The Molecular Biology of Chloroplasts and Mitochondria …978-0-306-48204...25 Assembly and Function of the Chloroplast ATP Synthase 477–500 Heinrich Strotmann, Noun Shavit and Stefan

The Molecular Biology of Chloroplastsand Mitochondria in Chlamydomonas

Advances in Photosynthesis

VOLUME 7

Series Editor:GOVINDJEE

University of Illinois, Urbana, Illinois, U.S.A.

Consulting Editors:

Jan AMESZ, Leiden, The NetherlandsEva-Mari ARO, Turku, Finland

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

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

Advances in Photosynthesis is an ambitious book series seeking to provide acomprehensive and state-of-the-art account of photosynthesis research. Pho-tosynthesis is the process by which higher plants, algae and certain speciesof bacteria transform and store solar energy in the form of energy-rich organ-ic molecules. These compounds are in turn used as the energy source forall growth and reproduction in these organisms. As such, virtually all lifeon the planet ultimately depends on photosynthetic energy conversion. Thisseries of multiauthored books spans topics from physics to agronomy, fromfemtosecond reactions to season long production, from the photophysics ofreaction centers to the physiology of whole organisms, and from X-ray crys-tallography of proteins to the morphology of intact plants. The intent of thisseries of publications is to offer beginning researchers, graduate students,and even research specialists a comprehensive current picture of the remark-able advances across the full scope of photosynthesis research.

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

The Molecular Biology ofChloroplasts and

Mitochondriain Chlamydomonas

Edited by

J.-D. RochaixM. Goldschmidt-Clermont

Departments of Molecular Biology and Plant Biology,University of Geneva,Geneva, Switzerland

and

S. MerchantDepartment of Chemistry and Biochemistry

and Molecular Biology Institute,University of California-Los Angeles,

Los Angeles, U.S.A.

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

eBook ISBN: 0-306-48204-5Print ISBN: 0-7923-5174-6

©2004 Kluwer Academic PublishersNew York, Boston, Dordrecht, London, Moscow

Print ©1998 Kluwer Academic Publishers

All rights reserved

No part of this eBook may be reproduced or transmitted in any form or by any means, electronic,mechanical, recording, or otherwise, without written consent from the Publisher

Created in the United States of America

Visit Kluwer Online at: http://kluweronline.comand Kluwer's eBookstore at: http://ebooks.kluweronline.com

Dordrecht

This book is dedicated

to Paul Levine for his pioneering studies onthe genetics of photosynthesis in Chlamydomonas

and to the memory of Ruth Sager for her seminalcontributions to organellar genetics.

ContentsPreface xvii

Color Plates CP-1

1 Introduction to Chlamydomonas 1–11Elizabeth H. Harris

SummaryI.II.III.IV.V.VI.VII.

Why Chlamydomonas?CellArchitectureLife CycleLaboratory strains of Chlamydomonas reinhardtiiGenetic AnalysisMolecular BiologyResources

AcknowledgmentReferences

1133467788

2 Perspectives on Early Research on Photosynthesis inChlamydomonas 13–23

Robert K. Togasaki and Stefan J. SurzyckiSummaryI.II.III.IV.V.VI.

General BackgroundThe Levine Laboratory in the Early 1960sEstablishment of Chlamydomonas reinhardtii as a Legitimate Model OrganismDevelopment of New TechniquesEmergence of New Research TargetsOld Experiments Becoming Reality


131314151819212122

3 Organization of the Nuclear Genome 25–40Carolyn D. Silflow

SummaryI.II.III.IV.IV.VI.

Introduction and ScopeGeneral Characteristics of the Nuclear GenomeOrganization of the GenomeCharacteristics of Chlamydomonas Genes Transcribed by Polymerase IIPhysical Mapping of the Chlamydomonas GenomeFuture Prospects

AcknowledgmentsReferences

252626263036373737

4 Nuclear Transformation: Technology and Applications 41–61Karen L. Kindle

SummaryI.II.

IntroductionA Brief History of C. reinhardtii Nuclear Transformation

424242

III.IV.V.VI.VII.VIII.IX.X.XI.

