Physiology and Biochemistry of Prokaryotes

674 Pages·2007·8.92 MB·English

by  White

The PHYSIOLOGY
and
BIOCHEMISTRY of
PROKARYOTES
THIRD EDITION
David White
Indiana University
New York Oxford
OXFORD UNIVERSITY PRESS
2007
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Library of Congress Cataloging-in-Publication Data
White, David, 1936–
The physiology and biochemistry of prokaryotes / David White.—
3rd ed.
p.;cm.
Includes bibliographical references and index.
ISBN-13: 978-0-19-530168-7 (cloth : alk. paper)
ISBN-10: 0-19-530168-4 (cloth : alk. paper)
1. Prokaryotes—Physiology. 2. Microbial metabolism.
[DNLM: 1. Bacteria—metabolism. 2. Archaea—physiology.
3. Prokaryotic Cells—physiology. QW 52 W583p 2006] I. Title.
QR88.W48 2006
571.2′93—dc22
2005013746
1 3 5 7 9 8 6 4 2
Printed in the United States of America on acid-free paper
PREFACE
The prokaryotes are a diverse assemblage of underlying principles of chemistry and physics
organisms that consists of the bacteria (also in explaining the various physiological and
called eubacteria) and the archaea (also called metabolic features of prokaryotic cells, and
archaebacteria). The text provides an updated thus provides the background for further
account of the major aspects of the prokary- advanced studies in this area.
otes, such as cell structure, metabolism, To help students learn the material and
developmental biology, adaptation to environ- prepare for examinations, each chapter ends
mental changes, and biofilm formation. The with a summary and study questions, as well as
text also covers cellular signaling pathways a section of references and notes. The literature
that allow individual bacterial cells to sense and cited can be consulted for more data supporting
respond to the environment, and also to signal the conclusions stated in the text and the notes
each other so that they can respond as a cooper- expand on topics mentioned in the text. The
ating population of organisms. It is written notes are particularly important. Not only do
primarily for advanced undergraduate and they contain references to review articles and
beginning graduate students, and those who research papers, but they also have vital back-
teach them. Topics include the structure and ground information as well as detailed expla-
function of the prokaryotic cell (Chapter 1), nations of text material, including descriptions
growth and cell division (Chapter 2), mem- of experimental approaches. Students are
brane and cytosol bioenergetics (Chapters 3 therefore urged to examine the notes, particu-
and 7), electron transport and photosynthetic larly when the text directs them to do so.
electron transport (Chapters 4 and 5), meta- This third edition of the text also contains
bolic regulation (Chapter 6), intermediary boxes, which offer interesting historical per-
metabolism (Chapters 8, 9, and 12–14), the spectives on earlier discoveries that established
metabolism of DNA, RNA, and protein, as well the central tenets of biochemistry from the
as how chromosomes are segregated during the end of the nineteenth century into the 1960s,
cell cycle (Chapter 10), cell wall, capsule, and and the people who made these discoveries.
polysaccharide biosynthesis (Chapter 11), From this material, the reader should gain
homeostasis (Chapter 15), solute transport an appreciation of the life-long effort of the
(Chapter 16), protein export and secretion many people who have contributed to our
(Chapter 17), adaptive and developmental understanding of the biochemical bases of how
changes, multicellular behavior, and the signal- cells function. Other boxes explain in more
ing that underlies these events (Chapter 18), detail topics discussed in the text. See the list-
and how bacteria respond to environmental ing of boxed material following the Table of
stress (Chapter 19). The text emphasizes the Contents.
xi
xii PREFACE
Most of the metabolic pathways that exist Most of the carboxyl groups are drawn as
in the prokaryotes are the same as those in all nonionized and the primary amino groups
living organisms, reflecting a unity in biochem- as nonprotonated. However, at physiological
istry dictated by principles of chemistry and pH these groups are ionized and protonated,
(with respect to bioenergetics) physics. On the respectively. The names of the organic acids
other hand, there is also a great deal of physio- indicate that they are ionized (e.g., acetate
logical diversity. The diversity of the prokary- rather than acetic acid).
