absorb what she or he can and then share in the
interactions that bring together the joint knowledge that one day will describe all of
cellular metabolism. Because new students interested in these systems are
2794_book.fm Page vi Sunday, September 24, 2006 9:17 AM

continually entering the field, a book such as this is an entry point for them, and it
is to these newcomers that I dedicate this limited preface.

David Baltimore
2794_book.fm Page vii Sunday, September 24, 2006 9:17 AM

The Editor
Sankar Ghosh, Ph.D., is currently a Professor of Immunobiology and Molecular
Biophysics and Biochemistry at Yale University School of Medicine. Dr. Ghosh
obtained his undergraduate education in Calcutta, India, before coming to the United
States in 1982 to pursue his Ph.D. at the Albert Einstein College of Medicine in
New York. After obtaining his Ph.D. in 1998 he joined the laboratory of Dr. David
Baltimore at the Whitehead Institute/Massachusettes Institute of Technology to carry
out postdoctoral studies in molecular immunology. During his postdoctoral fellow-
ship, Dr. Ghosh made major findings in the NF-κB field including establishing the
importance of phosphorylation in the regulation of NF-κB, and cloning the genes
encoding NF-κB p50, p65, and IκB genes. Dr. Ghosh then joined the faculty at Yale
in 1991, where he has continued to investigate mechanisms responsible for regulating
NF-κB activity.
2794_book.fm Page viii Sunday, September 24, 2006 9:17 AM
2794_book.fm Page ix Sunday, September 24, 2006 9:17 AM

Contributors
Albert S. Baldwin Tom Huxford
Lineberger Comprehensive Cancer San Diego State University
Center San Diego, California
University of North Carolina School of
Medicine Alain Israël
Chapel Hill, North Carolina Institut Pasteur
Paris, France
Yinon Ben-Neriah
Lautenberg Center for Immunology Michael Karin
Hadassah Medical School School of Medicine
Hebrew University University of California, San Diego
Jerusalem, Israel La Jolla, California

Lin-Feng Chen Steven C. Ley

Gladstone Institute of Virology and Division of Immune Cell Biology
Immunology National Institute for Medical Research
University of California, San Francisco London, England
San Francisco, California
Anu K. Moorthy
Gourisankar Ghosh University of California, San Diego
University of California, San Diego La Jolla, California
La Jolla, California
Vinay Tergaonkar
Warner C. Greene Laboratory of Genetics
Gladstone Institute of Virology and The Salk Institute for Biological Studies
Immunology La Jolla, California
University of California, San Francisco
San Francisco, California Inder M. Verma
Laboratory of Genetics
Hans Häcker The Salk Institute for Biological Studies
Laboratory of Gene Regulation and La Jolla, California
Signal Transduction
School of Medicine Sebo Withoff
University of California, San Diego Laboratory of Genetics
La Jolla, California The Salk Institute for Biological Studies
La Jolla, California
Matthew S. Hayden
Yale University School of Medicine
New Haven, Connecticut
2794_book.fm Page x Sunday, September 24, 2006 9:17 AM
2794_book.fm Page xi Sunday, September 24, 2006 9:17 AM

Contents
Chapter 1 The NF-κB Pathway: A Paradigm for Inducible Gene
Expression ............................................................................................1
Sankar Ghosh

Chapter 2 Structural Aspects of NF-κB and IκB Proteins ..................................9

Anu K. Moorthy, Tom Huxford, and Gourisankar Ghosh

Chapter 3 Regulation of IKK .............................................................................25

Hans Häcker and Michael Karin

Chapter 4 Control of NF-κB Activity by Ubiquitination...................................53

Steven C. Ley and Yinon Ben-Neriah

Chapter 5 Regulation of Nuclear NF-κB Action: A Key Role for

Posttranslational Modification ...........................................................87
Lin-Feng Chen and Warner C. Greene

Chapter 6 NF-κB in the Innate Immune System .............................................107

Matthew S. Hayden and Sankar Ghosh

Chapter 7 NF-κB in the Adaptive Immune System: Lymphocyte Survival

and Function .....................................................................................131
Matthew S. Hayden and Sankar Ghosh