Selectable MarkersMethods for Introducing DNA into the Nuclear Genome of C. reinhardtiiReporters and PromotersCharacteristics of Transformation EventsInsertional Mutagenesis and Gene TaggingGene Isolation by Complementation of a Mutant PhenotypeHomologous Recombination and Gene TargetingThe Use of Nuclear Transformation to Study Promoter FunctionConclusion


4345464851545456585858

5 Modes and Tempos of Mitochondrial and Chloroplast Genome Evolution inChlamydomonas: A Comparative Analysis

Aurora M. Nedelcu and Robert W. LeeSummaryI.II.III.

IV.V.

VI.

VII.

VIII.

IntroductionPhylogenetic Position of ChlamydomonasMonophyletic versus Polyphyletic Origin of Mitochondria and Plastids:The Chlamydomonas CaseEvolution of Mitochondrial and Chloroplast Genome Size in ChlamydomonasEvolution of Mitochondrial and Chloroplast Genome Organization inChlamydomonasEvolution of Mitochondril and Chloroplast Gene Structure and Organizationin ChlamydomonasEvolution of Mitochondrial and Chloroplast DNA Sequences inChlamydomonasConclusions


636464

6569

79

82

85878787

6 Uniparental Inheritance of Chloroplast Genomes 93–113E. Virginia Armbrust

SummaryI.II.III.IV.V.VI.VI.

IntroductionHistorical Overview of the Uniparental Inheritance of Chloroplast DNAMating-Type Control of Life Cycle EventsProtection of Plus Chloroplast DNAZygote Specific Elimination of Minus Chloroplast DNARegulation of Chloroplast DNA InheritanceEvolution of the Uniparental Inheritance of Organelle Genomes


93949598

101103108110110110

7 Replication, Recombination, and Repair in the ChloroplastGenetic System of Chlamydomonas 115–138

Barbara B. SearsSummaryI.II.III.IV.

IntroductionReplicationRecombinationRepair

115116116123130

viii

63–91

V. Perspectives and ConclusionsAcknowledgmentsReferences

133133133

8 Chloroplast Transformation and Reverse Genetics 139–149Michel Goldschmidt-Clermont

SummaryI.II.III.IV.V.VI.

IntroductionDelivery of DNA to the ChloroplastSelectable Markers and ReportersFate of Transforming DNAReverse GeneticsConclusion and Perspective


139140140140142147147148148

9 Chloroplast RNA Stability 151–163Jörg Nickelsen

SummaryI.II.III.IV.V.

IntroductionCell Cycle Dependent Regulation of Chloroplast RNA StabilityNuclear Mutants Affected in Chloroplast RNA StabilityTowards a Molecular Model of Chloroplast RNA Stabilization/DegradationConclusions and Perspectives


151152152154154161161161

10 Chloroplast RNA Synthesis and Processing 165–183David B. Stern and Robert G. Drager

SummaryI.II.

Transcription of Chloroplast GenesProcessing of Chloroplast mRNAs


165166171177177

11 RNA Splicing in the Chloroplast 183–195David L. Herrin, Tai-Chih Kuo and Michel Goldschmidt-Clermont

SummaryI.II.III.IV.

IntroductionGroup I IntronsGroup II Introns and Trans-SplicingPerspective


183184184190193193193

12 Regulation of Chloroplast Translation 197–217Charles R. Hauser, Nicholas W. Gillham and John E. Boynton

SummaryI.II.

IntroductionThe Role of Physiological and Environmental Factors in Translational Control

197198200

ix

III.

IV.V.

VI.VII.VIII.IX.

Current Biochemical and Genetic Approaches to Dissect Mechanisms ofTranslational RegulationCis-acting Sequences Involved in Translation InitiationTranslational Regulation Involves Interactions between cis-ActingSequences and trans-Acting FactorsRibosomes, Membranes and TethersTranslational Regulation of Complex AssemblyHow are the Regulatory Proteins Regulated?Is there Hierarchical Control of Chloroplast mRNA Translation?


202203

205209211212213214214

13 Chloroplast Protein Translocation 219–231Mireille C. Perret, Karen K. Bernd and Bruce D. Kohorn


IntroductionChloroplast ImportSorting of Proteins Within the ChloroplastThylakoid TranslocationMutations Affecting TranslocationPerspectives


219220220222223226228229229

14 Supramolecular Organization of the Chloroplast andof the Thylakoid Membranes 233–254

Jacqueline Olive and Francis-André WollmanSummaryI.II.III.IV.V.VI.

