Anoxygenic Photosynthetic Bacteria

Advances in Photosynthesis

VOLUME 2

Series Editor:GOVINDJEE

Department of Plant BiologyUniversity of Illinois, Urbana, Illinois, U.S.A.

Consulting Editors:Jan AMESZ, Leiden, The Netherlands

James BARBER, London, United KingdomRobert E. BLANKENSHIP, Tempe, Arizona, U.S.A.

Norio MURATA, Nagoya, JapanDonald R. ORT, Urbana, Illinois, U.S.A.

Advances in Photosynthesis provides an up-to-date account of research onall aspects of photosynthesis, the most fundamental life process on earth.Photosynthesis is an area that requires, for its understanding, a multidiscipli-nary (biochemical, biophysical, molecular biological, and physiological)approach. Its content spans from physics to agronomy, from femtosecondreactions to those that require an entire season, from photophysics of reac-tion centers to the physiology of the whole plant, and from X-ray crystallog-raphy to field measurements. The aim of this series of publications is topresent to beginning researchers, advanced graduate students and evenspecialists a comprehensive current picture of the advances in the variousaspects of photosynthesis research. Each volume focusses on a specificarea in depth.

The titles to be published in this series are listed on the backcover of this volume.

AnoxygenicPhotosynthetic Bacteria

Edited by

Robert E. BlankenshipDepartment of Chemistry and Biochemistry,

Arizona State University,Tempe, Arizona, U.S.A.

Michael T. MadiganDepartment of Microbiology,Southern Illinois University,Carbondale, Illinois, U.S.A.

and

Carl E. BauerDepartment of Biology,

Indiana University,Bloomington, Indiana, U.S.A.

KLUWER ACADEMIC PUBLISHERSNEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW

eBook ISBN: 0-306-47954-0Print ISBN: 0-7923-3681-X

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Dordrecht

Contents

Preface xxiii

Part I: Taxonomy, Physiology and Ecology

1 Taxonomy and Physiology of Phototrophic Purple Bacteria andGreen Sulfur Bacteria

Johannes F. Imhoff

SummaryI. IntroductionII. General Aspects of TaxonomyIII. General Aspects of PhysiologyIV. Description of the GroupsReferences

1–15

11345

11

2 Taxonomy, Physiology and Ecology of HeliobacteriaMichael T. Madigan and John G. Ormerod

SummaryI. IntroductionII. Taxonomy of HeliobacteriaIII. PhysiologyIV. Ecology and Isolation of HeliobacteriaAcknowledgmentsReferences

17–30

17181923272929

3 Taxonomy and Physiology of Filamentous Anoxygenic PhototrophsBeverly K. Pierson and Richard W. Castenholz

SummaryI. IntroductionII. Taxonomy and PhylogenyIII. PhysiologyAcknowledgmentReferences

Ecology of Phototrophic Sulfur BacteriaHans Van Gemerden and Jordi Mas

SummaryI. IntroductionII. Characteristic and Vertical Structure of the Habitats

v

31–47

323233364444

49–85

505050

4

53565860636372787979

87–103

878893

94101

105–122

105106106108111113116118120120

123–136

124124126127131134135135

III. Distribution and Abundance of Phototrophic Sulfur Bacteria in NatureIV. Contribution of Phototrophic Sulfur Bacteria to Primary ProductionV. Growth Rates in NatureVI. Loss ProcessesVII. Growth Balance, Maximum Biomass and Production in Phototrophic CommunitiesVIII. Environmental Factors Affecting Growth and Survival of Phototrophic Sulfur BacteriaIX. Case StudiesX. Concluding RemarksAcknowledgmentsReferences

5 Ecology of Thermophilic Anoxygenic PhototrophsRichard W. Castenholz and Beverly K. Pierson

SummaryI. IntroductionII. Chemical and Geographical Diversity of Thermal HabitatsIII. Principal Habitats of Thermophilic Anoxygenic Phototrophs and

the Environmental Requirements: Case StudiesReferences

6 Aerobic Anoxygenic PhototrophsKeizo Shimada

SummaryI. IntroductionII. Habitats and CultureIII. Photosynthetic ApparatusIV. Pigments and Other ComponentsV. Photosynthetic Activity and Electron Transfer SystemVI. Regulation of Pigment SynthesisVII. Evolution and TaxonomyAcknowledgmentsReferences

