Archaea : molecular and cellular biology PDF
Preview Archaea : molecular and cellular biology
Archaea MOLECULAR AND CELLULAR BIOLOGY This page intentionally left blank Archaea MOLECULAR AND CELLULAR BIOLOGY EDITED BY RICARDO CAVICCHIOLI School of Biotechnology and Biomolecular Sciences The University of New South Wales Sidney, Australia Washington, DC Copyright © 2007 ASM Press American Society for Microbiology 1752 N St., N.W. Washington, DC 20036-2904 Library of Congress Cataloging-in-Publication Data Archaea : molecular and cellular biology/edited by Rick Cavicchioli. p. ; cm. Includes bibliographical references and index. ISBN-13: 978-1-55581-391-8 (hardcover : alk. paper) ISBN-10: 1-55581-391-7 (hardcover : alk. paper) 1. Archaebacteria—Molecular aspects. I. Cavicchioli, Ricardo. [DNLM: 1. Archaea—genetics. 2. Archaea—physiology. 3. Biotechnology. 4. Evolution, Molecular. 5. Genome, Archaeal. QW 52 A669 2007] QR82.A69A735 2006 579.3(cid:2)21—dc22 2006034575 All rights reserved Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 Address editorial correspondence to ASM Press, 1752 N St., N.W., Washington, DC 20036-2904, U.S.A. Send orders to: ASM Press, P.O. Box 605, Herndon, VA 20172, U.S.A. Phone: 800-546-2416; 703-661-1593 Fax: 703-661-1501 E-mail: [email protected] Online: estore.asm.org Cover figure:Pyrodictiumcells after freeze-etching, exhibiting an S-layer with p6 symmetry (courtesy of Reinhard Rachel, Universität Regensburg) (see Chapter 14, Fig. 16A). CONTENTS Contributors • vii 9. Features of Aminoacyl-tRNA Synthesis Preface • xi Unique to Archaea • 198 Carla Polycarpo, Kelly Sheppard, Lennart Randau, Alexandre Ambrogelly, Alexander Machado Cardoso, Shuya Fukai, Stephanie Herring, Michael Hohn, Yuko Nakamura, Hiroyuki Oshikane, Sotiria 1. The Archaea: an Invitation to Palioura, Juan Carlos Salazar, Jing Yuan, Osamu Evolution • 1 Nureki, and Dieter Söll Carl R. Woese 10. Protein-Folding Systems • 209 2. General Characteristics and Important Frank T. Robb, Ryo Izuka, and Masafumi Yohda Model Organisms • 14 Arnulf Kletzin 11. Sensing, Signal Transduction, and Posttranslational Modification • 224 3. DNA Replication and Cell Cycle Peter J. Kennelly • 93 Si-houy Lao-Sirieix, Victoria L. Marsh, 12. Central Metabolism • 260 and Stephen D. Bell Michael J. Danson, Henry J. Lamble, and David W. Hough 4. DNA-Binding Proteins and Chromatin • 110 13. Methanogenesis • 288 Rachel Samson and John N. Reeve James G. Ferry and Kyle A. Kastead 5. Mechanisms of Genome Stability and 14. Proteinaceous Surface Layers of Archaea: Evolution • 120 Ultrastructure and Biochemistry • 315 Dennis W. Grogan Helmut König, Reinhard Rachel, and Harald Claus 6. Transcription: Mechanism and 15. Lipids: Biosynthesis, Function, and Regulation • 139 Evolution • 341 Michael Thomm Yan Boucher 7. RNA Processing • 158 16. Solute Transport • 354 Gabriele Klug, Elena Evguenieva-Hackenberg, Sonja V. Albers, Wil N. Konings, Arina D. Omer, Patrick P. Dennis, and Arnold J. M. Driessen and Anita Marchfelder 17. Protein Translocation into and across 8. Translation • 175 Archaeal Cytoplasmic Membranes • 369 Paola Londei Mechthild Pohlschröder and Kieran C. Dilks v vi CONTENTS 18. Flagellation and Chemotaxis • 385 21. Molecular Genetics of Archaea Ken F. Jarrell, Sandy Y. M. Ng, and Bonnie Chaban • 463 Kevin Sowers and Kimberly Anderson 19. Structure and Evolution of Genomes • 411 22. Biotechnology • 478 Patrick Forterre, Yvan Zivanovic, Marco Moracci, Beatrice Cobucci-Ponzano, and Simonetta Gribaldo Giuseppe Perugino, and Mosè Rossi 20. Functional Genomics • 434 23. Archaeosome Vaccines • 496 Francis E. Jenney, Jr., Sabrina Tachdjian, G. Dennis Sprott and Lakshmi Krishnan Chung-Jung Chou, Robert M. Kelly, and Michael W. W. Adams Index • 511 CONTRIBUTORS Michael W. W. Adams Chung-Jung Chou Department of Biochemistry & Molecular