IntroductionCell and Chloroplast MorphologyUltrastructural Organization of Thylakoid MembranesDynamic Aspects of Thylakoid Membrane OrganizationBiogenesisConclusion


234234235239246248250251251

15 Assembly of Photosystem II 255–285Jeanne Marie Erickson

SummaryI.II.III.IV.

V.

IntroductionDevelopmental Biogenesis of Photosystem IIAssembly of Photosystem II ComplexesAssembly of the Extrinsic Membrane Polypeptides of the PS IIOxygen-Evolving ComplexAssembly of Manganese: The Catalytic Center of the Oxygen-EvolvingComplex


255256257260

270

273277277

x

16 Functional Analysis of Photosystem II 287–322Stuart V. Ruffle and Richard T. Sayre

SummaryI. IntroductionII. The Photosystem II ComplexIII. The Chloroplast DNA Encoded Small Polypeptides of Photosystem IIIV. The Nucleus Encoded Polypeptides of the Photosystem II ComplexV. PerspectivesAcknowledgmentsReferences

287288289308311315315315

17 Structure and Function of Photosystem I 323–348Andrew N. Webber and Scott E. Bingham


IntroductionStructure of Photosystem INature and Function of Electron Transfer CofactorsAntenna Structure and FunctionFunction of Photosystem I SubunitsBiogenesis of Photosystem I


324324325328332333341344344

18 Reexamining the Validity of the Z-Scheme: Is Photosystem IRequired for Oxygenic Photosynthesis in Chlamydomonas? 349–362

Kevin Redding and Gilles PeltierSummaryI. The Z-Scheme of Oxygenic Photosynthesis and Alternative SchemesII. Electron Transport in the Absence of PS IIIII. Photosynthesis in the Absence of PS IIV. Putative Electron Transport Pathways Outside of the Z-SchemeV. Thermodynamic ConsiderationsVI. Evolutionary ConsiderationsVII. ConclusionsAcknowledgmentsReferences

349350351354357358358359359360

19 Assembly of Light-Harvesting Systems 363–376J. Kenneth Hoober, Hyoungshin Park, Gregory R. Wolfe,Yutaka Komine and Laura L. Eggink

SummaryI.II.III.IV.

Thylakoid Biogenesis in ChlamydomonasAnalysis of LHCII AssemblySite of Assembly of LHCII During Initial GreeningConclusions


363364366368371373373

xi

20 Pigment Biosynthesis: Chlorophylls, Heme, and Carotenoids 377–414Michael P. Timko

SummaryI.II.III.IV.V.VI.VII.VIII.

IntroductionTetrapyrroles and Their Derivatives—An OverviewFormation of ALAThe Pathway from ALA to Protoporphyrin IXThe Magnesium Branch—Chlorophyll FormationThe Iron Branch—Formation of HemeLight and Metabolic Regulation of Chlorophyll FormationCarotenoids


378378378379383388397398401406406

21 Glycerolipids: Composition, Biosynthesis and Function inChlamydomonas 415–431

Antoine TrémolièresSummaryIntroductionII.III.IV.V.VI.

Glycerolipid and Fatty Acid Composition of ChlamydomonasLipid Metabolic Pathway in Chlamydomonas spp.In vivo Modifications of Lipid Composition in ChlamydomonasMutants Affected in Lipid CompositionInvolvement of Lipids in the Functional Organization and the Biogenesisof the Photosynthetic Apparatus


415416417422425426

428429429

22 In vivo Measurements of Photosynthetic Activity: Methods 433–449Pierre Joliot, Daniel Béal and René Delosme

SummaryI.II.III.IV.V.VI.VII.VIII.

IntroductionKinetic Analysis of the Fluorescence YieldFluorescence Emission Spectra at Low TemperatureDelayed Fluorescence MeasurementsOxygen MeasurementsAbsorption SpectroscopyPhotoacoustic MeasurementsConclusion and Perspectives

Appendix A: Estimation of the Signal-to-Noise Ratio in FluorescenceMeasurements

Appendix B: Flash SpectrophotometerAcknowledgmentReferences

433434436439439439440443445

446446448448

23 New Digital Imaging Instrument For Measuring Fluorescence andDelayed Luminescence 451–458

Pierre Bennoun and Daniel BéalSummaryI.II.