Chapter 8 NF-κB and IKK as Key Mediators of Inflammation and

Oncogenic Progression ....................................................................159
Albert S. Baldwin

Chapter 9 NF-κB and Associated Human Genetic Pathologies ......................183

Alain Israël
2794_book.fm Page xii Sunday, September 24, 2006 9:17 AM

Chapter 10 Regulating the Master Regulator NF-κB: From Natural

Strategies to Rationally Designed Superdrugs ................................195
Sebo Withoff, Vinay Tergaonkar, and Inder M. Verma

Index ......................................................................................................................223
2794_book.fm Page 1 Sunday, September 24, 2006 9:17 AM

The NF-κB Pathway:

1 A Paradigm for Inducible
Gene Expression
Sankar Ghosh

CONTENTS

1.1 Introduction ......................................................................................................1

1.2 NF-κB/Rel Proteins..........................................................................................2
1.3 IκB Proteins .....................................................................................................4
1.4 IκB Kinase Complex .......................................................................................5
1.5 NF-κB Inducers and κB-Dependent Genes.....................................................6
References..................................................................................................................7

1.1 INTRODUCTION
The eukaryotic transcription factor NF-κB was first identified by Sen and Baltimore
20 years ago as a protein that bound to a specific decameric DNA sequence
(5´-GGGACTTTCC-3´) within the intronic enhancer of the immunoglobulin kappa
light chain gene in mature B and plasma cells but not pre-B cells [1]. Subsequently,
these same workers demonstrated induction of NF-κB:DNA binding in other cell
types in response to exogenously applied stimuli, such as phorbol esters, and showed
that this activation was independent of de novo protein synthesis [2]. In the decades
following its discovery, NF-κB has been shown to exist in most cell types, and
specific NF-κB binding sites termed κB sites have been identified in the promot-
ers/enhancers of a very large number of inducible genes. Similarly, the range of
biological factors and environmental conditions known to induce NF-κB activity
has been shown to be remarkably large and diverse. Efforts to understand how the
many intracellular signals evoked by such diverse stimuli can be integrated at the
level of activation of this transcription factor has led to fundamental insights about
many aspects of gene regulation and signal transduction. These insights in turn have
stimulated discoveries in different biological pathways.
In keeping with the enormous research activity targeted toward understanding
the regulation of NF-κB in different biological systems, a large number of reviews
have been, and are being, published discussing different features of this transcription
factor. However, the breadth of information makes it impossible for any particular

1
2794_book.fm Page 2 Sunday, September 24, 2006 9:17 AM

2 Handbook of Transcription Factors NF-kappaB

review, or even a collection of reviews, to provide an adequate summary of the

current knowledge about NF-κB. The purpose of this volume is to collect in one
place a number of chapters, written by leading authorities who were involved in
making the seminal discoveries that have shaped this field, in a form that emphasizes
current knowledge, with enough historical information to make the process of dis-
covery apparent. Significant effort has been invested in making the chapters similar
in style, giving this volume the feel of a textbook. It is also anticipated that with
input from the community, this handbook will be updated at regular intervals, to
ensure that the information included remains current and useful.
We begin this handbook on NF-κB by first providing a summary introduction
to the key features of this transcription factor. We believe this information will
provide an uninitiated reader easier access to the complexities in the NF-κB system.
Subsequent chapters will delve in greater detail into different regulatory features of
this transcription factor, culminating with a discussion of current efforts to develop
therapies aimed at inhibiting the aberrant activity of NF-κB in different diseases.

