Handbook of Glycosyltransferases and Related Genes Naoyuki Taniguchi • Koichi Honke Minoru Fukuda • Hisashi Narimatsu Yoshiki Yamaguchi • Takashi Angata Editors Handbook of Glycosyltransferases and Related Genes Second Edition Editors Naoyuki Taniguchi Yoshiki Yamaguchi RIKEN-Max-Planck Joint Research Center RIKEN-Max-Planck Joint Research Center for Systems Chemical Biology, RIKEN for Systems Chemical Biology, RIKEN Wako, Saitama, Japan Wako, Saitama, Japan Koichi Honke Takashi Angata Department of Biochemistry Institute of Biological Chemistry Kochi University Medical School Academia Sinica Nankoku, Kochi, Japan Taipei, Taiwan Minoru Fukuda Sanford Burnham Medical Research Institute La Jolla, CA, USA Hisashi Narimatsu Research Center for Medical Glycoscience (RCMG) National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, Ibaraki, Japan ISBN 978-4-431-54239-1 ISBN 978-4-431-54240-7 (eBook) ISBN 978-4-431-54241-4 (print and electronic bundle) DOI 10.1007/978-4-431-54240-7 Springer Tokyo Heidelberg New York Dordrecht London Library of Congress Control Number: 2014930991 # Springer Japan 2002, 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface Almost ten years have passed since the publication of the first edition of this book in 2002, and it is timely to renew and publish a second edition, because a large number of glycosyltransferases has been characterized since then. In the second edition, Springer introduced an online system for receiving a submitted manuscript of each chapter, which helped us to handle more than one hundred manuscripts much easier, and before publishing the printed version of the book, online articles are now being made available. It is no doubt that glycoscience has been, and will be in the future, playing a pivotal role in various fields of research in the life sciences. Last year, the US National Academy of Sciences published a report entitled “Transforming Glycoscience, A Roadmap for the Future.” This report emphasizes the role of glycans in health, energy and material science. However, many issues related to the structure and function of glycans remain to be clarified, and characterizing the structure and function of glycosyltransferases is essential for our understanding of glycans in health and disease. Moreover, gene technology is now a very common technique and many KO or transgenic mice have been developed which has permitted possible implication of various diseases such as autoimmune disease, diabetes, chronic obstructive pulmonary disease, and cancer metastasis, and auto- immune diseases to be clarified. In addition, the cause of some of the CGD (congenital disorders of glycosylation) including muscle dystrophy was found to be due to the lack of, or a mutation in, a certain glycosyltransferase gene. At present, almost 200 glycosyltransferase genes have been identified and encompass approximately 1 % of the whole human genome. There are still many proteins with unknown functions which belong to the glycosyltransferase family or its related genes. In this edition, 160 glycosyltransferases are listed and additional information such as X-ray crystallographic data and UniProt number have been also included. It is also known that the expression levels of glycosyltransferases are regulated by various factors such as nucleotide sugar levels, nucleotide transporter levels, chaperons, acceptor substrate levels, genetic or epigenetic regulation via transcrip- tion factors etc., and also their availability in the Golgi or ER etc. However, those underlying mechanisms of glycosyltransferase regulation are largely unknown. It is also not clear at present how glycosyltransferases act on specific glycoprotein(s) as acceptor substrates and how monosaccharide(s) are added at a specific site of the v vi Preface proteins and expressed in a tissue/cell/organ specific manner. These issues should be cleared in the next decade and will open a new field of glycobiology. Regarding industrial or pharmaceutical applications of glycosyltransferases, such as the synthesis of glycans using glycosyltransferases, it is still difficult for us to use a sole glycosyltransferase to synthesize glycans and/or glycoproteins, glycolipids and proteoglycans. Therefore a combination of glycosyltransferase and chemistry, namely, chemo-enzymatic techniques were being used. The biological significance of glycosyltransferases in terms of the growth and development, immune-system neuroscience, stem cell research, cancer biomarker discovery and antibody therapy etc. are still important areas of research which will likely develop in the future. This book is dedicated to the late Professor Robert Hill who was a genuine pioneer in the field of glycosyltransferase enzymology and the purification of glycosyltransferases which opened a new field of research for glycosyltransferase genes and their functions. Finally we wish to express our sincere thanks to all authors who took the time to contribute to this monograph. We particularly thank Ms. Fumi Ota at RIKEN Systems Glycobiology Research Group, who helped us in publishing this book. Finally we are very grateful to all staff members of the Springer Japan KK and Springer who generously edited the original draft of this book and the online version. October 10, 2013 Naoyuki Taniguchi Koichi Honke Minoru Fukuda Hisashi Narimatsu Yoshiki Yamaguchi Takashi Angata Editors About the Editors Naoyuki Taniguchi Group Director, RIKEN-Max-Planck Joint Research Center for Systems Chemical Biology, RIKEN, Wako, Saitama, Japan Naoyuki Taniguchi graduated from the Faculty of Medicine, Hokkaido University, and obtained his M.D. in 1967 and then Ph.D. in 1972 from the same university. He became Assistant Professor of the Department of Preventive Medicine, Hokkaido University, and Visiting Associate Professor at the Connell University Medical School, New York, in 1976. In 1986, he became Professor and Chair of the Department of Biochemistry at the Osaka University Medical School. In 2006, after retirement from the medical school, he became endowed Chair Professor of Osaka University. Meanwhile, he formed the Systems Glycobiology Research Group at RIKEN in 2007 and has been the Group Director since. His focus is on the structure and function of glycans, especially the role of N-linked glycoproteins in relation to the mechanism of the disease biomarker discovery and therapeutics. He has received several distinguished awards, such as IGO (International Glycoconjugate Organization) Award in 2001, Medal with Purple Ribbon from the Emperor of Japan in 2005, HUPO (Human Proteome Organization) Distinguished Service Award in 2009, and Japan Academy Prize in 2011. Taniguchi currently vii viii About the Editors serves as editor and editorial board member of many journals such as Journal of Biological Chemistry, Biochemical and Biophysical Research Communications, Proteomics, etc., and he himself has published more than 400 original papers and more than 50 reviews. He also served as President in the 75th Annual Meeting of the Japanese Biochemical Society and as Secretary General in the 20th IUBMB 11FAOBMB Congress. Recently, he has been elected as the President of the Society for Glycobiology for 2014. About the Editors ix Koichi Honke Professor, Department of Biochemistry, Kochi University Medical School, Nankoku, Kochi, Japan Koichi Honke is a Professor at Kochi University Medical School in Kochi, Japan. Honke graduated from Hokkaido University School of Medicine obtaining his M.D. in 1983. Since he started his research under the supervision of Prof. Akira Makita at Cancer Institute, Hokkaido University Medical School, in 1984, Honke has been studying the metabolism and function of glycolipids as well as glycoproteins. Honke worked at Osaka Medical Center