7 Bacteriochlorophyll-Containing Rhizobium SpeciesDarrell E. Fleischman, William R. Evans and lain M. Miller

SummaryI. IntroductionII. Relationship of Bacteriochlorophyll-containing Rhizobium Species to Other BacteriaIII. Characteristics of Aeschynomene Rhizobium BTAi 1 Grown ex plantaIV. Characteristics of Photosynthetic Rhizobium in the Symbiotic SystemV. ConclusionsAcknowledgmentsReferences

vi

Part II: Molecular Structure and Biosynthesis of Pigments and Cofactors

8

9

10

vii

208208208209217

219221222223226

207–230

137–151

137137138141149149149

153–177

153154154170170

Biosynthesis and Structures of the BacteriochlorophyllsMathias O. Senge and Kevin M. Smith

SummaryI. IntroductionII. Structural Chemistry of the BacteriochlorophyllsIII. Biosynthesis of the BacteriochlorophyllsIV. Degradation of the BacteriochlorophyllsAcknowledgmentsReferences

Biosynthesis and Structures of Porphyrins and HemesSamuel I. Beale

SummaryI. IntroductionII. The Early Common StepsAcknowledgmentsReferences

Lipids, Quinones and Fatty Acids of Anoxygenic Phototrophic Bacteria 179–205Johannes M. Imhoff and Ursula Bias-lmhoff

SummaryI. IntroductionII. Polar Lipids and Fatty AcidsIII. Apolar LipidsReferences

Part III. Membrane and Cell Wall Architecture and Organization

11 Anoxygenic Phototrophic Bacteria: Model Organisms for Studies onCell Wall Macromolecules

Jürgen Weckesser, Hubert Mayer and Georg Schulz

SummaryI. IntroductionII. Definition, Function, and Constituents of the Cell WallIII. Phylogenetic Relevance of Cell Wall ConstituentsIV. Structure of Lipopolysaccharide (LPS)V. Contribution of the Lipopolysaccharides (LPS) of Purple Bacteria to

Endotoxin ResearchVI. PorinVII. External Envelope LayersVIII. Concluding RemarksReferences

180180183198201

12 Structure, Molecular Organization, and Biosynthesis of Membranes ofPurple Bacteria 231–257

231232

233

242251251

Gerhart Drews and Jochen R. Golecki

SummaryI. IntroductionII. Structure and Supramolecular Organization of Cytoplasmic and Intracytoplasmic

MembranesIII. Biosynthesis of Membranes and the Assembly of the Functional Complexes

of the Photosynthetic ApparatusAcknowledgmentsReferences

13 Membranes and Chlorosomes of Green Bacteria: Structure, Compositionand Development 259–278

Jürgen Oelze and Jochen R. Golecki

Summary 259260260264267268274275275

I. IntroductionII. UltrastructureIII. Chemical CompositionIV. Supramolecular Organization of ChlorosomesV. Development of the Photosynthetic ApparatusVI. Open QuestionsAcknowledgmentsReferences

14 Organization of Electron Transfer Components and Supercomplexes 279–295André Verméglio, Pierre Joliot and Anne Joliot

Summary 279280281282284287292

I. IntroductionII. The Versatile Metabolism of the RhodospirillaceaeIII. Regulation of the Biosynthesis of the Electron Transfer ComponentsIV. Short Term Interactions Between Photosynthetic and Respiratory ActivitiesV. Organization of the Electron Carrier Proteins into SupercomplexesReferences

Part IV: Antenna Structure and Function

15 Theory of Electronic Energy Transfer 297–313

297298298303309312312

Walter S. Struve

SummaryI. IntroductionII. The Weak Coupling LimitIII. Unified Theory for Energy TransferIV. Temperature Dependence of Energy TransferAcknowledgmentsReferences

viii

16 Structure and Organization of Purple Bacterial Antenna ComplexesHerbert Zuber and Richard J. Cogdell

SummaryI.II.

Structure and Function of Antenna Complexes from Purple BacteriaStructure and Function of Antenna Polypeptides from Purple Bacteria.General Aspects

III. Amino Acid Sequences (Primary Structure) of Antenna Polypeptides.Sequence Homologies, Structural and Functional Features

IV. Structural and Functional Variability of the Antenna Polypeptides and Pigmentswithin the Antenna Complex

V. Possible Structural Organization of Polypeptides and BChl Molecules in theAntenna Complex Derived from Primary Structure Data (Primary Structure Models):Considerations on the Three-Dimensional Structure of Antenna Complexes

Note Added in ProofAcknowledgmentsReferences

316316

320

321

328

331342344344

17 Kinetics of Excitation Transfer and Trapping in Purple BacteriaVilly Sundström and Rienk van Grondelle

Summary

349–372

315–348

I. IntroductionII. Pigment-Protein Organization in LH1 and LH2III. Spectroscopy of the LH1 and LH2 Light-Harvesting AntennaeIV. Energy Transfer in LH2-Less Purple BacteriaV. Energy Transfer in LH2-Containing Purple BacteriaVI. Energy Transfer in Isolated Light-Harvesting Complexes and MutantsReferences

