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of Biology University Transport Carriers
ACADEMIC PUBLISHERS
Bacteria
BOSTON 1 LONDONBologna,
Zannoniof
in
by
of Prokaryotic 1 Electron Archaea
Respiration
and
Diversity
Edited
Davide
Department
Italy
""
ON
KLUWER
DOFRDRECHT
Contents
Editorial v
Preface
Color Plates CP-1
1 Evolution and Phylogenetic Analysis of Respiration 1-14
Jose Castresana
Summary 1
1. Introduction 2
Il . Chemical Composition of the Primitive Atmosphere and Oceans 2
II1 . Heterotrophic vs, Autotrophic Origin of Energy Conversion 3
IV. The Comparative Genomics Evidence on the Evolution of Respiration 3
V. Ancient Respiratory Mechanisms 5
V1 . Respiratory Mechanisms Evolved in Archaea 8
VII . The Last Universal Ancestor Was a Generalist Organism 8
Vlll . The Respiration- Eariy Hypothesis : Photosynthesis Came Later 9
Acknowledgments 10
References 10
2 NADH Dehydrogenase (NADH-Quinone Oxidoreductase) 15-40
Takao Yagi, Salvatore Di Bemardo, Eiko Nakamaru-Ogiso,
Mou-Chieh Kao, Byoung Boo Seo, and Akemi Matsuno-Magi
Summary 15
I. Introduction 16
ii. Genes and Regulations of H+-Translocating NADH-Quinone (Q)
Oxidoreductase (NDH-1) and NADH-Q Oxidoreductase (Non-Energy
Transducing, NDH-2) 17
111 . NDH-1 20
IV . NDH-2 31
Acknowledgments 33
References 33
3 Bacterial Hydroquinone:Cytochrome c Oxidoreductases.
Physiology, Structure and Function 41--55
Jason W, Cooley, Elisabeth Darrouzet and Fevzi DaIdal
Summary 41
I. Introduction 42
II. Experimental Systems Used in the Study of the Cyt bc, 44
III . Structure of the Cyt be, 46
IV. Function of the Cyt be, The Modified Q cycle
: 50
V. Diseases Associated with the Cyt bc1
51
Acknowledgments 53
References 53
4 Structure and Function of Succinate:Quinone Oxidoreductases and
the Role of Quinol :Fumarate Reductases in Fumarate Respiration 57-85
C. Roy D, Lancaster
Summary 58
I. Introduction 58
II, Organization of the sdh and frd Genes 61
III . Structure and Function of the Quinol : Fumarate Reductase (QFR) Subunits 62
IV. The Site(s) of Menaquinol Oxidation and Quinone Reduction 68
V. Catalytic Properties of Succinate :Quinone Reductases (SQRs) and
Quinol :Fumarate Reductases (QFRs) 69
VI . Electron Transfer 70
VII, Inhibition of SQR and QFR 74
VIII . The Function of Menaquinone in W. succinogenes Fumarate Respiration
and Reconstitution of the Electron Transfer Chains 74
IX. Energetics of Fumarate Respiration and the Mechanism of Ap Generation 77
X. Conclusions 80
Acknowledgments 81
References 81
5 Biochemical and Molecular Features of Terminal Oxidases 87--113
Junshi Sakamoto and Nobuhito Sone
Summary 88
I. Introduction 88
II . Diversity and Unity of Cytochrome Oxidases 89
II . SoxM-Type Oxidases 91
IV . SoxB-Type Oxidases 96
V. FixN-Type Oxidases 98
VI . Cytochrome bd 100
VII . Interaction with Cyt c and Quinoi : Cytochrome cOxidoreductase (QCR) 102
VIII. Energy-Yielding Terminal Oxidases 104
References 107
6 Structures of Bacterial Herne-Copper Oxidases 115-128
Jeff Abramson, Tatsuro Shimamura and So iwata
summary 115
I. Introduction 116
II. Structures of Cytochrome c Oxidases 116
III . Structure of Ubiquinol Oxidase 124
