Experimental Glycoscience: Glycobiology

475 Pages·2008·3.8 MB·English

by  Takeomi Murata, Taichi Usui (auth.), Naoyuki Taniguchi M.D., Ph.D., Akemi Suzuki M.D., Ph.D., Yukishige Ito Ph.D., Hisashi Narimatsu M.D., Ph.D., Toshisuke Kawasaki Ph.D., Sumihiro Hase Ph.D. (eds.)

Experimental Glycoscience
Glycobiology
GLY_VOL2_PR.indd I 6/30/2008 11:54:00 AM
N. Taniguchi, A. Suzuki, Y. Ito, H. Narimatsu,
T. Kawasaki, S. Hase (Eds.)
Experimental Glycoscience
Glycobiology
GLY_VOL2_PR.indd III 6/30/2008 11:54:00 AM
Naoyuki Taniguchi, M.D., Ph.D.
Professor, Department of Disease Glycomics, Research Institute for Microbial
Diseases, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan;
Systems Glycobiology Group, Advanced Science Institute, RIKEN, Wako,
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Akemi Suzuki, M.D., Ph.D.
Professor, Institute of Glycotechnology, Future Science and Technology Joint Research
Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
Yukishige Ito, Ph.D.
Chief Researcher, RIKEN Discovery Research Institute, Synthetic Cellular Chemistry
Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Hisashi Narimatsu, M.D., Ph.D.
Research Center for Medical Glycoscience, Advanced Industrial Science and
Technology, AIST Tsukuba, Central 2, Tsukuba, Ibaraki 305-8568, Japan
Toshisuke Kawasaki, Ph.D.
Professor, Research Center for Glycobiotechnology, Ritsumeikan University, 1-1-1
Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
Sumihiro Hase, Ph.D.
Professor, Graduate School of Science, Osaka University, 1-1 Machikaneyama,
Toyonaka, Osaka 560-0043, Japan
ISBN: 978-4-431-77921-6 Tokyo Berlin Heidelberg New York
eISBN: 978-4-431-77922-3
Library of Congress Control Number: 2008930135
Cover: A ribbon diagram of an infl uenza virus neuraminidase subtype N9. Image created by Dr. Yoshiki
Yamaguchi
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GLY_VOL2_PR.indd IV 7/8/2008 6:35:14 PM
Preface
There is growing interest in glycoscience, which is known to be one of the most important
research areas in the medical and life sciences. It is now clear that glycans are impli-
cated in various diseases such as cancer, immune diseases, infectious diseases, muscle-
degenerative diseases, neurodegenerative diseases, and diabetes. Glycans also play a
pivotal role in fertilization, growth and development, regeneration, and the aging process.
Moreover, glycans are likely targets for the discovery of biomarkers, vaccines, and drugs
for cancer and infl ammatory diseases.
For these reasons, scientists in every fi eld of research have realized that the application
of glycoscience contributes to the development of their research projects. They also have
a feeling, however, that glycoscience is technically diffi cult because of the heterogeneity
and complexity of glycans. It is evident that many researchers from different disciplines
who are not familiar with the specialized techniques used in glycoscience require detailed
advice.
Newly developed analytical techniques—namely, the development of mass spectrom-
etry, capillary electrophoresis, and high-performance liquid chromatography—and the
accumulated resources of cloned glycosyltransferase genes, lectins, chemically and/or
enzymatically synthesized compounds, bioinformatics, and KO mice or gene-targeting
animals have opened new avenues for glycoscience.
The Japan Consortium for Glycobiology and Glycotechnology (JCGG) published the
Japanese monograph entitled Glycoscience: A Door to Open the Future in 2006 written
by more than 150 glycoscientists to summarize recent advances in this fi eld in Japan and
to offer readers a broad introduction to glycoscience. This present book is the English
version but is largely modifi ed and updated. Many of the contributors are experts in their
respective fi elds and have made an effort to present their material in a manner that is
understandable to those with general knowledge but with a different background in the
biological sciences. The book is presented in three ways: 1) as a “cookbook” with which
researchers will be able to prepare the solutions described and follow “recipes” to com-
plete their experiments without needing to consult original research papers; 2) by
“concept,” which will allow researchers to search out the discipline, research equipment,
research device, or methodology required; and 3) as a “table” providing an overview of
the research data, among other information. For those who wish to delve into these topics,
we included several references at the end of each chapter for further reading. This book
will therefore be of interest to many scientists both in glycoscience and in the broader
fi elds of biology, chemistry, and medicine, as well as to postdoctoral fellows, students,
and young scientists.
