Archaea : molecular and cellular biology

555 Pages·2007·19.75 MB·English

by  Cavicchioli

Archaea
MOLECULAR AND CELLULAR BIOLOGY
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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.
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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