Biology, Department of Chemical and Biomolecular Davison Life Sciences Complex, Green Street, Engineering, North Carolina State University, University of Georgia, Athens, GA 30602-7229 EB-1, Box 7905, 911 Partners Way, Raleigh, NC 27695-7905 Sonja V. Albers Department of Microbiology, Groningen Harald Claus Biomolecular Sciences and Biotechnology Institute, Institut für Mikrobiologie und Weinforschung, University of Groningen, Kerklaan 30, 9751 NN Johannes Gutenberg-Universität, Becherweg 15, Haren, The Netherlands D-55099 Mainz, Germany Alexandre Ambrogelly Beatrice Cobucci-Ponzano Departments of Molecular Biophysics and Institute of Protein Biochemistry, National Research Biochemistry, Yale University, New Haven, Council, Via P. Castellino 111, 80131 Naples, Italy CT 06520-8114 Michael J. Danson Kimberly Anderson Centre for Extremophile Research, Department of Center of Marine Biotechnology, University of Biology and Biochemistry, University of Bath, Maryland Biotechnology Institute, 701 E. Pratt Street, Bath BA2 7AY, United Kingdom Baltimore, MD 21202 Patrick P. Dennis Stephen D. Bell Division of Molecular and Cellular Biosciences, MRC Cancer Cell Unit, Hutchison MRC Research National Science Foundation, 4201 Wilson Blvd., Centre, Hills Road, Cambridge CB2 2XZ, Arlington, VA 22230 United Kingdom Kieran C. Dilks Yan Boucher Biology Department, University of Pennsylvania, Department of Chemistry and Biomolecular Sciences, Philadelphia, PA 19104 Macquarie University, Sydney, NSW 2109, Australia Arnold J. M. Driessen Alexander Machado Cardoso Department of Microbiology, Groningen Departments of Molecular Biophysics and Biomolecular Sciences and Biotechnology Institute, Biochemistry, Yale University, New Haven, University of Groningen, Kerklaan 30, 9751 NN CT 06520-8114 Haren, The Netherlands Bonnie Chaban Elena Evguenieva-Hackenburg Department of Microbiology and Immunology, Institut für Mikrobiologie und Molekularbiologie, Queen’s University, Kingston, Ontario K7L 3N6, Universität Giessen, Heinrich-Buff-Ring 26-32, Canada 35392 Giessen, Germany vii viii CONTRIBUTORS James G. Ferry Kyle A. Kastead Department of Biochemistry and Molecular Biology, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, The Pennsylvania State University, University Park, PA 16802 PA 16802 Patrick Forterre Robert M. Kelly Unité Biologie Moléculaire du Gène chez les Department of Chemical and Biomolecular Extremophiles, Institut de Génétique et Microbiologie, Engineering, North Carolina State University, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France EB-1, Box 7905, 911 Partners Way, Raleigh, NC 27695-7905 Shuya Fukai Department of Biological Information, Graduate Peter J. Kennelly School of Bioscience and Biotechnology, Tokyo Department of Biochemistry, Mail Stop 0308, Institute of Technology, Yokohama-shi, Kanagawa Virginia Polytechnic Institute and State University, 226-8501, Japan Blacksburg, VA 24061 Simonetta Gribaldo Arnulf Kletzin Unité Biologie Moléculaire du Gène chez les Institute of Microbiology and Genetics, Darmstadt Extremophiles, Institut Pasteur, 25 rue du Dr. Roux, University of Technology, Schnittspahnstrasse 10, 75724 Paris Cedex 15, France D-64287 Darmstadt, Germany Dennis W. Grogan Department of Biological Sciences, University of Gabriele Klug Cincinnati, Cincinnati, OH 45221-0006 Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Heinrich-Buff-Ring 26-32, Stephanie Herring 35392 Giessen, Germany Departments of Molecular Biophysics and Biochemistry, Yale University, New Haven, Helmut König CT 06520-8114 Institut für Mikrobiologie und Weinforschung, Michael Hohn Johannes Gutenberg-Universität, Becherweg 15, Departments of Molecular Biophysics and D-55099 Mainz, Germany Biochemistry, Yale University, New Haven, CT 06520-8114 Wil N. Konings Department of Microbiology, Groningen David W. Hough