1.2 NF-κB/REL PROTEINS

In the majority of cell types NF-κB exists in the cytoplasm as homo- or heterodimers
of a family of structurally related proteins. Mammalian cells express five members
that contain a conserved N-terminal region called the Rel homology domain (RHD)
within which lies the DNA-binding and dimerization domains and the nuclear
localization signal (NLS) (Chapter 2). In unstimulated cells, NF-κB complexes are
sequestered in an inactive form via interaction with a monomer of an inhibitory
protein called IκB, which itself belongs to a structurally and functionally related
family of molecules. Signals that induce NF-κB activity cause degradation of IκB,
allowing NF-κB dimers to translocate to the nucleus and induce gene expression
(Figure 1.1). Although in most cases NF-κB activity must be induced, in certain cell
types, e.g., mature B cells, thymocytes, monocytes, macrophages, neurons, corneal
keratinocytes, vascular smooth muscle cells, and many tumor cells, NF-κB can also
be detected as a constitutively active, nuclear protein.
The first reports of purification of NF-κB DNA-binding subunits to homogeneity
identified two proteins with molecular weights of approximately 50 and 65 kDa
[3,4], respectively. Purification was performed using κB-site-specific DNA affinity
chromatography and the two proteins, referred to as p50 (also called NF-κB1) and
p65 (RelA), were subsequently shown to form heterodimers that bind specifically
to cognate κB-sites. The functional domains of NF-κB/Rel proteins were determined
after molecular cloning of p50, which revealed that the N-terminal 300 amino acids,
subsequently termed the Rel-homology domain, was highly homologous to the
oncogene v-Rel, its corresponding cellular homologue c-Rel and the Drosophila
protein Dorsal [4,5]. Further studies revealed that p65/RelA, p100/p52 (NF-κB2),
and Rel-B were also members of the mammalian Rel-family, thereby bringing the
total to five. Almost every combination of NF-κB/Rel proteins as homo- or het-
erodimers, in either the cytoplasm or nucleus of many different cell types, has been
described. For example, p50/p65 heterodimers are found in the cytoplasm of most
2794_book.fm Page 3 Sunday, September 24, 2006 9:17 AM

The NF-κB Pathway 3

NF-κB:IκB

Cytosol

Nucleus

FIGURE 1.1 The basic paradigm of the NF-κB signaling pathway. In uninduced cells, NF-κB
remains in the cytosol bound to inhibitory IκB proteins. Stimulation of cells leads to the
activation of the IκB kinase complexes that phosphorylate the IκB proteins. The phosphory-
lated IκB proteins are ubiquitinated and degraded, allowing the released NF-κB to translocate
to the nucleus and drive gene expression.

cells, whereas a constitutively active nuclear NF-κB in mature B cells is a dimer of

p50/c-Rel. Dimers of p52/c-Rel, p65/c-Rel, p65/p65, p50/p50, p52/p52, and p50/p52
have also been identified. RelB is a notable exception in that it only forms dimers
with p50 or p52. These RelB/p52-containing dimers are generated as a result of
signaling through the “alternative” NF-κB activation pathway (see Section 1.4 and
Chapters 2 and 3) and are believed to be the key dimeric form of NF-κB responsible
for expression of genes involved in lymphoid organogenesis.
Not all combinations of NF-κB/Rel proteins are transcriptionally active; and the
members of this family can be divided into two groups based upon their transacti-
vating ability (see Chapter 5 for a discussion of additional transcriptional require-
ments). First, p65, c-Rel, and RelB contain potent transactivation domains within
their C-terminal portions. In addition to its C-terminal domain, RelB also contains
an N-terminal leucine zipper-like region, and both these domains are required for
RelB to be fully active. However, neither p50 nor p52 contains any transactivating
regions and, as such, are transcriptionally inactive. Homo- or heterodimers of p50
and p52 have been shown to repress κB-dependent transcription in vivo, most likely
through recruitment of histone deacetylases to κB-sites. It is believed that p50
homodimers inhibit transcription by constitutively occupying κB sites that might
otherwise be bound by transactivating NF-κB/Rel proteins. One interesting property
of p50 and p52 homodimers is their ability to specifically associate with two atypical
members of the IκB family (see Section 1.3), namely the proto-oncogene BcL-3
and IκBζ. These interactions have been shown to induce κB-dependent transcription
by inhibiting DNA-binding of p50 and p52 homodimers, and by providing transac-
tivating potential to these normally inactive dimers.
In contrast to NF-κB/Rel molecules containing C-terminal transactivation
domains (p65, c-Rel, and RelB), p50 nor p52 is synthesized as large precursor