I would like to take this opportunity to introduce the JCGG which was launched 5
years ago (Yoshitaka Nagai, JCGG president, professor emeritus, The University of
Tokyo). The organization of this consortium is slightly different from that of the Con-
sortium for Functional Glycomics (CFG) in the United States. Instead of receiving offi -
cial support from the Japanese government for its operation, scientists took the initiative
for creating and supporting the consortium by using their existing government research
grants. Scientists who have been funded by different ministries of the Japanese govern-
ment, such as the Ministry of Education, Culture, Sports, Science and Technology
V
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VI Preface
(MEXT); the Japan Society for the Promotion of Science (JSPS); the Japan Science and
Technology Agency (JST); the Ministry of Economy, Trade and Industry (METI); the
New Energy and Industrial Technology Development Organization (NEDO); and the
Ministry of Health, Labour and Welfare, are involved in this effort. They have joined
together to form this consortium and to provide support through their individual research
grants.
The JCGG aims to facilitate the exchange of scientifi c information; the sharing of
resources, equipment, and facilities; the fostering of young scientists; and the construc-
tion of a database and infrastructures, among other goals. It also aims to launch national
research centers in Japan, such as a Systems Glycobiology Center, where glycobiology
can merge with such areas as nanotechnology, bioinformatics, and chemical biology to
pursue the goals mentioned above, including medical applications. The JCGG holds an
annual symposium in which more than 600 people usually participate.
On behalf of the editors, I gratefully acknowledge all those who contributed to this
volume despite their busy schedules. Special thanks are due to Mr. Keiichi Yoshida, the
secretary general of JCGG, for his skillful assistance in editing. I also thank Kinpodo,
Kyoto, who published the original Japanese version, for agreeing to publication of the
English version.
Thanks also go to the editorial staff members at Springer Japan, for their constant
support, patience regarding the deadline for the manuscript, and skill in directing the
production of this book.
I hope this publication will provide an impetus for future research.
On behalf of the editors,
Naoyuki Taniguchi, MD, PhD
February 10, 2008
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Editorial Board
Editors:
Naoyuki Taniguchi, M.D., Ph.D.
Department of Disease Glycomics, Research Institute for Microbial Diseases, Osaka
University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan;
Systems Glycobiology Group, Advanced Science Institute, RIKEN, Wako, 2-1 Hirosawa,
Wako, Saitama 351-0198, Japan
Akemi Suzuki, M.D., Ph.D.
Institute of Glycotechnology, Future Science and Technology Joint Research Center,
Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
Yukishige Ito, Ph.D.
RIKEN Discovery Research Institute, Synthetic Cellular Chemistry Laboratory,
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Hisashi Narimatsu, M.D., Ph.D.
Research Center for Medical Glycoscience, Advanced Industrial Science and Technol-
ogy, AIST Tsukuba, Central 2, Tsukuba, Ibaraki 305-8568, Japan
Toshisuke Kawasaki, Ph.D.
Research Center for Glycobiotechnology, Ritsumeikan University, 1-1-1 Noji-Higashi,
Kusatsu, Shiga 525-8577, Japan
Sumihiro Hase, Ph.D.
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka
560-0043, Japan
Co-editors:
Koichi Furukawa, M.D., Ph.D., School of Medicine, Nagoya University, Japan
Makoto Kiso, Ph.D., Faculty of Applied Biological Sciences, Gifu University, Japan
Tomoya Ogawa, Ph.D., RIKEN Yokohama Institute, Japan
Shoichi Kusumoto, Ph.D., Suntory Institute For Bioorganic Research, Japan
VII
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Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . V
Editorial Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . VII
Contents of Experimental Glycoscince: Glycochemistry . . . . . . . . . . . . . . . . . . . . XVI
List of Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . XVII
Part 1 Glycosyltransferase Genes
Section I Glycosyltransferases
Convenient Synthesis of Glycan-Related Oligosaccharides and
Their Transformation into Neoglycoconjugates Using Enzymatic
Methods
T. Murata, T. Usui . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Comparison of Glycosyltransferase Families Using the Profi le
Hidden Markov Model
N. Kikuchi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
N-Acetylglucosaminyltransferases Involved in N-Glycan
Biosynthesis
K. Inamori, N. Taniguchi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
UDP-N-Acetyl-d-Galactosamine:polypeptide
N-Acetylgalactosaminyltransferases (ppGaNTases,
pp-GalNAc-Ts, EC 2.4.1.41)
K. Tachibana . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Glycosyltransferase Family with b4GT Motif (b4Gal-T and
b4GalNAc-T Family)
T. Sato, H. Narimatsu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
b1,3-glycosyltransferase Gene Family and IGnT Gene Family
A. Togayachi, T. Sato, H. Narimatsu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
O-Mannosyltransferase and POMGnT1
T. Endo, H. Manya . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Glycosyltransferases Involved in O-fucose Glycan Synthesis
T. Okajima, T. Matsuda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Fucosyltransferase (a1,2/ a1,3/ a1,4-fucosyltransferases)
T. Kudo, H. Narimatsu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
FUT8 Assay
H. Ihara, H. Korekane, A. Matsumoto, N. Taniguchi . . . . . . . . . . . . . . . . . . . . 39
VIII
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Contents IX
Sialyltransferases
S. Tsuji . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Glucuronyltransferases Involved in the HNK-1 Biosynthesis
S. Kakuda, T. Kawasaki, S. Oka . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
a1,4-Linkage Glycosyltransferases