349350350352356361363366

18 Singlet Energy Transfer from Carotenoids to Bacteriochlorophylls 373–384Harry A. Frank and Ronald L. Christensen

SummaryI. Introduction

373374374378380381382

II. The Electronic Structure of Carotenoid Excited StatesIII. The Dynamics of Carotenoid Excited StatesIV. Implications for Energy TransferAcknowledgmentsReferences

19 Coupling of Antennas to Reaction CentersArvi Freiberg

385–398

385386386387388391393395396396

ix

SummaryI. IntroductionII. The Concept of a Photosynthetic UnitIII. Structure and Organization of Real Photosynthetic SystemsIV. Trapping of Energy by the Reaction CenterV. Detrapping of Excitation Energy from the Reaction CenterVI. Pigment-Protein Couplings According to High Hydrostatic Pressure StudiesVII. Concluding RemarksAcknowledgmentsReferences

20 399–435Antenna Complexes from Green Photosynthetic BacteriaRobert E. Blankenship, John M. Olson and Mette Miller

400400401408410413418422426427428428

SummaryI. IntroductionII. Chlorosome CompositionIII. In vitro Aggregates of Chlorosome ChlorophyllsIV. Spectroscopic Probes of Chlorosome StructureV.VI.

Structural Models for Pigment and Protein Organization in ChlorosomesKinetics and Pathways of Energy Transfer in Chlorosomes

VII.VIII.

The Fenna-Matthews-Olson (FMO) Bacteriochlorophyll a ProteinRedox Modulation of Energy Transfer in Green Photosynthetic Bacteria

IX. Evolutionary ConsiderationsAcknowledgmentsReferences

21 Structure-Function Relationships in Core Light-Harvesting Complexes (LHI)As Determined by Characterization of the Structural Subunit and byReconstitution Experiments 437–471

Paul A. Loach and Pamela S. Parkes-Loach

438439440449452

454456

457459460461464466467467

473–501

473474

478

478

480487495495496

SummaryI. IntroductionII. The Structural Subunit of LHIIII. Reconstitution of Subunit Complexes and LHI from Separately-Isolated ComponentsIV. Probing the BChl Binding Site by Reconstitution with BChl AnalogsV.

VI.VII.

VIII.IX.X.XI.XII.

Reconstitution of Car to Form Wild-Type LHI with BChl a and Polypeptides ofRb. sphaeroides and Rs. rubrumReconstitution of LHI-type Complexes Using Mixed PolypeptidesProbing Structural Requirements for Formation of the Subunit Complex and LHIby Reconstitution with Modified PolypeptidesAnalysis of Stabilizing Interactions in Subunit ComplexesAnalysis of Stabilizing Interactions in LHIImplications for the Structure of the Subunit ComplexesMinimal Structural Requirements to Form LHIInteraction of LHI with RC

AcknowledgmentsReferences

22 Genetic Manipulation of the Antenna Complexes of Purple BacteriaC. Neil Hunter

SummaryI.II.

IntroductionThe Effect of Genetic Alteration of Antennas on the Morphology of IntracytoplasmicMembranes

III. The Use of LH1-Only and LH1-RC Mutants to Facilitate Biochemical and StructuralStudies

IV.

V.VI.VII.

x

The Use of Antenna Mutants to Simplify Spectroscopic Studies of AntennaComplexes in a Membrane EnvironmentSite-Directed Mutagenesis of Bacterial Light Harvesting ComplexesHeterologous Expression of LH Genes in Rhodobacter sphaeroidesConcluding Remarks

References

Part V: Reaction Center Structure, Electron and Proton Transfer Pathways

23 The Structures of Photosynthetic Reaction Centers from Purple Bacteria asRevealed by X-Ray Crystallography 503–526

C. Roy D. Lancaster, Ulrich Ermler and Hartmut Michel

SummaryI. IntroductionII. Structural and Functional OverviewIII. Arrangement of the CofactorsIV. The Structure of the Protein SubunitsV.VI.

