Thermus Species

241 Pages·1995·3.24 MB·English

by  Richard Sharp (ed.)

Thermus Species
BIOTECHNOLOGY HANDBOOKS
Series Editors: Tony Atkinson and Roger F. Sherwood
Centre for Applied Microbiology and Research
Division of Biotechnology
Salisbury, Wiltshire, England
Volume 1 PENICILLIUM AND ACREMONIUM
Edited by John F. Peberdy
Volume 2 BACILLUS
Edited by Colin R. Harwood
Volume 3 CLOSTRIDIA
Edited by Nigel P. Minton and David]. Clarke
Volume 4 SACCHAROMYCES
Edited by Michael F. Tuite and Stephen G. Oliver
Volume 5 METHANE AND METHANOL UTILIZERS
Edited by]. Colin Murrell and Howard Dalton
Volume 6 PHOTOSYNTHETIC PROKARYOTES
Edited by Nicolas H. Mann and Noel G. Carr
Volume 7 ASPERGILLUS
Edited by]. E. Smith
Volume 8 SULFATE-REDUCING BACTERIA
Edited by Larry L. Barton
Volume 9 THERMUS SPECIES
Edited by Richard Sharp and Ralph Williams
A Continuation Order Plan is available for this series. A continuation order will bring
delivery of each new volume immediately upon publication. Volumes are billed only upon
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Thermus Species
Edited by
Richard Sharp
The Centre for Applied Microbiology and Research
Porton Down, Salisbury, England
and
Ralph Williams
Queen Mary and Westfield College
London, England
Springer Science+Business Media, LLC
Llbrary of Congress Cataloglng-ln-Publlcatlon Data
Thermus species I edited by Richard Sharp and Ralph Williams.
p. cm. -- (Biotechnology handbooks ; v. 9)
Includes bibliographical references and index.
ISBN 978-1-4613-5741-4 ISBN 978-1-4615-1831-0 (eBook)
DOI 10.1007/978-1-4615-1831-0
1. Thermophil ic bacteria. 1. Sharp. Richard (Richard J.)
II. Wi 11 iams. R. A. D. (Ralph Anthony David). 1938-
III. Series.
OR84.8.T46 1995
589.9·2--dc20 95-12394
CIP
ISBN 978-1-4613-5741-4
© 1995 Springer Science+Business Media New York
Originally published by Plenum Press in 1995
Softcover reprint of the hardcover Ist edition 1995
10987654321
AII rights reserved
No part of this book may be reproduced, stored in a retrieval system, or transmitted in any
form or by any means, electronic, mechanical, photocopying, microfilming, recording, or
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Contributors
Gudni A. Alfredsson • University of Iceland, Institute of Biology, Mi
crobiology Laboratory, Armuli lA, IS-I08 Reykjavik, Iceland
Peter L. Bergquist • Bacterial Genetics and Microbiology, School of
Biological Sciences, University of Auckland, New Zealand
Doug Cossar • Cangene Corporation, 3403 American Drive, Missis
sauga, Ontario, Canada, L4V IT4
Milton S. da Costa • Departmento de Zoologia, Universidade de
Coimbra, 3049 Coimbra Cedex, Portugal
Melanie L. Duffield • Centre for Applied Microbiology and Research,
Porton Down, Salisbury, Wiltshire SP4 OJG, United Kingdom
Jakob K. Kristjansson • University of Iceland, Institute of Biology,
Microbiology Laboratory, ArmUli lA, IS-I08 Reykjavik, Iceland
Hugh W. Morgan • Thermophile Research Unit, University of Wai
kato, Private Bag 3105, Hamilton, New Zealand
Tairo Oshima • Department of Life Science, Tokyo Institute of Tech
nology, Nagatsuta, Yokohama, Japan
Neil D. H. Raven • Centre for Applied Microbiology and Research,
Porton Down, Salisbury, Wiltshire SP4 OjG, United Kingdom
Richard Sharp • Centre for Applied Microbiology and Research, Por
ton Down, Salisbury, Wiltshire SP4 OJG, United Kingdom
Ralph Williams • Queen Mary & Westfield College, Biochemistry De
partment, Faculty of Basic Medical Sciences, Mile End Road, London
E 14 NS, United Kingdom
v
Preface
There is considerable interest in thermophile microorganisms, in their
environments, their ability to survive at temperatures which normally
denature proteins, but more importantly, as a valuable resource for bio
technology.
