Nucleic Acids and Molecular Biology

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Series Editors Hans J. Gross, Janusz M. Bujnicki

Yo Kikuchi Elena Y. Rykova (Eds.) l

Extracellular Nucleic Acids

Editors Yo Kikuchi Department of Environmental and Life Sciences Toyohashi University of Technology 441-8580 Toyohashi-city, Aichi Japan [email protected] Series Editors Hans J. Gross Institut fu¨r Biochemie Biozentrum Am Hubland 97074 Wu¨rzburg Germany

Elena Y. Rykova Institute of Chemical Biology and Fundamental Medicine, Lavrentjeva Prospect, 8 630090 Novosibirsk Russia [email protected]

Janusz M. Bujnicki International Institute of Molecular and Cell Biology Laboratory of Bioinformatics and Protein Engineering Trojdena 4 02-109 Warsaw Poland

ISSN 0933-1891 e-ISSN 1869-2486 ISBN 978-3-642-12616-1 e-ISBN 978-3-642-12617-8 DOI 10.1007/978-3-642-12617-8 Springer Heidelberg Dordrecht London New York Library of Congress Control Number: 2010931462 # Springer-Verlag Berlin Heidelberg 2010 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, 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. Cover design: WMXDesign GmbH, Heidelberg Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)

Preface

Nucleic acids have a wide variety of functions in the main systems of life, gene maintenance, and expression, and therefore nucleic acids as functional forms have been believed to exist only inside cells. Extracellular nucleic acids have long been known, but these nucleic acids were initially presumed to be derived from cells lysed by natural cell death or viruses and considered to be of limited importance. However, these extracellular nucleic acids have recently emerged as important players in the fields of medical and environmental microbiology. In recent years, extracellular nucleic acids have been shown to be involved in not only microbial evolution as genetic elements but to also have structural roles in bacterial communities, such as biofilms. Circulating nucleic acids have been found in human blood in normal and pathologic states. Moreover, they are expected to be the low invasive markers for diagnosis of several diseases. Extracellular nucleic acids have attracted attention as active modulators of the immune system in higher organisms. This volume of the Nucleic Acids and Molecular Biology series is devoted to the extracellular nucleic acids, which are found in different biological fluids in the highest organisms and in the extracellular milieu of bacterial communities. Applications of the phenomena are also important topics for consideration. Recently, characterization and the role of extracellular DNA of the bacterium Pseudomonas aeruginosa were clearly described by Tolker-Nielsen and colleagues. Chiang and Tolker-Nielsen begin this volume by describing new roles of extracellular DNA in bacterial biofilm formation. Extracellular DNAs in the environment are thought to be used as genetic donors in natural transformation of several organisms. The following two chapters are related to evolution and microbial ecology. Lang and Beatty introduced extracellular DNAs packed in virus-like particles. Tani and Nasu discuss extracellular DNAs and microbial diversity from a global viewpoint. Extracellular DNAs of high molecular weight seem to be more stable than previously imagined. Kaneko and Itaya describe a new technique for introduction of large DNAs from lysed cells into other species mimicking horizontal gene transfer in nature. Chapter 5 by Kikuchi also presents technology-oriented topics.

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Preface

The physiology and biotechnology of a marine bacterium are described. In addition to the extracellular DNA, analysis of extracellular RNAs of this organism is described. A newly developed method for production of RNA drugs using this bacterium is also presented. One of the current hot topics in biology, systemic RNA interference, in which some RNAs interfere with gene expression, is strongly related to the subject of extracellular RNAs. Timmons reviews these topics and leads to the following chapters for higher organisms. Extracellular nucleic acids circulating in the human blood were first considered to be products of cell degradation. Later on, concentration and composition of the circulating nucleic acids were found to be significantly changed in the blood of patients with different pathologies, including cancer, compared with healthy subjects. Rykova et al. review the recent progress in the investigation of the circulating DNA and RNA as markers of cancer and other disorders, such as diabetes, trauma, stroke, myocardial infarction, complications in transplantation, etc. Development of the low invasive diagnostics of pregnancy-associated and fetal disorders based on the circulating DNA and RNA markers is described by Tsang and Lo. Tewari and Mitchell discuss the assessment of microRNAs as a promising approach for cancer diagnostics. Questions are brought up, which remain to be resolved to develop robust assays for the pathologies diagnosis and prognosis relevant for clinical use. Gahan and Stroun present data highlighting appearance of extracellular nucleic acids in the human blood and indicating their important biological roles in normal and pathologic states of the organism. The chapter provides evidence that circulating nucleic acids can play signaling roles under normal conditions and become causative factors in the disease development. One of the important properties of nucleic acids and their metabolites is their potential to be active modulators of the immune system, which is detailed in two chapters. Koyama et al. describe the recognition and immune response of “nonself” nucleic acids during infection and “self” nucleic acids in autoimmune disorders. Some clinical applications of nucleic acids that utilize their immunogenic potential are illustrated. Klinman and Klaschik give the detailed description of the gene expression regulation by unmethylated CpG DNA triggered by Toll-like receptor 9 (TLR9). Synergistic modulation of gene expression by TLR9 and TLR3 ligands is also discussed. This volume covers almost all current fields related to extracellular nucleic acids, including the fields of basic biology, ecology, and medical sciences. These are currently emerging fields of study. The reviews presented in this book will provide readers current knowledge into these exciting fields and also stimulate discussion to address new frontiers. Toyohashi, Japan Novosibirsk, Russia