Cofactor Conformation and Protein-Cofactor InteractionsThe Structure of Mutant Reaction Centers

VII. ConclusionsReferences

24 The Pathway, Kinetics and Thermodynamics of Electron Transfer in Wild Type527–557and Mutant Reaction Centers of Purple Nonsulfur Bacteria

Neal W. Woodbury and James P. Allen

SummaryI. IntroductionII. The Reaction Center of Rhodobacter sphaeroidesIII. Reaction Center MutantsIV. The Ground State Optical Spectrum of Reaction CentersV. The Spectral and Kinetic Properties of P*VI. The StateVII. The Product of Initial Charge SeparationVIII. Electron Transfer to the Primary QuinoneIX. Electron Transfer from the Primary to Secondary QuinoneX. The Thermodynamics of Reaction Center Electron TransferXI. Reaction Center Symmetry and the Direction of Electron TransferXII. The Pathway and Mechanism of Initial Electron TransferXIII. The Role of the Reaction Center Protein in Electron TransferAcknowledgmentsReferences

25 Theoretical Analyses of Electron-Transfer ReactionsWilliam W. Parson and Arieh Warshel

SummaryI. IntroductionII. Phenomenological Descriptions of Electron-Transfer ReactionsIII. Microscopic Calculations of Electron-Transfer ParametersAcknowledgmentsReferences

xi

503504505506508512521523523

528528529531532533538540542543543545547551552552

559–575

559560562564572572

26 Proton-Coupled Electron Transfer Reactions of in Reaction Centers fromPhotosynthetic Bacteria 577–594

M. Y. Okamura and G. Feher

SummaryI. IntroductionII.III.

Structure of the Bacterial Reaction Center Near the SiteThe Quinone Reduction Cycle

IV. Properties of the QuinonesV. Effects of Site-Directed Mutagenesis on Electron and Proton Transfer RatesVI. Mechanism of Proton Coupled Electron TransferVII. Pathways for Proton TransferNote Added in ProofAcknowledgementsReferences

27 The Recombination Dynamics of the Radical Pair in External Magnetic and595–626Electric Fields

Martin Volk, Alexander Ogrodnik and Maria-Elisabeth Michel-Beyerle

SummaryI. The Magnetic Field EffectII. Temperature Dependent Recombination Dynamics of in Native RCs of Various

Photosynthetic BacteriaIII. The Effect of Genetic Mutations on the Recombination Dynamics ofIV. Recombination Dynamics of in an External Electric FieldV. Observation of the Recombination Dynamics of in Delayed Fluorescence:

Evidence for an Energetic Inhomogeneity ofVI. Recombination Dynamics as a Unique Diagnostic Tool: ConclusionsAcknowledgmentsReferences

28 Infrared Vibrational Spectroscopy of Reaction CentersWerner Mäntele

SummaryI. Introduction: What Can We Learn About Reaction Centers From Infrared

Spectroscopy?II. Technical Aspects of Infrared Spectroscopy of Reaction CentersIII.IV.

From Bands to Bonds: Strategies for Band AssignmentsLight-Induced Difference Spectroscopy of Charge Separation in Reaction Centers

V. Electrochemically-lnduced FTIR Difference SpectraVI. Vibrational Modes of the Quinones and Their Host SitesVII. RC-Associated CytochromesVIII. ConclusionsAcknowledgmentsReferences

xii

577578579580581583587589590590590

596596

598611612

615618621621

627–647

627

628628631632634635642643643644

649–66329 Bacterial Reaction Centers with Modified Tetrapyrrole ChromophoresHugo Scheer and Gerhard Hartwich

SummaryI. IntroductionII. Selectivity of the ExchangeIII. Static Spectroscopy of Reaction Centers with Modified PigmentsIV. StabilizationV. Time-Resolved SpectroscopyVI. Open Problems and OutlookAppendix: Updated Procedure for Pigment ExchangeAcknowledgmentsReferences

30 The Reaction Center from Green Sulfur BacteriaUte Feiler and Günter Hauska

SummaryI. IntroductionII. Composition of the Reaction CenterIII. Electron Transfer Within the Reaction CenterIV. Genes Encoding Reaction Center ProteinsV. Comparison with Other Reaction CentersVI. ConclusionsAcknowledgmentsReferences

31 The Antenna-Reaction Center Complex of HeliobacteriaJan Amesz

SummaryI. IntroductionII. Pigments and Spectral PropertiesIII. The Primary Electron Donor and the Antenna-Reaction Center ComplexIV. The Primary Charge SeparationV. Transfer and Trapping of Excitation EnergyVI. Secondary Electron TransportVII. Concluding RemarksReferences

32 Biochemical and Spectroscopic Properties of the Reaction Center of the GreenFilamentous Bacterium, Chloroflexus aurantiacus