The first reported isolation of Thermus by Tom Brock was in 1969.
This initiated the present era of thermophilic research with the realization
that where liquid water is available, there may be no limits to the temper
ature at which microorganisms can grow. Considerable research into the
ecology, physiology, metabolism, and thermostable enzymes of thermo
philes has led to their evaluation for a range of industrial and commercial
processes. The past fifteen years have been an explosive period of dis
covery of many new genera and species, including the descriptions of a
new fundamental kingdom-the Archaea.
Much of the current research has been focused on the Archaea; but it
is significant that during this period, the original type strain YT-l of
Thermus aquaticus described by Brock has provided a major step forward in
molecular biology. DNA polymerase from strain YT-I has proved to be the
major success in the commercialization of enzymes from thermophilic
microorganisms to date.
The ease with which Thermus strains can be handled in laboratories
without specialized equipment, together with the large investment in de
scribing their structure, metabolism, and genetics, should ensure a con
tinuing effort in Thermus research.
This book brings together many groups that have isolated and con
tributed to our knowledge of Thermus. It covers aspects of ecology and
isolation, taxonomy, physiology, molecular biology and genetics, cell struc
ture and biotechnology. This volume aims primarily at established re
searchers in universities, research institutes, and industry, but it introduc
es this important group of thermophilic bacteria to undergraduates and
postgraduates who are interested in thermophilic microorganisms as po
tential biotechnological tools and as fascinating laboratory curiosities.
Richard Sharp
Ralph Williams
VB
Contents
Chapter 1
The Taxonomy and Identification of Thermus ............... .
Ralph Williams and Richard Sharp
I. Introduction and General Properties of Thermus ............ 1
2. Cell Wall Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.1. Peptidoglycan..................................... 4
3. Pigments and Lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3.1. Pigments.......................................... 4
3.2. Menaquinones..................................... 5
3.3. Fatty Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.4. Complex Lipids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
4. Phenotypic Properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
4.1. Physiological and Biochemical Tests. . . . . . . . . . . . . . . . . . 6
4.2. Numerical Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
5. Nucleic Acid Studies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.1. DNA Base Composition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.2. DNA:DNA Homology............................... 22
5.3. Ribosomal RNA Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . 24
6. The Species of Thermus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
6.1. The Yellow-Pigmented and Colorless Species. . . . . . . . . . 34
6.2. The Taxonomic Position of Thermus ruber. . . . . . . . . . . . . . 39
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Chapter 2
Ecology, Distribution, and Isolation of Thermus . . . . . . . . . . . . . . 43
Gudni A. Alfredsson and Jakob K. Kristjansson
1. Ecology and Distribution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
1.1. Characteristics of the Thermal Environment. . . . . . . . . . . 43
IX
x CONTENTS
1.2. Different Thermal Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . 44
1.3. Habitats of Thermus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
1.4. Sources of Organic Compounds for Thermus. . . . . . . . . . . . 46
1.5. Thermus and Oligotrophy . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
1.6. Effects of Some Environmental Factors . . . . . . . . . . . . . . . . 50
1.7. Rotund Bodies and Their Possible Function. . . . . . . . . . . . 54
1.8. Distribution of Thermus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
2. Isolation of Thermus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
2.1. Introduction....................................... 56
2.2. Physiological and Nutritional Characteristics. . . . . . . . . . . . 56
2.3. Sampling and Enumeration. . . . . . . . . . . . . . . . . . . . . . . . . . 56
2.4. Culture Media and Isolation .......... . . . . . . . . . . . . . . . 57
2.5. Growth Conditions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Chapter 3
Physiology and Metabolism of Thermus . . . . . . . . . . . . . . . . . . . . . . 67
Richard Sharp, Doug Cossar, and Ralph Williams
1. Enzymes of the Main Metabolic Pathways. . . . . . . . . . . . . . . . . . . 67
1.1. Glycolysis and Gluconeogenesis. . . . . . . . . . . . . . . . . . . . . . . 67
1.2. The Tricarboxylic Acid and Glyoxylate Cycles. . . . . . . . . . 69
1.3. Amino Acid Metabolism ............................. 70
2. Utilization of Substrates for Growth and Energy. . . . . . . . . . . . . 71
2.1. Amino Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
2.2. Carbohydrates...................................... 72
2.3. Carboxylic Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
3. Energetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
3.1. Electron Acceptors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
