Archaea: Evolution, Physiology, and Molecular Biology

438 Pages·2007·31.85 MB·English

by  Roger A. Garrett

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Archaea
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Archaea
Evolution, Physiology, and Molecular Biology
Edited by Roger A. Garrett and Hans-Peter Klenk
GARPR 9/21/06 3:51 PM Page iv
© 2007 by Blackwell Publishing Ltd
except for editorial material and organization © 2007 by Roger Garrett and
Hans-Peter Klenk
BLACKWELL PUBLISHING
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9600 Garsington Road, Oxford OX4 2DQ, UK
550 Swanston Street, Carlton, Victoria 3053, Australia
The right of Roger Garrett and Hans-Peter Klenk to be identified as the Authors of the
Editorial Material in this Work has been asserted in accordance with the UK Copyright,
Designs, and Patents Act 1988.
All rights reserved. No part of this publication may be reproduced, stored in a retrieval
system, or transmitted, in any form or by any means, electronic, mechanical,
photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs,
and Patents Act 1988, without the prior permission of the publisher.
First published 2007 by Blackwell Publishing Ltd
1 2007
Library of Congress Cataloging-in-Publication Data
Archaea : evolution, physiology, and molecular biology / edited by Roger Garrett and
Hans-Peter Klenk.
p. ; cm.
Includes bibliographical references and index.
ISBN-13: 978-1-4051-4404-9 (hardback : alk. paper)
ISBN-10: 1-4051-4404-1 (hardback : alk. paper)
1. Archaebacteria—Genetic aspects. 2. Molecular biology.
I. Garrett, Roger A. (Roger Antony), 1943– . II. Klenk, Hans-Peter.
[DNLM: 1. Archaea. 2. Archaea—genetics. 3. Evolution, Molecular.
QW 50 A669 2007]
QR82.A69A73 2007
579.3′21—dc22
2006009421
A catalogue record for this title is available from the British Library.
Set in 10 on 12pt Meridien
by SNP Best-set Typesetter Ltd, Hong Kong
Printed and bound in Singapore
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Contents
List of contributors vii 9 Specialist Article
Preface xi Plasmids 105
Georg Lipps
1 Introductory Chapter
The birth of the Archaea: a personal 10 Specialist Article
retrospective 1 Integration mechanisms: possible role in
Carl R. Woese genome evolution 113
Qunxin She, Haojun Zhu and
2 Review
Xiaoyu Xiang
Natural history of the archaeal domain 17
Patrick Forterre, Simonetta Gribaldo and 11 Review
Celine Brochier-Armanet Genetics 125
Moshe Mevarech and Thorsten Allers
3 Specialist Article
The root of the tree: lateral gene transfer
12 Specialist Article
and the nature of the domains 29
Genetic properties of Sulfolobus
David A. Walsh, Mary Ellen Boudreau,
acidocaldarius and related Archaea 137
Eric Bapteste and W. Ford Doolittle
Dennis W. Grogan
4 Review
Diversity of uncultivated Archaea: 13 Review
perspectives from microbial ecology and Chromatin and regulation 147
metagenomics 39 John N. Reeve and Kathleen Sandman
Christa Schleper
14 Review
5 Specialist Article DNA replication and the cell cycle 159
Nanoarchaeota 51 Victoria L. Marsh and Stephen D. Bell
Harald Huber and Reinhard Rachel
15 Review
6 Review
DNA repair 171
Families of DNA viruses infecting
Malcolm F. White
hyperthermophilic Crenarchaea 59
David Prangishvili 16 Review
Transcriptional mechanisms 185
7 Review
Michael Thomm and Winfried Hausner
Features of the genomes 75
Hans-Peter Klenk
17 Specialist Article
8 Specialist Article Transcriptional regulation in