IntroductionSetup for Fluorescence and Delayed Luminescence Video Imaging

451452452

xii

III.IV.

V.

Digital Fluorescence Imaging Related to Photosynthetic Electron TransferDigital Fluorescence Imaging Related to the Permanent ThylakoidElectrochemical GradientDigital Delayed Luminescence Imaging Related to Light-Induced andPermanent Thylakoid Electrochemical Gradient


452

453

455457457

24 The Structure, Function and Biogenesis Of CytochromeComplexes 459–476

Francis-André WollmanSummaryI.II.III.IV.V.VI.

General TraitsBiochemical and Structural StudiesFunctional StudiesThe pet GenesBiogenesis and AssemblyConcluding Remarks


460460461463466467472474474

25 Assembly and Function of the Chloroplast ATP Synthase 477–500Heinrich Strotmann, Noun Shavit and Stefan Leu


IntroductionStructure ofMolecular Genetics ofMechanism ofRegulation ofConclusions

References

477478478482487492494494

26 Molecular Aspects of Components of the Ferredoxin/ThioredoxinSystems 501–514

Jean-Pierre Jacquot, Mariana Stein, Stéphane Lemaire,Paulette Decottignies, Pierre Le Maréchal and Jean-MarkLancelin

SummaryI.II.III.IV.

IntroductionFerredoxin Dependent SystemsThioredoxin Dependent SystemsConclusion


501502505508511512512

27 Genetic Engineering of Rubisco 515–527Robert J. Spreitzer

SummaryI.II.

IntroductionChloroplast Genetic Screening and Selection

515516518

xiii

III. Directed Mutagenesis and Chloroplast TransformationIV. Rubisco Nuclear MutantsV. Conclusion and PerspectiveAcknowledgmentsReferences

521523524524524

28 Acquisition. Acclimation to Changing Carbon Availability 529–547Martin H. Spalding

SummaryI.II.III.

IntroductionPhotosynthetic Carbon AssimilationInduction of the CCM and Related Adaptations to Limiting


529530530539544544

29 Regulation of Starch Biosynthesis 549–567Steven G. Ball


Starch: Structure and FunctionThe Starch PathwayThe Genetics of Starch BiosynthesisA Model Explaining the Biogenesis of the Plant Starch GranuleFuture Prospects


549550554559563564565565

30 State Transition and Photoinhibition 569–596Nir Keren and Itzhak Ohad

SummaryI.II.III.IV.

IntroductionState Transition: The PhenomenonLight Stress: Photoinhibition and RecoveryConcluding Remarks and Perspectives


569570574578590590590

31 Synthesis of Metalloproteins Involved in Photosynthesis:Plastocyanin and Cytochromes 597–611

Sabeeha MerchantSummaryI.II.III.IV.

IntroductionCopper-Responsive Synthesis of Plastocyanin and CytochromeGenetic Analysis of Chloroplast Metalloprotein AssemblyConclusions


598598600605608608609

32 Responses to Deficiencies in Macronutrients 613–635John P. Davies and Arthur R. Grossman

SummaryI. Introduction

614614

xiv

II. Nutrients in the EnvironmentIII. Specific ResponsesIV. Common ResponsesV. Model Integrating the Responses to Nutrient DeprivationVI. Regulation of the Responses to Nutrient DeprivationVII. Identification of Mutants Deficient in the Acclimation to Nutrient DeprivationAcknowledgmentsReferences

615617622626627629630630

33 Nitrogen Assimilation and its Regulation 637–659Emilio Fernández, Aurora Galván and Alberto Quesada


Introduction. Pathways for Nitrogen Assimilation in ChlamydomonasAssimilation of AmmoniumAssimilation of Amino AcidsAssimilation of PurinesAssimilation of Nitrate and NitriteConcluding Remarks


638638639642643645654655655

34 Mitochondrial Genetics 661–674Claire Remacle and René F. Matagne


VII.