Reiner Feick, Judith A. Shiozawa and Angelika Ertlmaier

SummaryI. IntroductionII. Biochemical Composition of the Chloroflexus aurantiacus Reaction CenterIII. Structure-Function Relationships of the RC ComplexIV. The Primary PhotochemistryV. Summary and ConclusionsAcknowledgmentsReferences

xiii

649650650655658658659659660660

665–685

666666667670675678681681682

687–697

687688688689691692693694695

699–708

699700700702704706706706

Part VI: Cyclic Electron Transfer Components and Energy Coupling Reactions

33 Cytochrome BiogenesisRobert G. Kranz and Diana L. Beckman

SummaryI. Introduction: Topological and Biosynthetic Distinctions Among CytochromesII. Transport of Apocytochromes to the Appropriate Subcellular LocationsIII. Components Required Specifically for Cytochrome c BiogenesisIV. Synthesis of c-Type Cytochromes in Other Bacteria and in Eukaryotes:

Analogous ComponentsV. Future DirectionsAcknowledgmentsReferences

34 Cytochromes, Iron-Sulfur, and Copper Proteins Mediating Electron Transferfrom the Cyt Complex to Photosynthetic Reaction Center Complexes

T. E. Meyer and Timothy J. Donohue725–745

SummaryI. IntroductionII. What Proteins Participate in Light-Dependent Reaction Center Reduction?III. How Do Electron Donors Interact with Membrane-Bound Redox Complexes?IV. What Insights Has Genetics Provided About Electron Donors to Reaction Center

Complexes?V. Future PerspectivesAcknowledgmentsReferences

726726730734

736740741741

35 Mutational Studies of the Cytochrome ComplexesKevin A. Gray and Fevzi Daldal

747–774

SummaryI. Cytochrome ComplexII. Mutational ApproachesIII. Conclusions and PerspectivesAcknowledgmentsReferences

747748759767768769

36 Reaction Center Associated Cytochromes 775–805Wolfgang Nitschke and Stella M. Dracheva

SummaryI. IntroductionII. A Brief History of Reaction Center Associated CytochromesIII. Tetraheme Cytochrome SubunitsIV. Nature of RC Associated Cytochromes in Photosynthetic EubacteriaV. Some Considerations with Respect to EvolutionAcknowledgmentsReferences

776776777782797799800800

xiv

709–723

709710711712

717721721721

37 The Proton-Translocating ATP Synthase-ATPase Complex 807–830

807808809815824825825

Zippora Gromet-Elhanan

SummaryI. IntroductionII. The ComplexIII. TheIV. Mechanism of Action of the ATP SynthaseAcknowledgmentsReferences

38 Proton-Translocating Transhydrogenase and NADH Dehydrogenase inAnoxygenic Photosynthetic Bacteria 831–845

J. Baz Jackson

SummaryI. IntroductionII. The Structure of TranshydrogenaseIII. Bioenergetics and Kinetics of TranshydrogenaseIV. Structure of NADH DehydrogenaseV. Integration Of NADH Dehydrogenase and Transhydrogenase in MetabolismVI. Concluding RemarksReferences

831832833835837838841841

Part VII: Metabolic Processes

39 Sulfur Compounds as Photosynthetic Electron Donors 847–870Daniel C. Brune

SummaryI. IntroductionII. Types of Anoxygenic Phototrophs and Their Sulfur-Oxidizing CapabilitiesIII. Electron Transport in Purple and Green Sulfur BacteriaIV. Pathways of Sulfide and Thiosulfate Oxidation and Catalytic EnzymesV. Considerations for Future ResearchAcknowledgmentsReferences

847848849854856864865865

40 Carbon Metabolism in Green Bacteria 871–883Reidun Sirevåg

SummaryI. IntroductionII. Mechanisms of Autotrophic Carbon Dioxide AssimilationIII. The Assimilation of Organic CarbonIV. Carbon Containing Reserve Materials and Endogenous MetabolismVI. Evolution of Metabolic Pathways Involved in Carbon Metabolism of Green BacteriaReferences

871872872876878879881

xv

41 The Biochemistry and Metabolic Regulation of Carbon Metabolism andFixation in Purple BacteriaF. Robert Tabita

885–914

SummaryI. IntroductionII. Central Pathways for Organic Carbon MetabolismIII. Calvin Reductive Pentose Phosphate PathwayIV. Alternative Assimilatory RoutesV. ConclusionsAcknowledgmentsReferences

885886886891906908908908

42 Microbiology of Nitrogen Fixation by Anoxygenic Photosynthetic BacteriaMichael T. Madigan

915–928

SummaryI. BackgroundII. Nitrogen Fixation by Purple and Green BacteriaIII. Phototrophic Rhizobia and Other Bacteriochlorophyll a-Containing SpeciesIV. Ecological Aspects of Fixation by Anoxygenic Photosynthetic BacteriaV. Concluding RemarksAcknowledgmentsReferences