Sulfolobus genomes: mechanisms of Haloarchaea 199
rearrangement and change 95 Felicitas Pfeifer, Torsten Hechler,
Kim Brügger, Xu Peng and Roger A. Garrett Sandra Scheuch and Simone Sartorius-Neef
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vi CONTENTS
18 Specialist Article 23 Specialist Article
Aminoacyl-tRNAs: deciphering and Metabolism of inorganic sulfur
defining the genetic message 207 compounds in Archaea 261
Alexandre Ambrogelly, Juan Carlos Salazar, Arnulf Kletzin
Kelly Sheppard, Carla Polycarpo,
Hiroyuki Oshikane, Yuko Nakamura, 24 Specialist Article
Shuya Fukai, Osamu Nureki and Dieter Söll Methyl-coenzyme M reductase in
methanogens and methanotrophs 275
19 Specialist Article Rudolf K. Thauer and Seigo Shima
Translational mechanisms and protein
synthesis 217 25 Specialist Article
Paola Londei Methylation of metal(loid)s by
Methanoarchaea: production of volatile
20 Review derivatives with high ecotoxicological
Expanding world of small noncoding impact and health concern 285
RNAs in Archaea 229 Klaus Michalke, Jörg Meyer and
Arina Omer, Maria Zago and Reinhard Hensel
Patrick P. Dennis
26 Review
21 Specialist Article Biotechnology 295
Transcriptomics, proteomics, and Ksenia Egorova and
structural genomics of Pyrococcus furiosus 239 Garabed Antranikian
Michael W. W. Adams, Francis E. Jenney Jr,
Chung-Jung Chou, Scott Hamilton-Brehm, Wolfram Zillig 323
Farris L. Poole II, Keith R. Shockley, References 325
Sabrina Tachdjian and Robert M. Kelly Index 377
22 Specialist Article
The glycolytic pathways of Archaea:
evolution by tinkering 247
John van der Oost and Bettina Siebers
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Contributors
M. W. W. Adams Department of Biochemistry and C.-J. Chou Department of Chemical and
Molecular Biology, University of Georgia Athens, Biomolecular Engineering, North Carolina State
Georgia 30602-7229, USA University, Raleigh, NC 27695-7905, USA
T. Allers Institute of Genetics, University of P. P. Dennis Division of Molecular and Cellular
Nottingham, Queen’s Medical Centre, Nottingham Biosciences, National Science Foundation, 4201
NG7 2UH, United Kingdom Wilson Blvd., Alexandria, Virginia 22230, USA
A. Ambrogelly Department of Molecular W. F. Doolittle Department of Biochemistry and
Biophysics and Biochemistry, Yale University, Molecular Biology, Dalhousie University, 5850
New Haven, Connecticut 06520-8114, USA College Street, Halifax, Nova Scotia B3H 1X5,
Canada
G. Antranikian Institute of Technical
Microbiology, Hamburg University of Technology, K. Egorova Institute of Technical Microbiology,
Kasernenstraße 12, 21073 Hamburg, Germany Hamburg University of Technology,
Kasernenstraße 12, 21073 Hamburg, Germany
E. Bapteste Department of Biochemistry and
Molecular Biology, Dalhousie University, 5850 P. Forterre Unité Biologie Moléculaire du Gène
College Street, Halifax, Nova Scotia B3H 1X5, chez les Extremophiles, Institut Pasteur, 25 rue du
Canada Dr. Roux, 75724 Paris Cedex 15, France
S. D. Bell MRC Cancer Cell Unit, Hutchison MRC S. Fukai Department of Biological Information,
Research Centre, Hills Road, Cambridge CB2 2XZ, Graduate School of Bioscience and Biotechnology,
United Kingdom Tokyo Institute of Technology, Yokohama-shi,
Kanagawa 226-8501, Japan
M. E. Boudreau Department of Biochemistry and
Molecular Biology, Dalhousie University, 5850 R. A. Garrett Danish Archaea Centre, Institute