otes is in part due to adaptations to the different There are two distinct evolutionary lines of
habitats in which they grow. The habitats range prokaryotes commonly referred to as eubac-
in pH from approximately 1 to 12, tempera- teria and archaebacteria. However, this ter-
tures from below 2 °C to over 100 °C, pressures minology implies a specific relationship between
as great as several thousand atmospheres (at eubacteria and archaebacteria, whereas at the
the bottom of the oceans), habitats without molecular level, the archaebacteria are not any
oxygen, and habitats with salt concentrations more related to the eubacteria than they are to
that can reach saturating levels. the eukaryotes. In recognition of this fact,
The physiological types among the prok- Woese et al. suggested that the eubacteria be
aryotes mirror the diversity in the habitats referred to simply as bacteria and that the
and the sources of nutrient. Thus there are archaebacteria be called archaea.1 That ter-
aerobes, anaerobes, and facultative anaerobes; minology is followed in this text.
heterotrophs, autotrophs, phototrophs, and
chemolithotrophs; and alkaliphiles (alkalo-
philes), acidophiles, and halophiles. Some of
Acknowledgments
these physiological types are found only among
the prokaryotes, with rare exceptions. For
example, among microorganisms that have I would like to express gratitude to the follow-
been cultured in the laboratory, the ability to ing individuals who kindly and carefully
live indefinitely in the absence of air (anaerobic reviewed portions of this edition: Carl Bauer,
growth) is confined almost entirely to prokary- Yves Brun, Jim Drummond, Martin Dworkin,
otes. Also, growth using the energy extracted Pat Foster, Clay Fuqua, Heidi Kaplan, Larry
from inorganic compounds (lithotrophy) seems Shimkets, and Ashley Williams, as well as the
not to have evolved in the eukaryotes and is anonymous reviewers. I also want to thank the
restricted to certain groups of prokaryotes. The many individuals who helped me by reviewing
same can be said about the ability to reduce the first two editions. I would also like to thank
nitrogen gas to ammonia (nitrogen fixation), the team at Oxford University Press for helping
although this characteristic is more widespread me with this edition, including the senior editor
among the prokaryotes than is lithotrophy. for life sciences, Peter Prescott, Kaity Cheng,
Another typically prokaryotic capability is the the editorial assistant for Life Sciences, Barbara
use of inorganic compounds such as nitrate and Mathieu, the production editor, and Brenda
sulfate as electron acceptors during respiration Griffing, the copy editor. This edition, like the
(anaerobic respiration). first two editions, was illustrated by Eric J.
The organization of the text is according to White.
topics rather than organisms, although the
physiology of specific groups of prokaryotes is
REFERENCE
emphasized. This pattern of organization lends
itself to the elucidation of general principles of
1. Woese, C. R., Kandler, O., and M. L. Wheelis.
physiology, metabolism, responses to environ-
1990. Towards a natural system of organisms:
mental challenges, and cellular/multicellular proposal for the domains Archaea, Bacteria and
development. Eucarya. Proc. Natl. Acad. Sci. USA87:4576–4579.