915916918923924925925925

43 The Biochemistry and Genetics of Nitrogen Fixation by PhotosyntheticBacteria 929–947

Paul W. Ludden and Gary P. Roberts

Summary 929930935943944

I. Background and Historical IntroductionII. Regulation of Nitrogenase by Reversible ADP-ribosylationAcknowledgmentsReferences

44 Aerobic and Anaerobic Electron Transport Chains in Anoxygenic PhototrophicBacteria 949–971

Davide Zannoni

949950951960964964

SummaryI. IntroductionII. Dark Aerobic Electron Transport ChainsIII. Dark Anaerobic Electron Transport ChainsAcknowledgmentsReferences

45 Storage Products in Purple and Green Sulfur Bacteria 973–990Jordi Mas and Hans Van Gemerden

SummaryI. General Characteristics of the Storage Inclusions of Phototrophic Sulfur BacteriaII. Environmental Conditions Leading to the Accumulation of Storage Compounds

973974979

xvi

III. Physiological Role of Storage CompoundsIV. Storage Compounds in Natural Populations of Phototrophic Sulfur BacteriaV. Physical Consequences of the Accumulation of Storage CompoundsVI. Concluding RemarksAcknowledgmentReferences

980983984987988988

46 Degradation of Aromatic Compounds by Nonsulfur Purple BacteriaJane Gibson and Caroline S. Harwood

991–1003

SummaryI. IntroductionII. PhysiologyIII. BiochemistryIII. Regulation and GeneticsV. EcologyVI. Comparative AspectsAcknowledgmentsReferences

47 Flagellate Motility, Behavioral Responses and Active Transport in PurpleNon-Sulfur Bacteria 1005–1028

Judith P. Armitage, David J. Kelly and R. Elizabeth Sockett

SummaryI. IntroductionII. Motility and BehaviorIII. Solute TransportIV. Future PerspectiveAcknowledgmentsReferences

1006100610071018102410251025

Part VIII: Genetics and Genetic Manipulations

48 Genetic Manipulation of Purple Photosynthetic BacteriaJoAnn C. Williams and Aileen K. W. Taguchi

SummaryI. IntroductionII. Genetic ManipulationIII. Gene MappingIV. Gene Cloning and SequencingV. MutagenesisVI. Gene ExpressionVII. ConclusionsAcknowledgmentsReferences

1029–1065

1030103010301033103510431048105110511051

xvii

991992992993999

1001100110011002

49 Physical Mapping of Rhodobacter capsulatus: Cosmid Encyclopedia andHigh Resolution Genetic Map 1067–1081

Michael Fonstein and Robert Haselkorn

Summary 1067I. Introduction 1068II. Low Resolution Physical Mapping of the Genome of Rhodobacter capsulatus 1068III. High Resolution Physical Mapping 1075IV. Comparison with the Existing Genetic Map 1075V. Comparison of the Chromosomal Maps of Different Rhodobacter Strains 1075VI. Possible Applications of the Minimal Cosmid Set of Rhodobacter capsulatus SB1003 1078Acknowledgment 1078Note Added in Proof 1079References 1079

50 Structure and Sequence of the Photosynthesis Gene ClusterMarie Alberti, Donald H. Burke and John E. Hearst

SummaryI. IntroductionII. Biosynthetic PathwaysIII. The Genetic MapIV. Functional Assignments of the Open Reading Frames (ORFs) in the SequenceV. Potential Regulatory SequencesVI. ConclusionAcknowledgmentsReferences

1083–1106

108310841084108810901096110111021103

51 Genetic Analysis of Fixation GenesJanet Lee Gibson

SummaryI. IntroductionII. cbb GenesIII. Regulation of cbb Gene ExpressionIV. Mutational AnalysisV. Transcriptional Regulatory GenesVI. Expression of cbb Genes in Heterologous SystemsVII. ConclusionsAcknowledgmentsReferences

1107–1124

1108110811091113111511161119112111211122

52 Genetic Analysis and Regulation of Bacteriochlorophyll Biosynthesis 1125–1134

SummaryI. IntroductionII. Genetics of Protoporphyrin BiosynthesisIII. Regulation of BChl BiosynthesisIV. ConclusionsReferences