Biomolecular Sciences and Biotechnology Institute, Centre for Extremophile Research, Department of University of Groningen, Kerklaan 30, 9751 NN Biology and Biochemistry, University of Bath, Haren, The Netherlands Bath BA2 7AY, United Kingdom Lakshmi Krishnan Ryo Izuka Laboratory of Bio-Analytical Chemistry, Graduate Institute for Biological Sciences, 100 Sussex Drive, School of Pharmaceutical Sciences, The University of National Research Council of Canada, Ottawa, Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Ontario K1A 0R6, Canada Japan Henry J. Lamble Ken F. Jarrell Centre for Extremophile Research, Department of Department of Microbiology and Immunology, Biology and Biochemistry, University of Bath, Queen’s University, Kingston, Ontario K7L 3N6, Bath BA2 7AY, United Kingdom Canada Si-houy Lao-Sirieix Francis E. Jenney, Jr. Department of Biochemistry & Molecular Biology, MRC Cancer Cell Unit, Hutchison MRC Research Davison Life Sciences Complex, Green Street, Centre, Hills Road, Cambridge CB2 2XZ, University of Georgia, Athens, GA 30602-7229 United Kingdom CONTRIBUTORS ix Paola Londei Mechthild Pohlschröder Department of Medical Biochemistry, Biology and Biology Department, University of Pennsylvania, Physics (DIBIFIM), Università degli Studi di Bari Philadelphia, PA 19104 (Policlinico), Bari, Italy Carla Polycarpo Anita Marchfelder Departments of Molecular Biophysics and Molekulare Botanik, Universität Ulm, Albert- Biochemistry, Yale University, New Haven, Einstein-Allee 11, 89069 Ulm, Germany CT 06520-8114 Victoria L. Marsh Reinhard Rachel MRC Cancer Cell Unit, Hutchison MRC Research Lehrstuhl für Mikrobiologie, Universität Regensburg, Centre, Hills Road, Cambridge CB2 2XZ, Universitätsstraße 31, D-93053 Regensburg, United Kingdom Germany Lennart Randau Marco Moracci Departments of Molecular Biophysics and Institute of Protein Biochemistry, National Research Biochemistry, Yale University, New Haven, Council, Via P. Castellino 111, 80131 Naples, Italy CT 06520-8114 Yuko Nakamura John N. Reeve Department of Biological Information, Graduate Department of Microbiology, Ohio State University, School of Bioscience and Biotechnology, Tokyo Columbus, OH 43210 Institute of Technology, Yokohama-shi, Kanagawa 226-8501, Japan Frank T. Robb Center of Marine Biotechnology, University of Sandy Y. M. Ng Maryland Biotechnology Institute, 701 E. Pratt Street, Department of Microbiology and Immunology, Baltimore, MD 21202 Queen’s University, Kingston, Ontario K7L 3N6, Canada Mosè Rossi Institute of Protein Biochemistry, National Research Osamu Nureki Council, Via P. Castellino 111, 80131 Naples, Italy Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Juan Carlos Salazar Institute of Technology, Yokohama-shi, Kanagawa Departments of Molecular Biophysics and 226-8501, Japan Biochemistry, Yale University, New Haven, CT 06520-8114 Arina D. Omer Department of Biochemistry and Molecular Biology, Rachel Samson University of British Columbia, Vancouver, Department of Microbiology, Ohio State University, BC V6T 1Z3, Canada Columbus, OH 43210 Hiroyuki Oshikane Kelly Sheppard Department of Biological Information, Graduate Departments of Molecular Biophysics and School of Bioscience and Biotechnology, Tokyo Biochemistry, Yale University, New Haven, Institute of Technology, Yokohama-shi, CT 06520-8114 Kanagawa 226-8501, Japan Dieter Söll Sotiria Palioura Departments of Molecular Biophysics and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Biochemistry, Yale University, New Haven, CT 06520-8114 CT 06520-8114 Kevin R. Sowers Giuseppe Perugino Center of Marine Biotechnology, University of Institute of Protein Biochemistry, National Research Maryland Biotechnology Institute, 701 E. Pratt Council, Via P. Castellino 111, 80131 Naples, Italy Street, Baltimore, MD 21202
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