CONTENTS
Boxed Material x
Preface xi
Symbols xiii
Conversion Factors, Equations, and Units of Energy xv
Definitions xvii
Chapter 1. Structure and Function 1
1.1 Phylogeny 3
1.2 Cell Structure 6
1.3 Summary 44
Study Questions 45
Chapter 2. Growth and Cell Division 53
2.1 Measurement of Growth 53
2.2 Growth Physiology 55
2.3 Cell Division 64
2.4 Growth Yields 70
2.5 Growth Kinetics 71
2.6 Steady State Growth and Continuous Growth 73
2.7 Summary 74
Study Questions 75
Chapter 3. Membrane Bioenergetics: The Proton Potential 83
3.1 The Chemiosmotic Theory 83
3.2 Electrochemical Energy 84
3.3 The Contributions of the ∆Ψand the ∆pH to the Overall ∆p
in Neutrophiles, Acidophiles, and Alkaliphiles 90
3.4 Ionophores 91
3.5 Measurement of the ∆p 93
3.6 Use of the ∆pto Do Work 94
3.7 Exergonic Reactions that Generate a ∆p 98
3.8 Other Mechanisms for Creating a ∆Ψor a ∆p 102
3.9 Halorhodopsin, a Light-Driven Chloride Pump 112
3.10 The ∆pand ATP Synthesis in Alkaliphiles 112
3.11 Summary 112
Study Questions 114
v
vi CONTENTS
Chapter 4. Electron Transport 120
4.1 Aerobic and Anaerobic Respiration 121
4.2 The Electron Carriers 121
4.3 Organization of the Electron Carriers in Mitochondria 125
4.4 Organization of the Electron Carriers in Bacteria 128
4.5 Coupling Sites 130
4.6 How a Proton Potential Might Be Created at the Coupling Sites: Q Loops,
Q Cycles, and Proton Pumps 132
4.7 Patterns of Electron Flow in Individual Bacterial Species 137
4.8 Summary 144
Study Questions 145
Chapter 5. Photosynthesis 149
5.1 The Phototrophic Prokaryotes 149
5.2 The Purple Photosynthetic Bacteria 152
5.3 The Green Sulfur Bacteria (Chlorbiaceae) 157
5.4 Cyanobacteria and Chloroplasts 159
5.5 Efficiency of Photosynthesis 161
5.6 Photosynthetic Pigments 162
5.7 The Transfer of Energy from the Light-Harvesting Pigments to
the Reaction Center 168
5.8 The Structure of Photosynthetic Membranes in Bacteria 169
5.9 Summary 169
Study Questions 170
Chapter 6. The Regulation of Metabolic Pathways 173
6.1 Patterns of Regulation of Metabolic Pathways 173
6.2 Kinetics of Regulatory and Nonregulatory Enzymes 175
6.3 Conformational Changes in Regulatory Enzymes 178
6.4 Regulation by Covalent Modification 178
6.5 Summary 179
Study Questions 179
Chapter 7. Bioenergetics in the Cytosol 181
7.1 High-Energy Molecules and Group Transfer Potential 181
7.2 The Central Role of Group Transfer Reactions in Biosynthesis 186
7.3 ATP Synthesis by Substrate Level Phosphorylation 188
7.4 Summary 194
Study Questions 195
Chapter 8. Central Metabolic Pathways 196
8.1 Glycolysis 198
8.2 The Fate of NADH 204
8.3 Why Write NAD+Instead of NAD, and NADH Instead of NADH? 204
2
8.4 A Modified EMP Pathway in the Hyperthermophilic Archaeon
Pyrococcus furiosus 204
8.5 The Pentose Phosphate Pathway 205
8.6 The Entner–Doudoroff Pathway 210
8.7 The Oxidation of Pyruvate to Acetyl–CoA: The Pyruvate
Dehydrogenase Reaction 213
8.8 The Citric Acid Cycle 214
8.9 Carboxylations that Replenish Oxaloacetate: The Pyruvate and
Phosphoenolpyruvate Carboxylases 219
8.10 Modification of the Citric Acid Cycle into a Reductive (Incomplete) Cycle
During Fermentative Growth 220
CONTENTS vii
8.11 Chemistry of Some of the Reactions in the Citric Acid Cycle 221
8.12 The Glyoxylate Cycle 223
8.13 Formation of Phosphoenolpyruvate 224
8.14 Formation of Pyruvate from Malate 225
8.15 Summary of the Relationships Between the Pathways 226
8.16 Summary 226
Study Questions 228
Chapter 9. Metabolism of Lipids, Nucleotides, Amino Acids, and Hydrocarbons 230
9.1 Lipids 230
9.2 Nucleotides 238
9.3 Amino Acids 243
9.4 Aliphatic Hydrocarbons 248