IntroductionMitochondrial GenomeMitochondria and the Electron Transport ChainMutations Affecting the Mitochondrial GenomeTransmission of Mitochondrial Genes in Meiotic ZygotesTransmission of Mitochondrial Genes in Vegetative Zygotes andMapping of Mitochondrial Mutations by Recombinational AnalysisMitochondrial Transformation


661662662664665668

669671672672

35 Chlororespiration, Sixteen Years Later 675–683Pierre Bennoun


IntroductionThe Thylakoid Electrochemical Gradient Present in the DarkReduction of Plastoquinone in the DarkOxidation of Plastoquinol in the DarkConclusion

Cautionary NoteAcknowledgmentsReferences

675676676678680680682682682

36 Perspectives 685–703Lauren J. Mets and Jean-David Rochaix

SummaryI.II.

IntroductionThe Niche of Chlamydomonas in Photosynthesis Research

685686687

xv

III. Forefront Problems in Photosynthesis and Organelle ResearchAcknowledgmentsReferences

696700700

Index 705

xvi

Preface

The Molecular Biology of Chloroplasts andMitochondria in Chlamydomonas is the seventhvolume to be published in the series Advances inPhotosynthesis of Kluwer Academic Publishers(Series Editor: Govindjee). Volume 1 dealt with TheMolecular Biology of Cyanobacteria; Volume 2 withAnoxygenic Photosynthetic Bacteria; Volume 3 withBiophysical Techniques in Photosynthesis; Volume 4with Photosynthesis and the Environment; andVolume 6 with Lipids in Photosynthesis: Structure,Function and Genetics.

The main goal of this book is to provide acomprehensive overview of current research withthe green alga Chlamydomonas on chloroplast andmitochondrial biogenesis and function, with specialemphasis on the assembly and structure-functionrelationships ofthe constituents ofthe photosyntheticapparatus. The editors have encouraged thecontributors of this volume to emphasize theparticular features of Chlamydomonas that makethis unicellular organism uniquely suited for study-ing photosynthesis and its multiple regulatorymechanisms operating under various environmentaland stress conditions. A second, but equally importantaim is to show that current research in photosyn-thesis is multidisciplinary and combines moleculargenetics, biochemical, biophysical and physiologicalapproaches. Although Chlamydomonas has alsoproven to be apowerful system forunderstanding thestructure, function and assembly of flagella, thistopic is not covered in the book.

Chlamydomonas research would not have reachedits present status without the pioneering studies ofthe late Ruth Sager and of Paul Levine. Organellargenetic analysis of this alga started over 40 years agowhen Ruth Sager discovered that during crossescertain traits were transmitted uniparentally to theprogeny from the mating-type plus parent, but notfrom the mating-type minus parent. These uniparentaltraits were shown later to be specified by thechloroplast genome. Sager also found that, in rarecases, the uniparental traits ofboth parents could beinherited and that the analysis of their segregationpattern during crosses could be used to construct agenetic map. The potential ofusing C. reinhardtii for

a genetic dissection of photosynthesis was firstrecognized by Paul Levine. Together with hiscoworkers, he initiated a long-range genetic approachwhich proved to be highly successful. It providedgenetic support for the linear Z scheme ofphotosynthesis and led to the identification of newcomponents of the photosynthetic electron transferchain such as the Rieske protein ofthe cytochromecomplex.

During the past 20 years, the powerful techniquesof molecular biology and genetics, and thedevelopment of methods for efficient nuclear andchloroplast transformation of C. reinhardtii havegreatly enhanced the potential of this organism as anexperimental system for studying chloroplastbiogenesis. This has led to impressive advances inour understanding of the regulation of chloroplastgene expression and it has provided important newinsights into the complex cooperative interplaybetween the chloroplast and nuclear compartmentsin the assembly of the photosynthetic apparatus. Atthe same time, the ability to manipulate the chloroplastgenome with surgical precision has opened the doorfor a detailed structure-function analysis ofphotosynthetic complexes in vitro, and thanks to therefinements and new developments in spectroscopicand fluorescence techniques, also in vivo. We feelstrongly that a book on these recent exciting advancesin research on photosynthesis in Chlamydomonas istimely and important.