3.2. The Electron Transport Chain. . . . . . . . . . . . . . . . . . . . . . . . 73
3.3. ATP Synthetase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
3.4. Defenses against Oxygen Toxicity. . . . . . . . . . . . . . . . . . . . . 74
4. Microbial Growth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.1. Medium Development and Growth Requirements. . ... . . 75
4.2. Growth Kinetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
4.3. Growth and Pigmentation. . . ... .. .. . . . .. . . . . . . . . . . . . . 81
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
CONTENTS xi
Chapter 4
Enzymes of Thermus and Their Properties. . . . . . . . . . . . . . . . . . . 93
Melanie L. Duffield and Doug Cossar
1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
2. Thermal Stability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
2.1. Proposed Mechanisms of Thermal Stability . . . . . . . . . . . 9S
2.2. Examples of Thermal Stability. . .. . .. . .. . . . . . . . . . . . . 101
3. Oxidoreductases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
3.1. Lactate Dehydrogenase ............. . . . . . . . . . . . . . . . 101
3.2. Malate Dehydrogenase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
3.3. NADP-Dependent Isocitrate Dehydrogenase. . . . . . . . . . 104
3.4. 3-Isopropylmalate Dehydrogenase. . . . . . . . . . . . . . . . . . . 105
3.5 Ferredoxin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
3.6 Glyceraldehyde-3-Phosphate Dehydrogenase. . . . . . . . . . 107
3.7. L-Alanine Dehydrogenase. . . . . . . . . . . . . . . . . . . . . . . . . . lOS
3.S. NADH Dehydrogenase. . .. . . . . . . . . . . . .. . . . . . .. . . . .. lOS
3.9. NADH Oxidase.. . . . . . ... . .. . . . . . . . . . . . . .... . . . . . . 109
3.10. Catalase.......................................... 110
3.11. Superoxide Dismutase ............................. 110
3.12. Cytochromes...................................... 111
4. Transferases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
4.1. tRNA Methyltransferases . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
4.2. Phosphofructokinase.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
4.3. Phosphoglycerokinase...... . . . . . . . . . . . . . . . . . . . . . . . . 114
4.4. RNA Polymerases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.5. DNA Polymerases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5. Hydrolases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5.1. Proteases..... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5.2. Carbohydrases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
5.3. Alkaline Phosphatase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
5.4. Ribonucleases...... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5.5. EFTu............................................ 120
5.6. Asparaginase..................................... 121
5.7. Inorganic Pyrophosphatase. . . . . . . . . . . . . . . . . . . . . . . . . 122
5.S. ATPase.......................................... 122
5.9. DNA Endonucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
6. Lyases. . . . . . . . .. . .... . . . . . . .. . . .. . . . . . .. . . . . . . .. . . . . . . . 124
6.1. Anthranilate Synthetase. . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
6.2. Enolase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
xii CONTENTS
6.3. Fumarase.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
6.4. Tryptophan Synthetase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
7. Isomerases ............. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
7.1. D-Xylose Isomerase. .... . . . . . . . . . . . . . . . . . . . . . . . ... . . 126
8. Ligases. . . . . . . .. . . . . . . . .. . . .. . . . . . . . . . .. . . . . . . . . . . . . . . .. 127
8.1. Aminoacyl tRNA Synthetase. . . . . . . . . . . . . . . . . . . . . . . . .. 127
8.2. Succinyl-CoA Synthetase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
8.3. DNA Ligase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
9. Miscellaneous. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
9.1. Chaperonins....................................... 131
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Chapter 5
The Cell Walls and Lipids of Thermus . . . . . . . . . . . . . . . . . . . . . . . 143
Milton S. da Costa
1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
2. Cell Wall Structure and Composition. . . . . . . . . . . . . . . . . . . . . . . 143
3. Lipid Composition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
3.1. Respiratory Quinones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
3.2. Polar Lipids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 145
3.3. Fatty Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
3.4. Carotenoids........................................ 150
4. Temperature-Induced Alterations in Lipids. . . . . . . . . . . . . . . . . 151
4.1. Polar Lipids. . . . . . . . . . . . . . . . . . . . .. . . . .. . . . .. . .. . . . . . 151
4.2. Fatty Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
5. Final Considerations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Chapter 6
Genetics of Thermus: Plasmids, Bacteriophage,
Potential Vectors, Gene Transfer Systems . . . . . . . . . . . . . . . . . . . . 157
Neil D. H. Raven
1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
2. Thermus Plasmids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158