112511261126112811311132

xviii

Alan J. Biel

53 Genetic Analysis and Regulation of Carotenoid Biosynthesis:Structure and Function of the crt Genes and Gene Products

Gregory A. Armstrong1135–1157

SummaryI. IntroductionII. Early Developments in the Genetics of Carotenoid BiosynthesisIII. Mapping, Cloning and Sequencing of Carotenoid Biosynthesis GenesIV. Regulation of Carotenoid BiosynthesisV. Functional and Structural Conservation of the crt Gene ProductsVI. Perspectives for the FutureAcknowledgmentsReferences

54 A Foundation for the Genetic Analysis of Green Sulfur, Green Filamentousand Heliobacteria

Judith A. Shiozawa1159–1173

SummaryI. Some Relevant Physiological and Biochemical CharacteristicsII. The GenomeIII. Genetic ManipulationIV. Concluding RemarksAcknowledgmentsReferences

1159116011611170117011711171

Part IX: Regulation of Gene Expression

55 Regulation of Hydrogenase Gene ExpressionPaulette M. Vignais, Bertrand Toussaint and Annette Colbeau

1175–1190

SummaryI. IntroductionII. Hydrogenases of Photosynthetic Bacteria Belong to the Class of [NiFe]HydrogenasesIII. Regulation of Hydrogenase GenesIV. Conclusions and PerspectivesAcknowledgmentsReferences

1175117611781180118511861186

56 Regulation of Nitrogen Fixation GenesRobert G. Kranz and Paul J. Cullen

1191–1208

SummaryI. Introduction: Nitrogen Fixation (nif) Genes; Transcriptional Control by

Fixed Nitrogen and Oxygen

1191

11921193119512011204120412051205

II. General Models Describing nif Regulatory MechanismsIII. Regulatory Components Related to Other Bacterial ProteinsIV. Regulatory Components Unique to Anoxygenic Phototrophs (Or Are They)?V. The Alternative Nitrogen Fixing Systems: Aspects Concerning Gene RegulationVI. Future Studies and PerspectivesAcknowledgmentsReferences

xix

113611361137

1148

11371143

115311541154

57 Organization of Photosynthesis Gene TranscriptsJ. Thomas Beatty

1209–1219

SummaryI. IntroductionII. Transcripts of Rb. capsulatus Photosynthesis GenesIII. Transcripts of Rb. sphaeroides Photosynthesis GenesIV. Transcripts of Rhodospirillum rubrum Photosynthesis GenesV. Transcripts of Rhodopseudomonas viridis Photosynthesis GenesVI. Transcripts of Rubrivivax gelantinosus Photosynthesis GenesVII. Transcripts of Chloroflexus aurantiacus Photosynthesis GenesVIII. Prospects for the Future and Concluding RemarksAcknowledgmentsReferences

12101210121112141215121512151216121612171217

58 Regulation of Photosynthesis Gene Expression 1221–1234

SummaryI. IntroductionII. The Photosynthesis Gene ClusterIII. cis-Acting Regulatory SitesIV. trans-Acting Regulatory CircuitsV. Concluding remarksAcknowledgmentsReferences

12211221122212231227123112311231

59 Post-Transcriptional Control of Photosynthesis Gene Expression 1235–1244

SummaryI. IntroductionII. Control of Photosynthesis Gene Expression on the Level of mRNA StabilityIII. 23S rRNA Processing in RhodobacterIV. Evidence for Translational or Post-Translational Regulation of Photosynthesis

Gene ExpressionV. Concluding RemarksAcknowledgmentsReferences

1235123612361240

1241124212421242

Part X: Applications

60 Polyesters and Photosynthetic Bacteria: From Lipid Cellular Inclusions toMicrobial Thermoplastics 1245–1256

R. Clinton Fuller

Gabriele Klug

Carl E. Bauer

12451246124612481248

SummaryI. IntroductionII. PHAs as Prokaryotic InclusionsIII. Occurrence of PHAs in Anoxygenic Phototrophic BacteriaIV. Biosynthesis of PHAs in Rhodospirillum rubrum

xx

V. Regulation of PHA MetabolismVI. Polymer Production and Material PropertiesVII. Structure and Function of PHA InclusionsAcknowledgmentsReferences

12481250125212551255

61 Imaging Spectroscopy and Combinatorial Mutagenesis of theReaction Center and Light Harvesting II Antenna 1257–1268

Ellen R. Goldman and Douglas C. Youvan

Summary 12571258125812611262126612671267

I. IntroductionII. The Role of Mutagenesis in Photosynthesis ResearchIII. Massively Parallel Screening of MutantsIV. Combinatorial Cassette MutantsV. Conclusions and ProspectusAcknowledgmentsReferences