College Street, Halifax, Nova Scotia B3H 1X5, of Molecular Biology, Copenhagen
Canada University, Sølvgade 83H, DK-1307 Copenhagen K,
Denmark
C. Brochier-Armanet EA EGEE (Evolution,
Génome, Environnement), Université Aix-Marseille S. Gribaldo Unité Biologie Moléculaire du Gène
I, Centre Saint-Charles, Case 36, 3 Place Victor chez les Extremophiles, Institut Pasteur, 25 rue du
Hugo, 13331 Marseille, Cedex 3, France Dr. Roux, 75724 Paris Cedex 15, France
K. Brügger Danish Archaea Centre, Institute of D. W. Grogan Department of Biological Sciences,
Molecular Biology, Copenhagen University, 614 Rieveschl Hall, ML 0006, University of
Sølvgade 83H, DK-1307 Copenhagen K, Denmark Cincinnati, Cincinnati, Ohio 45221-0006, USA
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viii CONTRIBUTORS
S. Hamilton-Brehm Department of Biochemistry M. Mevarech Department of Molecular
and Molecular Biology, University of Georgia Microbiology & Biotechnology, Tel-Aviv University,
Athens, Georgia 30602-7229, USA Tel-Aviv 69978, Israel
W. Hausner University of Regensburg, Department K. Michalke Department of Microbiology and
of Microbiology, Universitätsstraße 31, 93053 Geography, University Duisburg-Essen, Campus
Regensburg, Germany Essen, Universitätsstraße 5, 45117 Essen, Germany
T. Hechler Institute of Microbiology and Genetics, Y. Nakamura Department of Biological
Darmstadt University of Technology, Information, Graduate School of Bioscience and
Schnittspahnstrasse 10, 64287 Darmstadt, Germany Biotechnology, Tokyo Institute of Technology,
Yokohama-shi, Kanagawa 226-8501, Japan
R. Hensel Department of Microbiology and
Geography, Universität Duisburg-Essen, O. Nureki Department of Biological Information,
Campus Essen, Universitätsstraße 5, 45117 Essen, Graduate School of Bioscience and Biotechnology,
Germany Tokyo Institute of Technology, Yokohama-shi,
Kanagawa 226-8501, Japan
H. Huber University of Regensburg, Department of
A. Omer Department of Biochemistry and
Microbiology and Archaea Center,
Molecular Biology, University of British Columbia,
Universitätsstraße 31, 93053 Regensburg, Germany
2146 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
F. E. Jenney Jr Department of Biochemistry and
Molecular Biology, University of Georgia Athens,
H. Oshikane Department of Biological
Georgia 30602-7229, USA
Information, Graduate School of Bioscience and
Biotechnology, Tokyo Institute of Technology,
R. M. Kelly Department of Chemical and
Yokohama-shi, Kanagawa 226-8501, Japan
Biomolecular Engineering, North Carolina State
University, Raleigh, NC 27695-7905, USA
X. Peng Danish Archaea Centre, Institute of
Molecular Biology, Copenhagen University,
H.-P. Klenk e.gene Biotechnologie, Pöckinger
Sølvgade 83H, DK-1307 Copenhagen K, Denmark
Fußweg 7a, 82340 Feldafing, Germany
F. Pfeifer Institute of Microbiology and Genetics,
A. Kletzin Institute of Microbiology and Genetics,
Darmstadt University of Technology,
Darmstadt University of Technology,
Schnittspahnstrasse 10, 64287 Darmstadt, Germany
Schnittspahnstrasse 10, 64287 Darmstadt, Germany
C. Polycarpo Department of Molecular Biophysics
G. Lipps University of Bayreuth, Biochemistry,
and Biochemistry, Yale University, New Haven,
95440 Bayreuth, Germany
Connecticut 06520-8114, USA
P. Londei Department of Medical Biochemistry, F. L. Poole II Department of Biochemistry and
Biology and Physics (DIBIFIM), Università degli Molecular Biology, University of Georgia Athens,
