Front Cover

Secondary Endosymbioses

Copyright

Contents

Contributors

Preface

Chapter One: The Convoluted Evolution of Eukaryotes With Complex Plastids

1. Introduction

2. Diversity of Plastids

2.1. Primary Plastids

2.2. Complex Plastids

3. Plastid vs Host Data: Divergent View on the Tree of Eukaryotes

3.1. Plastid Evidence Support a Single Origin

3.2. Host Lineages Are Not Monophyletic

4. How Often Have Red Algal-Derived Plastids Spread?

4.1. The Chromalveolate Hypothesis

4.2. Plastid Loss and Plastid Dependency

4.3. Serial Eukaryote-to-Eukaryote Endosymbioses

5. Complex Algae and Genome Mosaicism

6. Concluding Remarks

Acknowledgements

References

Chapter Two: Let There Be Light: A Contemporary Primer on Primary Plastid Endosymbiosis

1. Introduction

2. The ABCs of Primary Endosymbiosis

3. The Polychromatic Puzzle Pieces of Plastid Primary Endosymbiosis

4. Paulinella chromatophora: A Primary Plastid Revival Tour

5. Lost in the Light: Unexpected Insights From Nonphotosynthetic Primary Plastids

6. Three Decades of Primary Plastid Genomics

7. Concluding Thoughts: Too Much Sequencing, Not Enough Experimenting?

Acknowledgements

References

Chapter Three: Secondary Plastids of Stramenopiles

1. Introduction

1.1. Diversity of Stramenopiles

2. Endosymbiotic Origins

2.1. Endosymbiotic Histories of Stramenopiles

2.2. Chimeric Origins of Stramenopile Plastids

3. Structure of Stramenopile Plastids

3.1. Stramenopile Plastid Organisation

3.2. Stramenopile Plastid Genomes

4. Biochemistry and Physiology

4.1. Plastid Biogenesis

4.2. Photosynthesis and Photoprotection

4.3. Central Carbon Metabolism

4.4. Primary and Secondary Metabolism Pathways

4.5. Nutrient Acquisition

4.6. Plastid-Mitochondria Interactions

5. Evolutionary Dynamics

5.1. Loss of Photosynthesis

5.2. Transient Symbioses and Kleptoplasty

5.3. Tertiary and Higher Endosymbioses

6. Concluding Remarks

Acknowledgements

References

Chapter Four: Plastid Complexity in Dinoflagellates: A Picture of Gains, Losses, Replacements and Revisions

1. Introduction

2. Unusual Features of Dinoflagellates That Might Impact Their Endosymbionts

3. The Peridinin Plastid

4. Plastid Reduction and Loss

5. Plastid Replacement

5.1. Complex Plastids Derived From Haptophytes

5.2. Complex Plastids Derived From Green Algae

5.3. Complex Plastid Endosymbionts Derived From Diatoms

5.4. Kleptoplasts

6. Evolution of Plastids in Dinoflagellates: A Case to Revise Contemporary Notions

6.1. Scenario 1: A Common Plastid Was Gained Before the Divergence of Myzozoans

6.1.1. Rationale

6.1.2. Caveats

6.2. Scenario 2: Plastids Were Gained Independently After Divergence From the Common Myzozoan Ancestor

6.2.1. Rationale

6.2.2. Caveats

6.3. Scenario 3: A Common Plastid Was Present in the Myzozoan Common Ancestor, but the Dinoflagellate Peridinin Plastid R ...

6.3.1. Rationale

6.3.2. Caveats

7. Conclusion

Acknowledgements

References

Chapter Five: The Dark Side of the Chloroplast: Biogenesis, Metabolism and Membrane Biology of the Apicoplast

1. Introduction: Apicomplexan Parasites

2. Discovery of the Apicoplast

3. The 'Delayed Death' Phenomenon

4. The Evolution of the Apicoplast

5. Apicoplast Division and Segregation

6. Protein Targeting to the Apicoplast

7. Integrating Metabolism of the Apicoplast With That of the Parasite

7.1. Isoprenoid Synthesis

7.2. Fe-S Cluster Synthesis

7.3. Fatty Acid, Lipoic Acid and Phospholipid Synthesis

7.4. Haem Synthesis

8. Conclusions and Perspectives

Acknowledgements

References

Chapter Six: Chromerids and Their Plastids

1. Introduction

2. Morphology and Life Cycles of Chrompodellids

3. Chromerid Plastid Ultrastructure and Pigmentation

4. Divergent Plastid Genomes of Chromerid Algae

5. Nuclear and Mitochondrial Genomes of Chromerids

6. Roles of Chromerid Plastids in Cellular Metabolism

7. Ambiguity of Chromerid Plastid Sequence-Based Phylogenies

8. The Origin of Chromerid Plastids

Acknowledgements

References

Chapter Seven: Biology of Haptophytes: Complicated Cellular Processes Driving the Global Carbon Cycle