The first part of the book provides a generalintroduction to Chlamydomonas (Chapter 1, Harris),a historical chapter on early research on photo-synthesis in this organism (Chapter 2, Togasaki andSurzycki) and chapters on nuclear genome organi-zation (Chapter 3, Silflow), nuclear transformation(Chapter 4, Kindle), mitochondrial and chloroplastgenome evolution (Chapter 5, Nedelcu and Lee),chloroplast uniparental inheritance (Chapter 6,Armbrust), chloroplast DNA metabolism (Chapter 7,Sears) and chloroplast transformation and reversegenetics (Chapter 8, Goldschmidt-Clermont). Thesecond part includes several chapters on chloroplastgene expression: RNA stability (Chapter 9,Nickelsen), RNA processing (Chapter 10, Stern and

xvii

Drager), splicing (Chapter 11, Herrin et al.) andtranslation (Chapter 12, Hauser et al.). Proteintargeting in the chloroplast is discussed in Chapter 13(Perret et al.). The third part includes articles on thebiosynthesis and function of thylakoid membranes(Chapter 14, Olive and Wollman), Photosystem II(Chapter 15, Erickson; Chapter 16, Ruffle and Sayre),Photosystem I (Chapter 17, Webber and Bingham;Chapter 18, Redding and Peltier), LHCII (Chapter19, Hoober et al.), pigments (Chapter 20, Timko),glycerolipids (Chapter 21, Trémolières), thecytochrome complex (Chapter 24, Wollman), theATP synthase (Chapter 25, Strotmann et al.),ferredoxin and thioredoxin (Chapter 26, Jacquot etal.) and of ribulose 1,5 bisphosphate carboxylase-oxygenase (Chapter 27, Spreitzer). In addition,Chapters 22 (Joliot et al.) and 23 (Bennoun and Beal)describe new and powerful techniques used formeasurements of photosynthetic activity in vivo.These techniques are particularly suited forChlamydomonas. The fourth part includes chapterson uptake (Chapter 28, Spalding) and starchbiosynthesis (Chapter 29, Ball). Several articles aredevoted to the responses of Chlamydomonas tovarious stress conditions, such as high light(Chapter 30, Keren and Ohad), copper deficiency(Chapter 31, Merchant) and macronutrient depri-vation (Chapter 32, Davies and Grossman). Nitrogenassimilation and its regulation is discussed inChapter 33 (Fernández et al.). Chapter 34 (Remacleand Matagne) describes mitochondrial genetics and

Chapter 35 (Bennoun) discusses the current modelsof chlororespiration. The last Chapter (36, Mets andRochaix) offers a perspective on research onphotosynthesis with Chlamydomonas.

We thank the authors for their invaluablecontributions which we hope will make this bookvery useful for researchers and students interested inphotosynthesis and organellar biology in Chlamy-domonas. The book is also intended for a wideaudience, but is specifically designed for advancedundergraduate and graduate students and researchersin the fields of biochemistry, molecular biology,physiology, biophysics, plant biology, phycology andbiotechnology. We also hope that this book willstimulate scientists outside the Chlamydomonasresearch community to use this organism for theirstudies.

We wish to express our gratitude to Larry Orr forhis patience with inexperienced editors, generoushelp and remarkable efficiency, to Govindjee for hiscontinued interest and for his many helpfulsuggestions, and to Nicolas Roggli and MichaelHippler for their help in designing the cover graphics.Finally, we hope that by showing the extraordinarypower and uniqueness of Chlamydomonas as aresearch tool in photosynthesis and by documentingthe fast pace of progress achieved in the past yearswith this unicellular organism, this book will helppromote Chlamydomonas as the ‘green yeast’ amongthe plant research community.

Jean-David RochaixMichel Goldschmidt-Clermont

Sabeeha Merchant

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J. -D. Rochaix, M. Goldschmidt-Clermont and S. Merchant (eds): The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas,pp. CP-1–CP-7. © 1998 Kluwer Academic Publishers. Printed in The Netherlands.

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The Molecular Biology of Chloroplasts and Mitochondria …978-0-306-48204...25 Assembly and Function of the Chloroplast ATP Synthase 477–500 Heinrich Strotmann, Noun Shavit and Stefan