62 Waste Remediation and Treatment Using Anoxygenic PhototrophicBacteria

Michiharu Kobayashi and Michihiko Kobayashi1269–1282

1269126912701271127212721282

SummaryI. Distribution and Interrelationship with Other OrganismsII. Growth Acceleration by SymbiosisIII. Ecological Variation of Anoxygenic Phototrophic Bacteria in Organic SewageIV. Purification of Waste Water by Anoxygenic Phototrophic BacteriaV. The Use of ByproductsReferences

Index 1283

xxi

Preface

The editors are proud to present AnoxygenicPhotosynthetic Bacteria to students and researchersin the field of photosynthesis. We feel that this bookwill be the definitive volume on non-oxygen evolvingphotosynthetic bacteria for years to come, as it isliterally loaded with the most recent informationavailable in this field. Contributors were given thefreedom to develop topics in depth, and althoughthis has lead to a lengthy volume, readers can beassured that nothing of significance in the field ofanoxygenic photosynthetic bacteria has beenneglected.

We have organized the book along ten majorthemes: (1) Taxonomy, physiology and ecology, (2)Molecular structure of pigments and cofactors,(3)Membrane and cell wall structure, (4) Antennastructure and function, (5) Reaction center structureand electron/proton pathways, (6) Cyclic electrontransfer, (7) Metabolic processes, (8) Genetics, (9),Regulation of gene expression, and (10) Applications.For each theme, several chapters, written by leadingexperts in the field, combine to paint a detailedpicture of the current state of affairs of research inthat area. The editors have also tried to provideample cross-references between chapters to helpguide the reader to all of the coverage on a particulartopic.

The last time a comprehensive volume onanoxygenic photosynthetic prokaryotes was pub-lished was in 1978. This was the landmark volumeThe Photosynthetic Bacteria, edited by R. K. Claytonand W. R. Sistrom, and published by Plenum Press inNew York. That book brought together in one placethe state of current knowledge on the ecology,physiology, taxonomy, ultrastructure, biochemistry,biophysics and genetics of this diverse group ofbacteria. As a testament to its value as a referencebook, every copy of The Photosynthetic Bacteriathat any of the three editors of the present volumehave ever seen was tattered from years of almostconstant use and stained with coffee and cell extractsof various colors. The Photosynthetic Bacteria had a

tremendous impact on a generation of scientists inmany disciplines and will remain a classic for manyyears to come.

Thus it was with some trepidation that we undertookwhat was in essence the same task that faced Claytonand Sistrom 17 years earlier. The field has changeddramatically in that time in nearly every one of theareas mentioned above, perhaps most noticeably inthe area of genetics and related topics. A singlechapter on this subject sufficed in 1978, whereas 14of the 62 chapters in the present volume have ‘gene’or ‘genetic’ in the title and nearly every chaptermakes use of information obtained using mutants.

Another area of bacterial photosynthesis that hasseen tremendous progress in 17 years is structuralstudies. There is only one protein structure determinedusing X-ray diffraction that appears as a figure in the1978 volume, whereas dozens of structural figuresare included in this volume, including reactioncenters, antenna complexes, electron transfer proteinsand porins. An even more dramatic difference is thatthere is only a single, partial amino acid sequence inthe 1978 volume, while there are literally hundredsof sequences in this book. The emphasis in everyarea covered in this book, from taxonomy and ecologyall the way to biophysics has continually shiftedmore and more toward analysis at the molecularlevel.

This is the second volume in a series titled‘Advances in Photosynthesis,’ with Govindjee as theseries editor. The series provides an up to date accountof all aspects of the process of photosynthesis. Astatement of the scope of the series and a list ofprevious and upcoming titles can be found on theback cover.

We would like to dedicate this volume to HowardGest, who is unquestionably the father of modernresearch involving photosynthetic bacteria. He hasalso greatly influenced the careers of each of theeditors as either a collaborator, mentor or colleagueand to all of us as a friend.

Special thanks go to Larry Orr, without whose

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extraordinary talents and hard work this effort couldnever have come to fruition. Larry prepared all thecamera ready copy and is primarily responsible forthe layout and ‘look’ of the book.

Finally, we thank our wives, Liz, Nancy and Chrisand children, Larissa, Sam, Scott and Kevin for theirpatience and understanding of the time needed tocomplete this volume.

Robert E. BlankenshipMichael T. MadiganCarl E. Bauer

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Color Plates

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R. E. Blankenship, M. T. Madigan and C. E. Bauer (eds): Anoxygenic Photosynthetic Bacteria, pp. CP1–CP10.© 1995 Kluwer Academic Publishers. Printed in The Netherlands.

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