1. Introduction

2. Morphology of Haptophytes

2.1. Haptonema

2.2. Coccoliths

2.3. Organic Scales

2.4. Siliceous Scales

3. Life Cycle and Ecology of Haptophytes

4. Phylogeny and Classification of Haptophytes

5. Photosynthesis and Calcification of Haptophytes

5.1. General Features of the CO2-Concentrating Mechanism in Marine Phytoplankton

5.2. CCM as Excess Energy Dissipation System in Coccolithophores

5.3. Functional Link Between Calcification and Photosynthesis

5.4. Molecular Components Involved in Ion Transport

6. Initial Process of Photosynthetic Carbon Metabolism

6.1. Active Anaplerotic ß-Carboxylation

6.2. Metabolite Transport Across Four Chloroplast Membranes

7. Complex Fate of Fixed Carbon in Haptophytes

7.1. Unique Photosynthetic Products

7.2. ß-Glucans

7.3. Alkenones

7.4. Acid Polysaccharides

7.5. Mannitol

7.6. Dimethylsulphoniopropionate

8. Carbon Partitioning into Alkenones, β-Glucans, and Other Compounds in E. huxleyi

9. Physiological Differences Between Diatoms and Coccolithophores

10. Concluding Remarks

Acknowledgements

References

Chapter Eight: Cryptomonads: A Model Organism Sheds Light on the Evolutionary History of Genome Reorganization in Seconda ...

1. Introduction: General Characteristics of Cryptomonad Protists

2. Secondary Organisms: Cryptomonads

2.1. Challenges for Cryptomonad Classification

2.2. The Secondary Plastid of Cryptomonads

2.3. Insight Into Plastid Evolution in Secondary Endosymbiosis-Various States of Cryptomonad Plastids

2.4. The Phylogenetic Position of Cryptomonads in the Eukaryotic Tree of Life

3. Nucleomorph Genomics: A Model for Investigation of Genome Reorganization Between Eukaryotes

3.1. Reductive Genome Evolution of Endosymbionts

3.2. The Discovery of Nucleomorphs

3.3. The Three Chromosomes and Genome Size Diversity

3.4. Compaction of Nucleomorph Genomes

3.5. Are Nucleomorphs in an Intermediate State or End-Point of Reductive Genome Evolution?

3.5.1. Limited Number of Plastid-Related Genes in Nucleomorph Genomes

3.5.2. Lineage Specific and Convergent Loss of Genes

3.5.3. Nucleomorphs Are "Frozen"

3.6. Genome Comparisons Between Prokaryotic and Eukaryotic Reduced Genomes

3.6.1. Comparison Between Plastid and Mitochondrial Genome Evolution

3.6.2. The Hypothetical Proteins With No Similarity to Known Proteins

3.6.3. Genome Rearrangement Frequency

4. Concluding Remarks

Acknowledgements

References

Chapter Nine: Secondary Plastids of Euglenophytes

1. Introduction: What Are the Euglenophytes and Why to Care About Them

2. Origin of Euglenophyte Plastids: Early or Late, Green or Red?

3. Plastid Morphology: Display of Diversity

4. Plastid Genomes: Sped-Up Evolution and Introns Gone Haywire

5. Plastid Biogenesis and Housekeeping: How to Make It and How to Control It

6. Plastid Metabolism: A Factory With Redundant Production Lines

7. Secondary Osmotrophy and Plastid Bleaching: Plastids That Forgot How to Plastid

8. Conclusions

Acknowledgements

References

Chapter Ten: Chlorarachniophytes With Complex Secondary Plastids of Green Algal Origin

1. Introduction

2. Origin of Chlorarachniophytes

3. Taxonomy of Chlorarachniophytes

4. Phylogeny and Morphological Evolution in Chlorarachniophytes

5. Nucleomorph Genomes of Chlorarachniophytes

6. Convergent Evolution of Nucleomorph Genomes in Chlorarachniophytes and Cryptophytes

7. Plastid Genomes of Chlorarachniophytes

8. Protein Targeting Into Chlorarachniophyte Plastids

9. Evolutionary Mosaicism of Chlorarachniophyte Nuclear Genomes

References

Subject Index

Author Index

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