Genetics and Molecular Biology of Anaerobic Bacteria

722 Pages·1993·36.64 MB·English

by  Thomas Leisinger

Brock/ Springer Series in Contemporary Bioscience
Genetics and Molecular
Biology of Anaerobic Bacteria
Brock/ Springer Series in Contemporary Bioscience
Series Editor: Thomas D. Brock
University of Wisconsin-Madison
Tom Fenchel
ECOLOGY OF PROTOZOA:
The Biology of Free-living Phagotrophic Protists
Johanna Dobereiner and Fabio O. Pedrosa
NITROGEN-FIXING BACTERIA IN NONLEGUMINOUS
CROP PLANTS
Tsutomu Hattori
THE VIABLE COUNT: Quantitative and Environmental Aspects
Roman Saliwanchik
PROTECTING BIOTECHNOLOGY INVENTIONS:
A ( uide for Scientists
Hans G. Schlegel and Botho Bowien (Editors)
AUTOTROPHIC BACTERIA
Barbara Javor
HYPERSALINE ENVIRONMENTS: Microbiology and Biogeochemistry
Ulrich Sommer (Editor)
PLANKTON ECOLOGY: Succession in Plankton Communities
Stephen R. Rayburn
THE FOUNDATIONS OF LABORATORY SAFETY:
A Guide for the Biomedical Laboratory
Gordon A. McFeters (Editor)
DRINKING WATER MICROBIOLOGY:
Progress and Recent Developments
Mary Helen Briscoe
A RESEARCHER'S GUIDE TO SCIENTIFIC AND
MEDICAL ILLUSTRATIONS
Max M. Tilzer and Colette Serruya (Editors)
LARGE LAKES: Ecological Structure and Function
Jurgen Overbeck and Ryszard ]. Chr6st (Editors)
AQUATIC MICROBIAL ECOLOGY:
Biochemical and Molecular Approaches
John H. Andrews
COMPARATIVE ECOLOGY OF MICROORGANISMS
AND MACROORGANISMS
(Continued after index)
Madeleine Sebald
Editor
Genetics and Molecular
Biology of Anaerobic Bacteria
With 186 Figures
Springer-Verlag
New York Berlin Heidelberg London Paris
Tokyo Hong Kong Barcelona Budapest
Madeleine Sebald
Unite des Anaerobies
Institut Pasteur
75724 Paris, France
Cover photograph: Clostridium bifermentans DSM 631. Reproduced from The Prokaryotes, Second
Edition, Vol. II. p. 1803. © 1992 Springer-Verlag, New York.
Library of Congress Cataloging-in-Publication Data
Genetics and molecular biology of anaerobic bacteria / Madeleine
Sebald, editor.
p. cm. - (Brock/Springer series in contemporary bioscience)
Includes bibliographical references and index.
ISBN 978-1-4615-7089-9 ISBN 978-1-4615-7087-5 (eBook)
DOl 10.1007/978-1-4615-7087-5
1. Anaerobic bacteria-Genetics. 2. Anaerobic bacteria-Molecular
Aspects. I. Sebald, Madeleine. II. Series.
QR89.5.G46 1992
589.9'01'5-dc20 91-28037
CIP
Printed on acid-free paper.
© 1993 Springer-Verlag New York, Inc.
Softcover reprint of the hardcover 1st edition 1993
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9 8 7 6 5 4 321
Preface
The field of bacterial genetics has been restricted for many years to Escherichia
coli and a few other genera of aerobic or facultatively anaerobic bacteria such as
Pseudomonas, Bacillus, and Salmonella. The prevailing view up to recent times
has been that anaerobic bacteria are interesting organisms but nothing is known
about their genetics. To most microbiologists, anaerobic bacteria appeared as a
sort of distant domain, reserved for occasional intrusions by taxonomists and
medical microbiologists. By the mid-1970s, knowledge of the genetics and
molecular biology of anaerobes began to emerge, and then developed rapidly.
This was the result of advances in molecular biology techniques, but also im
portantly because of improvements in basic techniques for culturing
anaerobes and for understanding their biochemistry and other areas of in
terest. Investigations in this field were also stimulated by a renewal of interest
in their ecology, their role in pathology and in biotransformations, and in the
search for alternative renewable sources of energy.