Yo Kikuchi Elena Y. Rykova

Contents

1

Extracellular DNA as Matrix Component in Microbial Biofilms . . . . . 1 Wen-Chi Chiang and Tim Tolker-Nielsen

2

Gene Transfer Agents and Defective Bacteriophages as Sources of Extracellular Prokaryotic DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Andrew S. Lang and J. Thomas Beatty

3

Roles of Extracellular DNA in Bacterial Ecosystem . . . . . . . . . . . . . . . . . . 25 Katsuji Tani and Masao Nasu

4

Stable Extracellular DNA: A Novel Substrate for Genetic Engineering that Mimics Horizontal Gene Transfer in Nature . . . . . . 39 Shinya Kaneko and Mitsuhiro Itaya

5

Extracellular Nucleic Acids of the Marine Phototrophic Bacterium Rhodovulum sulfidophilum and Related Bacteria: Physiology and Biotechnology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Yo Kikuchi

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Systemic RNAi in C. elegans from the Viewpoint of RNA as Extracellular Signals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Lisa Timmons

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Circulating Nucleic Acids in Health and Disease . . . . . . . . . . . . . . . . . . . . . . 93 E.Y. Rykova, P.P. Laktionov, and V.V. Vlassov

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Circulating MicroRNAs in Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 Patrick S. Mitchell and Muneesh Tewari

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Biology and Diagnostic Applications of Cell-Free Fetal Nucleic Acids in Maternal Plasma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 Jason C.H. Tsang and Y.M. Dennis Lo

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The Biology of Circulating Nucleic Acids in Plasma and Serum (CNAPS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 P.B. Gahan and M. Stroun

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Modulation and Regulation of Gene Expression by CpG Oligonucleotides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191 Dennis Klinman and Sven Klaschik

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Immune Recognition of Nucleic Acids and Their Metabolites . . . . . . 209 Shohei Koyama, Shizuo Akira, and Ken J. Ishii

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229

Contributors

Shizuo Akira Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan J. Thomas Beatty Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada Wen-Chi Chiang Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark P.B. Gahan King’s College London, Anatomy and Human Sciences, London Bridge, London SE1 1UL, UK Ken J. Ishii Laboratory of Vaccine Science, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan, [email protected]; Laboratory of Adjuvant Innovation, National Institute of Biomedical Innovation, 7-6-8 Asagi Saito, Ibaraki, Osaka 567-0085, Japan Mitsuhiro Itaya Institute for Advanced Biosciences, Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan

Keio

University,

Shinya Kaneko Graduate School of Bioscience and Biotechnology, Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan Yo Kikuchi Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho 441-8580 Toyohashi, Japan, [email protected]

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Contributors

Sven Klaschik Cancer and Inflammation Program, National Cancer Institute, NCI in Frederick, Frederick, MD 21702, USA Dennis Klinman Laboratory of Experimental Immunology, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA Shohei Koyama Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai-city, Miyagi 980-8575, Japan P.P. Laktionov Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrentjeva Prosp., Novosibirsk 630090, Russia Andrew S. Lang Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada, [email protected] Y.M. Dennish Lo Li Ka Shing Institute of Health Sciences and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China, [email protected] Patrick S. Mitchell Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop D4-100, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA Masao Nasu Department of Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka, 565-0871, Japan, [email protected] Elena Y. Rykova Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Lavrentiev Prosp., 8, Novosibirsk 630090, Russia, [email protected] M. Stroun OncoXL, Eclosion, 14m chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland, [email protected] Katsuji Tani Department of Environmental Science and Microbiology, Faculty of Pharmaceutical Sciences, Osaka-ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-0854, Japan Muneesh Tewari Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop D4-100, Seattle, WA 98109 USA, [email protected]; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

Contributors

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Lisa Timmons Department of Molecular Biosciences, University of Kansas Lawrence, KS, USA Tim Tolker-Nielsen Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark, [email protected] Jason C.H. Tsang Li Ka Shing Institute of Health Sciences and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China V.V. Vlassov Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrentjeva Prosp., Novosibirsk 630090, Russia