J. Nakayama, K. Furukawa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Glycosyltransferases Involved in the Biosynthesis of Glycolipids
K. Furukawa, A. Tsuchida, K. Furukawa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Sialyltransferases and Other Enzymes Involved in the Biosynthesis of
Gangliosides
K. Furukawa, K. Furukawa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Heparan Sulfate Synthases and Related Genes
S. Mizumoto, H. Kitagawa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Chondroitin Sulfate Biosynthesis and Related Genes
H. Watanabe, K. Kimata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Biosynthesis of Keratan Sulfate
A. Seko, K. Yamashita . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Hyaluronan Synthase Assay
N. Itano . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Glycosylphosphatidylinositol-Anchored Protein Biosynthesis and Related
Genes in Mammalian Cells
Y. Maeda, T. Kinoshita . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Cloning of Genes for N-linked Oligosaccharide Synthesis in Endoplasmic
Reticulum
K. Nakayama, Y. Jigami . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Section II Sugar-Modifi ed Enzymes
N-acetylglucosamine-6-O-sulfotransferases
K. Uchimura, T. Muramatsu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Sulfotransferases Involved in Sulfation of Glycosaminoglycans
O. Habuchi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Sulfatide Synthase
K. Honke . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
CMP-N-acetylneuraminic Acid Hydroxylase
A. Suzuki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Section III Transporters
Nucleotide Sugar Transporter Genes and Their Functional Analysis
S. Nishihara . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
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X Contents
Section IV Glycosidases
Processing Enzymes Involved in N-glycan Biosynthesis and Related
Genes: the Golgi N-glycan Processing a-mannosidase II and a-
mannosidase IIx
T.O. Akama, M.N. Fukuda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Sialidase Genes
T. Miyagi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Release of Sugar Chains from Glycosphingolipids
M. Ito . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Heparan Sulfate Endosulfatase Assay
K. Keino-Masu, M. Masu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Sphingolipid Activator Proteins
J. Matsuda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Section V Animal Lectins
Affi nity Purifi cation of Recombinant Galectins
J. Iwaki, J. Hirabayashi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Siglec Family
T. Angata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Part 2 Functional Analyses of Sugar Chains
Section VI Immunology
NKT Cells and Their Recognition of Glycolipids
K. Seino, M. Taniguchi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Carbohydrate Ligands for Selectins in Immune Cell Traffi cking
R. Kannagi, K. Ohmori . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Carbohydrate Recognition by Cytokines and Its Relevance to Their
Physiological Activities
K. Fukushima, K. Yamashita . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Detection of Mouse MGL1/CD301a by a Specifi c Monoclonal Antibody
K. Denda-Nagai, K. Suzuki, M. Goda, A. Kudo, H. Kawakami, T. Irimura . . 158
Roles of Serum Lectins in Host Defense
N. Kawasaki, B.Y. Ma, T. Kawasaki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Siglec-2 Is a Key Molecule for Immune Response
T. Tsubata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Galectin and Immune System: Toward Clinical Applications
M. Hirashima . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Section VII Brains and Nerves
Novel Glycolipids in Developing Brain: Determination by
Nano-LC/MS/MS
Y. Hirabayashi, Y. Nagatsuka, S. Ito . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
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Contents XI
Functional Roles of the HNK-1 Carbohydrate and Polysialic Acid in the
Nervous System
Y. Kizuka, S. Oka . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Neuronal Function of Sulfatide
K. Honke . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Accumulation of Alzheimer b-amyloid via Ganglioside Clusters
K. Matsuzaki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Chondroitin Sulfate Proteoglycans and Neuronal Network Formation
N. Maeda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Processing of Glycosyltransferases by Alzheimer’s b-secretase (BACE1)
S. Kitazume, S. Takashima, Y. Hashimoto . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Chondroitin Sulfate Proteoglycans: A Key Substance for Central Nervous
System Injury Repair
A. Oohira . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Section VIII Quality Control of Proteins
A Cytoplasmic Peptide: N-Glycanase and ER-Associated Degradation
T. Suzuki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Ubiquitination of Glycoproteins in the Cytosol
T. Tai . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Degradation of Misfolded Glycoproteins in the Endoplasmic Reticulum
N. Hosokawa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Section IX Golgi and Lysosomal Diseases
Retrograde Transport of Glycolipid-Bound Toxins
R. Misaki, T. Taguchi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Degradation of Hyaluronan and Its Disorder
M. Yanagishita, K.A. Podyma-Inoue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Recent Advances in Enzyme Replacement Therapy for Lysosomal
Diseases
K. Itoh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Section X Infections
Developing an Assay System for the Hemagglutinin Mutations
Responsible for the Binding of Highly Pathogenic Avian Infl uenza
A Viruses to Human-Type Receptors
Y. Suzuki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Helicobacter pylori Growth Assay for Glycans
J. Nakayama . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Binding Properties of Clostridium botulinum Type C Progenitor Toxin
A. Nishikawa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
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