9.5 Summary 251
Study Questions 253
Chapter 10. Macromolecular Synthesis 255
10.1 DNA Replication, Chromosome Separation, and Chromosome Partitioning 255
10.2 RNA Synthesis 280
10.3 Protein Synthesis 293
10.4 Summary 306
Study Questions 308
Chapter 11. Cell Wall and Capsule Biosynthesis 318
11.1 Peptidoglycan 318
11.2 Lipopolysaccharide 323
11.3 Extracellular Polysaccharide Synthesis and Export in Gram-Negative Bacteria 328
11.4 Levan and Dextran Synthesis 333
11.5 Glycogen Synthesis 333
11.6 Summary 333
Study Questions 334
Chapter 12. Inorganic Metabolism 336
12.1 Assimilation of Nitrate and Sulfate 336
12.2 Dissimilation of Nitrate and Sulfate 338
12.3 Nitrogen Fixation 341
12.4 Lithotrophy 345
12.5 Summary 355
Study Questions 356
Chapter 13. C Metabolism 359
1
13.1 Carbon Dioxide Fixation Systems 359
13.2 Growth on C Compounds Other than CO: The Methylotrophs 375
1 2
13.3 Summary 378
Study Questions 380
Chapter 14. Fermentations 383
14.1 Oxygen Toxicity 383
14.2 Energy Conservation by Anaerobic Bacteria 384
14.3 Electron Sinks 386
14.4 The Anaerobic Food Chain 386
14.5 How to Balance a Fermentation 387
14.6 Propionate Fermentation via the Acrylate Pathway 388
14.7 Propionate Fermentation via the Succinate–Propionate Pathway 389
viii CONTENTS
14.8 Acetate Fermentation (Acetogenesis) 391
14.9 Lactate Fermentation 392
14.10 Mixed-Acid and Butanediol Fermentation 394
14.11 Butyrate Fermentation 397
14.12 Ruminococcus albus 400
14.13 Summary 401
Study Questions 402
Chapter 15. Homeostasis 404
15.1 Maintaining a ∆pH 404
15.2 Osmotic Pressure and Osmotic Potential 407
15.3 Summary 413
Study Questions 414
Chapter 16. Solute Transport 417
16.1 The Use of Proteoliposomes to Study Solute Transport 417
16.2 Kinetics of Solute Uptake 418
16.3 Energy-Dependent Transport 419
16.4 How to Determine the Source of Energy for Transport 429
16.5 Drug-Export Systems 430
16.6 Bacterial Transport Systems in Summary 431
16.7 Summary 431
Study Questions 434
Chapter 17. Protein Transport 438
17.1 The Sec System 439
17.2 The Translocation of Membrane-Bound Proteins 443
17.3 The E. coliSRP 445
17.4 Protein Translocation of Folded Proteins; the Tat System 445
17.5 Extracellular Protein Secretion 447
17.6 Folding of Periplasmic Proteins 457
17.7 Summary 459
Study Questions 460
Chapter 18. Microbial Development and Physiological Adaptation: Varied Responses to
Environmental Cues and Intercellular Signals 467
18.1 Introduction to Two-Component Signaling Systems 469
18.2 Responses by Facultative Anaerobes to Anaerobiosis 474
18.3 Response to Nitrate and Nitrite: The Nar Regulatory System 480
18.4 Response to Nitrogen Supply: The Ntr Regulon 484
18.5 Response to Inorganic Phosphate Supply: The Pho Regulon 489
18.6 Effect of Oxygen and Light on the Expression of Photosynthetic
Genes in the Purple Photosynthetic Bacterium Rhodobacter capsulatus 491
18.7 Response to Osmotic Pressure and Temperature:
Regulation of Porin Synthesis 492
18.8 Response to Potassium Ion and External Osmolarity: Stimulation of
Transcription of the kdpABCOperon by a Two-Component Regulatory System 494
18.9 Acetyl-Phosphate Is a Possible Global Signal in Certain
Two-Component Systems 494
18.10 Response to Carbon Sources: Catabolite Repression, Inducer Expulsion,
Permease Synthesis 496
18.11 Virulence Factors: Synthesis in Response to Temperature, pH, Nutrient,
Osmolarity, and Quorum Sensors 502
18.12 Chemotaxis 509
18.13 Photoresponses 519
CONTENTS ix
18.14 Aerotaxis 522
18.15 Introduction to Bacterial Development and to Quorum Sensing 522
18.16 Myxobacteria 523