The initial idea for this book came from Thomas D. Brock. When Dr. Brock
requested my opinion about two years ago on the feasibility of publishing a
book on the genetics of anaerobic bacteria, as a part of the Brock/Springer
Series in Contemporary Bioscience, I answered positively but I was apprehen
sive about assuming the role of editor. However, I was soon reassured by the
enthusiastic commitment of those I approached to contribute. Eventually,
thanks to the caring cooperation of the contributors, the task became relatively
easy.
I have tried to include most of the available data on the genetics and molecu
lar biology of both developing and developed topics, and it is my hope that
this book will furnish up-to-date information both to those entering and to
those already involved in anaerobic microbiology. I also hope it will show that
anaerobes are less distant than may be perceived.
Finally, I should like to express my gratitude to Thomas D. Brock, to the
contributors, and also to the reviewers. It is a pleasure to acknowledge the
assistance of Morris Goldner of the University of Toronto in the editorial pro-
cess.
Madeleine Sebald
v
Contents
Preface v
Contributors xiii
Introduction xix
1 Plasmids, Phages, and Gene Transfer in
Methanogenic Bacteria 1
Thomas Leisinger and Leo Meile
2 Methanogen Genes and the Molecular Biology of
Methane Biosynthesis 13
John R. Palmer and John N. Reeve
3 Genes for Stable RNAs and Their Expression
in Archaea 36
Michael Thomm and Winfried Hausner
4 Molecular Biology of the Acetoclastic Methanogen
Methanothrix soehngenii 54
Rik I.L. Eggen and Willem M. de Vos
5 Mutations 64
Madeleine Sebald
6 Conjugative Gene Transfer in Clostridia 98
Michael Young
7 Transformation and Electrotransformation
in Clostridia 111
Gilles Reysset
8 Vectors for Use in Clostridium acetobutylicum 120
Nigel P. Minton, Tracy-Jane Swinfield,
vii
viii Contents
John K. Brehm, Sarah M. Whelan, and
John D. Oultram
9 Antibiotic Resistance Determinants of Clostridium
perfringens 141
Julian I. Rood
10 Genetics and Molecular Biology of Antibiotic
Resistance in Clostridium difficile: General and
Specific Overview 156
Herbert Hachler and Fritz H. Kayser
11 Genetics and Molecular Biology of Chloramphenicol
Acetyltransferase of Clostridium butyricum 174
Walter L. Staudenbauer and Wolfgang Dubbert
12 The Role of Bacteriophages and Plasmids in the
Production of Toxins and Other Biologically Active
Substances by Clostridium botulinum and
Clostridium novyi 179
Mel W. Eklund
13 Molecular Biology of Clostridial ADP-
Ribosyltransferases and Their Substrates 195
Klaus Aktories, Gertrud Koch, and Ingo Just
14 Gene Cloning and Organization of the Alpha-Toxin
of Clostridium perfringens 211
Richard W. Titball, Helen Yeoman, and
Sophie E.C. Hunter
15 Gene Cloning, Organization, and Expression of
6-Toxin of Clostridium perfringens 227
Rodney K. Tweten
16 Molecular Biology of Clostridium perfringens
Enterotoxin 235
Per Einar Granum and Gordon S.A.B. Stewart
17 Molecular Genetic Studies of UV-Inducible
Bacteriocin Production in Clostridium perfringens 248
Stewart T. Cole and Thierry Garnier
18 Genome Mapping of Clostridium perfringens
Type A Strains 255
Stewart T. Cole and Bruno Canard
Contents ix
19 Molecular Biology of the Clostridium difficile Toxins 264
Christoph von Eichel-Streiber
20 Gene Cloning and Expression in Escherichia coli of
Clostridial Sialidases 290
Peter Roggentin and Roland Schauer
21 Cloning and Expression of Clostridium
acetobutylicum Genes Involved in Carbohydrate
Utilization 301
Peter Verhasselt andJos Vanderleyden