Acknowledgment 127
References 127
7 Functional Aspects of Heme-Copper Terminal Oxidases 129-153
Peter Brzezinski, Gisela Larsson and Pia Adelroth
Summary 130
l. Introduction 130
11 . Structures 131
lit . General Design of a Proton Pump 134
IV. Intramolecular Electron and Proton Transfer 134
V . Reaction of the Reduced Enzyme With Oxygen 139
VI . Putative Specific Proton Pumping Mechanisms 144
Vil . Current issues and Unresolved Questions 145
Acknowledgments 145
References 146
8 The Nay--Translocating NADH-Quinone Reductase of Marine and
Moderately Halophilic Bacteria 155-174
Maki Hayashi and Tsutomu Unemoto
Summary 155
I. Introduction 156
11. Redox-Driven Na+ Pump of Vibrio alginolyticus 156
Ill . Other Components of the Respiratory Chain of V. alginolyticus 156
IV. Catalytic Properties and Sub-Unit Structure of Na+-NQR 159
V. Mechanism of Energy Coupling 164
VI. Inhibitor Studies 168
VII. Distribution of the Na+-NQR 169
Vill . Bioenergetics of Marine Bacteria 170
References 171
9 Microbial Molybdenum-Containing Enzymes in Respiration:
Structural and Functional Aspects 175-202
Alastair G. McEwan, Ulrike Kappler and ChristopherA, MCDet%Itt
Summary 176
I. Introduction 176
11. Phylogeny of Enzymes of the Dimethylsulfoxide (DMSO) Reductase Family 179
III . Respiratory Processes Involving Molybdenum Enzymes 180
IV . Organization of Electron Transport Pathways 186
V . Structural Studies of Prokaryotic Respiratory Molybdenum Enzymes 189
VI . Mechanism of Molybdenum-Containing Enzymes 194
References 196
10 The Pyrroloquinoline Quinone (PQQ)-Containing
Dehydrogenases 203-225
Christopher Anthony
Summary 203
1. Introduction 204
11. The Physiological Roles of the Quinoprotein Dehydrogenases and
Their Electron Transport Chains 205
111 . The Structures of the PQQ-Containing Quinoprotein Dehydrogenases 208
IV. The Dehydrogenases 209
Acknowledgments 222
References 222
11 Biogenesis of Cytochrome c 227-250
Elisabeth Enggist and Linda Thony-Meyer
Summary 228
I. Introduction 228
II. Prokaryotic Genes for Cytochrome c Maturation 229
111 . Apo-Cytochrome c 232
1V. Heme 236
V. Heme Ligation 242
VI, Open Questions 244
Acknowledgment 245
References 246
12 Bacterial Hemoglobins : Old Proteins with `New' Functions?
Roles in Respiratory and Nitric Oxide Metabolism 251-286
Guanghui Wu, Laura M. Wainwright, Jorge Membrillo-
Hernandez and Robert K. Poole
Summary 252
I. Introduction to Globins-Definition and the Classical View 253
II . The Vitreoscilla Globin, Vgb, and other Single Domain
Myoglobin-like Globins 255
III . Truncated Globins 262
IV, Flavohemoglobins 266
V. Evolution of Globins 278
VI. Concluding Remarks 279
Acknowledgments 280
References 280
13 Oxidases as Redox Sensors in Pigment Synthesis 287-309
Jeong-!l Oh and Samuel Kaplan
Summary 287
I. Introduction 288
11 . Overview of PS Gene Regulation 292
111 . cbb3 Cytochrome c Oxidase 295
IV, cbb~-PrrBA Signal Transduction Pathway 299
V. Redox State of the Quinone Pool and PS Gene Expression 302
VI. Concluding Remarks 305
Addendum Added in Proof 305
Acknowledgments 305
References 305
Subject Index 3'11
Species Index 321
Gene and Gene Product Index 325