18.17 CaulobacterDevelopment: Control of DNA Replication and
Cell Cycle Genes 534
18.18 Sporulation in Bacillus subtilis 539
18.19 Competence in Bacillus subtilis 550
18.20 Bioluminescence 552
18.21 Systems Similar to LuxR/LuxI in Nonluminescent Bacteria 561
18.22 Biofilms 564
18.23 Summary 570
Study Questions 572
Chapter 19. How Bacteria Respond to Environmental Stress 599
19.1 Heat-Shock Response 599
19.2 Repairing Damaged DNA 603
19.3 The SOS Response 608
19.4 Oxidative Stress 611
19.5 Summary 613
Study Questions 614
Index 617
1
Structure and Function
The prokaryote (procaryote) domains are the structures, called appendages. The appendages
Bacteria and the Archaea. Prokaryotes are include pili and flagella. Pili (sing., pilus), which
defined as organisms that have no membrane- are of different types, serve different functions.
bound nucleus. (The prefix pro, borrowed Depending upon the type, pili are used for
from Greek pro, means earlier than or before; adhesion to other cells when that becomes
karyote, borrowed from Greek káryon, means necessary for colonization, for movement on
kernel or nut.) Besides lacking a nucleus, solid surfaces via a form of gliding motility
prokaryotes are devoid of organelles such as called twitching, and for mating. Flagella (sing.
mitochondria, chloroplasts, and Golgi vesicles. flagellum) are used by single cells to swim in
However, as you will learn from reading this liquid, as well as a form of group swimming on
chapter, their cell structure is far from simple moist solid surfaces called swarming.
and reflects the evolution of prokaryotes into In addition, it turns out that the poles of non-
quite sophisticated organisms that are the most spherical bacteria cells are physiologically and
successful in inhabiting diverse ecological niches. structurally different from the rest of the cell,
Despite the absence of organelles compar- and sometimes the cell poles in the same cell
able to those found in eukaryotic cells, prokar- differ from each other. This is obvious, for
yotes’ metabolic activities, cell division activities, example, when flagella or pili protrude from
and intracellular signaling activities that regu- one or both cell poles, or when a cell pole is
late metabolism and cell development are distinguished by having a stalk, as is the case for
compartmentalized and/or localized to specific Caulobacter, discussed in Chapter 18. In other
sites within the cell. For example, as this cases the differences between poles are less
chapter will point out, compartmentalization obvious, as shown, for example, in the discus-
occurs within multienzyme granules that house sion of the polar localization of the chemotaxis
enzymes for specific metabolic pathways, in proteins in Chapter 18. As also discussed in
intracellular membranes within the cytosol, Chapter 18, in Myxococcus the two gliding
within the cell membrane, within a special com- motility engines, the A and S engines, are not
partment called the periplasm in gram-negative only in opposite cell poles, but actually switch
bacteria, within the cell wall itself, and within poles on a regular basis. This is an example
various inclusion bodies that house specific of the dynamic interplay that can take place
enzymes, storage products, or photosynthetic between the various parts of a prokaryotic cell.
pigments. It has become recently clear that prokaryotes
As this chapter points out, the external struc- even have an internal protein cytoskeleton, a
ture of prokaryotic cells also has specialized property previously thought to be restricted to
1