22 Cloning and Expression of Clostridium
acetobutylicum Genes Involved in Solvent
Production 317
George N. Bennett and Daniel J. Petersen
23 Molecular Analysis of Glutamine Synthetase Genes
and Enzymes of Clostridium and Bacteroides 344
David R. Woods
24 Phospholipid Biosynthetic Enzymes of Butyric
Acid-Producing Clostridia 354
Howard Goldfine
25 The Clostridium pasteurianum Ferredoxin Gene 363
Jesse C. Rabinowitz
26 Organization of the Nitrogen Fixation Genes
in Clostridium pasteurianum 373
John L. Johnson, Shu-Zhen Wang, and
Jiann-Shin Chen
27 Cloning and Sequencing of the
Clos~ridium
pasteurianum Genes Encoding Molybdenum-Pterin
Binding Proteins 382
Stephen M. Hinton
28 Cloning, Sequencing, and Expressions of Genes
Encoding Enzymes of the Autotrophic Acetyl-CoA
Pathway in the Acetogen Clostridium
thermoaceticum 389
Thomas A. Morton, Chih-Fong Chou, and
Lars G. Ljungdahl
x Contents
29 Genes and Proteins Involved in Cellulose
Degradation by Mesophilic Clostridia 407
Jean-Pierre Belaich, Anne Belaich, Christian Gaudin,
and Chantal Bagnara
30 Genes and Proteins Involved in Cellulose and Xylan
Degradation by Clostridium thermocellum 412
Jean-Paul Aubert, Pierre Beguin, and Jacqueline
Millet
31 Nucleotide Sequence of the Gene and Primary
Structure of the Thermophilic p-Amylase from
Clostridium thermosulfurogenes 423
Hideo Yamagata and Shigezo Vdaka
32 The a-Amylase-Pullulanase (apu) Gene from
Clostridium thermohydrosulfuricum: Nucleotide
Sequence and Expression in Escherichia coli 432
Hannes Melasniemi
33 Molecular Biology of Xylan Utilization by
Thermoanaerobes 443
Michael Bagdasarian, Yong-Eok Lee, Chanyong Lee,
Menghsiao Meng, and J. Gregory Zeikus
34 Genetics and Molecular Biology of
Sulfate-Reducing Bacteria 456
Gerrit Voordouw and Judy D. Wall
35 Gene Transmission, MLS, and Tetracycline
Resistance in Bacteroides 474
Francis L. Macrina and C. Jeffrey Smith
36 Transfer of Beta-Lactam Antibiotic Resistance
in Bacteroides 490
Kunitomo Watanabe and Kazue Veno
37 Genetics of 5-Nitroimidazole Resistance in
Bacteroides 494
Gilles Reysset, Wen-Jin Su, and Madeleine Sebald
38 Genetics of Polysaccharide Utilization
Pathways of Colonic Bacteroides Species 505
Abigail A. Salyers, Peter Valentine, and Vivian Hwa
Contents xi
39 Molecular Biology of the Fimbriae of Dichelobacter
(Previously Bacteriodes) nodosus 517
John S. Mattick, Matthew Hobbs, Peter T. Cox, and
Brian P. Dalrymple
40 Genetic Exchange in Pigmented Bacteroides 546
Donald G. Guiney
41 Porphyromonas gingivalis: Gene Cloning of
Determinants of Pathogenicity 552
Barry C. McBride, Umadatt Singh, and Angela Joe
42 Cloning, Structure, and Expression of Genes of the
Anaerobic Rumen Bacteria 569
RM. Teather, H.J. Gilbert, and G.P. Hazlewood
43 Antigenic Characterization, Taxonomy, and
Genetics of Treponema hyodysenteriae 586
R Sellwood
44 Nucleic Acid Hybridization for Identification and
Detection of Gram-Negative Anaerobes 605
Ulf B. Gobel and Klaus Pelz
45 Molecular Biology of Bile Acid 7a-Dehydroxylation
in an Intestinal Eubacterium Species 618
Darrell H. Mallonee and Phillip B. Hylemon
46 Cloning and Expression in Escherichia coli of Three
Amylase Genes of a Strictly Anaerobic
Thermophile, Dictyoglomus thermophilum, and 629
Their Nucleotide Sequences
Sueharu Horinouchi and Teruhiko Beppu
47 A Novel Class of Industrially Important
Debranching Enzymes: The Thermoanaerobic
Amylopullulanases 640
Robert D. Coleman
Appendix: A List of Strict Anaerobes 654
J. Gregory Zeikus, Monique Hermann,
Michel Magot, and Madeleine Sebald
Index 675