Studi di Bari (Policlinico), Bari, Italy Georgia 30602-7229, USA
V. L. Marsh MRC Cancer Cell Unit, Hutchison D. Prangishvili Unité de Biologie Moléculaire du
MRC Research Centre, Hills Road, Cambridge CB2 Gène chez les Extrêmophiles, Institut Pasteur, rue
2XZ, United Kingdom Dr. Roux 25, 75724 Paris Cedex 15, France
J. Meyer Department of Microbiology and R. Rachel University of Regensburg, Department
Geography, University Duisburg-Essen, Campus of Microbiology and Archaea Center,
Essen, Universitätsstraße 5, 45117 Essen, Germany Universitätsstraße 31, 93053 Regensburg, Germany
GARPR 9/15/06 3:32 PM Page ix
CONTRIBUTORS ix
J. N. Reeve Department of Microbiology, Ohio S. Tachdjian Department of Chemical and
State University, Columbus, Ohio 43210, USA Biomolecular Engineering, North Carolina State
University, Raleigh, NC 27695-7905, USA
J. C. Salazar Department of Molecular Biophysics
and Biochemistry, Yale University, New Haven, R. K. Thauer Max-Planck-Institute for Terrestrial
Connecticut 06520-8114, USA Microbiology, Karl-von-Frisch-Strasse, 35043
Marburg, Germany
K. Sandman Department of Microbiology, Ohio
State University, Columbus, Ohio 43210, USA M. Thomm University of Regensburg, Department
of Microbiology, Universitätsstraße 31, 93053
S. Sartorius-Neef Institute of Microbiology and Regensburg, Germany
Genetics, Darmstadt University of Technology,
Schnittspahnstrasse 10, 64287 Darmstadt, Germany
J. van der Oost Laboratory of Microbiology,
Wageningen University, Hesselink van
S. Scheuch Institute of Microbiology and Genetics,
Suchtelenweg 4, 6703 CT Wageningen, The
Darmstadt University of Technology,
Netherlands
Schnittspahnstrasse 10, 64287 Darmstadt, Germany
D. A. Walsh Department of Biochemistry and
C. Schleper University of Bergen, Department of
Molecular Biology, Dalhousie University, 5850
Biology, Jahnebakken 5, N-5020 Bergen, Norway
College Street, Halifax, Nova Scotia B3H 1X5,
Canada
K. Sheppard Department of Molecular Biophysics
and Biochemistry, Yale University, New Haven,
M. F. White Centre for Biomolecular Sciences,
Connecticut 06520-8114, USA
University of St Andrews, St Andrews, Fife KY16
9ST, United Kingdom
S. Shima Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Strasse, 35043
C. R. Woese Department of Microbiology,
Marburg, Germany
University of Illinois, 601 South Goodwin Ave.,
Urbana, Illinois 61801-3709, USA
Q. She Danish Archaea Centre, Institute of
Molecular Biology and Physiology, Copenhagen
University, Sølvgade 83H, DK-1307 Copenhagen K, X. Xiang Danish Archaea Centre, Institute of
Denmark Molecular Biology and Physiology, Copenhagen
University, Sølvgade 83H, DK-1307 Copenhagen K,
K. R. Shockley Department of Chemical and Denmark
Biomolecular Engineering, North Carolina State
University, Raleigh, NC 27695-7905, USA M. Zago Department of Biochemistry and
Molecular Biology, University of British Columbia,
B. Siebers Department of Microbiology and 2146 Health Sciences Mall, Vancouver, British
Geography, University Duisburg-Essen, Campus Columbia V6T 1Z3, Canada
Essen, Universitätsstraße 5, 45117 Essen, Germany
H. Zhu Danish Archaea Centre, Institute of
D. Söll Departments of Molecular Biophysics and Molecular Biology and Physiology, Copenhagen
Biochemistry and Chemistry, Yale University, New University, Sølvgade 83H, DK-1307 Copenhagen K,
Haven, Connecticut 06520-8114, USA Denmark
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