Genome Evolution of Photosynthetic Bacteria

Series Editors

Preface

Contributors

Chapter One. A Time to Scatter Genes and a Time to Gather Them: Evolution of Photosynthesis Genes in Bacteria

Abstract

1 Introduction

2 Photosynthesis Genes of Cyanobacteria and Plants

3 Evolution of the Photosynthesis Gene Set

4 Photosynthesis and the Emergence of Life

Acknowledgements

References

Chapter Two. Molecular Markers for Photosynthetic Bacteria and Insights into the Origin and Spread of Photosynthesis

Abstract

1 Introduction

2 Molecular Signatures for Different Phyla of Photosynthetic Bacteria

3 Origin and Spread of Photosynthesis Based Upon Molecular Signatures in Key BChl Biosynthesis Proteins

Abbreviations

Acknowledgements

References

Chapter Three. Properties and Evolutionary Implications of the Heliobacterial Genome

Abstract

1 Introduction

2 Heliobacterial Photosynthesis

3 Heliobacteria as ‘Phototrophic Clostridia’

4 Thoughts on Heliobacteria and the Evolution of Photosynthesis

Acknowledgements

References

Chapter Four. Green Bacteria: Insights into Green Bacterial Evolution through Genomic Analyses

Abstract

1 Introduction

2 Sulfur Metabolism

3 Reverse TCA Cycle

4 Bacteriochlorophyll Biosynthesis in Green Bacteria

5 Chlorosome Structure and Assembly

6 Type-1 RCs

7 Evolution of Green Bacteria

8 Granick Hypothesis

9 Thoughts on Evolution of Photosynthesis

Abbreviations

Acknowledgements

References

Chapter Five. Comparison of Photosynthesis Gene Clusters Retrieved from Total Genome Sequences of Purple Bacteria

Abstract

1 Introduction

2 Retrieval of Photosynthesis Gene Sequences of Purple Bacteria From Genomic DNA Databases

3 Sequence Comparison of Photosynthetic Gene Products

4 Comparison of Gene Arrangements in PGCs of Purple Bacteria

5 Phylogenetic Analyses of Genes in PGCs and Horizontal Gene Transfer

6 Conclusion and Perspectives

Acknowledgements

References

Chapter Six. The Living Genome of a Purple Nonsulfur Photosynthetic Bacterium: Overview of the Rhodobacter sphaeroides Transcriptome Landscapes

Abstract

1 Transcriptomics as a Tool to Assess Metabolic Changes and Understand Regulatory Networks

2 Metabolic Versatility Requires Transcriptome Flexibility: R. sphaeroides Transcriptome Landscapes of Diverse Growth Modes

3 The Effects of O2 and Light: A Transcriptome Perspective

4 The Key O2- and Light-Responsive Regulons

5 Conclusions and Perspectives

Acknowledgements

References

Chapter Seven. The Evolution of the Purple Photosynthetic Bacterial Light-Harvesting System

Abstract

1 Introduction

2 Method

3 Results of the Phylogenetic Analysis

4 Discussion

Acknowledgements

References

Chapter Eight. Role and Evolution of Endogenous Plasmids in Photosynthetic Bacteria

Abstract

1 Introduction

2 Occurrence and Distribution of Endogenous Plasmids in the Anaerobic Anoyxgenic Phototrophic Bacteria

3 Functional Roles of Endogenous Plasmids in Phototrophic Bacteria

4 Evolution of Endogenous Plasmids

5 Conclusions and Perspectives

Acknowledgements

References

Chapter Nine. Evolution of Bacteriophytochromes in Photosynthetic Bacteria

Abstract

1 Introduction

2 Variation in the Bacteriophytochrome Output Domains

3 Distribution of the Different Types of Bacteriophytochromes

4 Bacteriophytochromes in Rhodopseudomonas palustris

5 Future Perspectives

Acknowledgements

References

Chapter Ten. Iron homeostasis in the Rhodobacter genus

Abstract

1 Introduction

2 Ferrous Iron Uptake

3 Ferric Iron Uptake

4 Iron ABC Transporters

5 Heme Iron Usage

6 Managing Iron Toxicity

7 Iron Homeostasis Regulators

8 Conclusion

References

Chapter Eleven. Genes Associated with the Peculiar Phenotypes of the Aerobic Anoxygenic Phototrophs

Abstract

1 Introduction

2 Abundance and Diversity Through Culturing and Sequencing

3 Phylogeny and Speculations on Evolution

4 Nutritional Requirements, Carbon Metabolism and the Associated Metabolic Pathways

5 Photosynthetic Pigments and their Association with the Photosynthetic Operon

6 Photosynthetic Apparatus Organisation and Genes

7 Unsolved Mysteries and Concluding Remarks

Acknowledgements

References

Chapter Twelve. Evolutionary Divergence of Marine Aerobic Anoxygenic Phototrophic Bacteria as Seen from Diverse Organisations of Their Photosynthesis Gene Clusters

Abstract

1 Introduction

2 Diverse Structures of PGCs

3 Expression of PGC

4 Evolution of AAPB

5 Summary and Future Perspectives

Acknowledgement

References

Chapter Thirteen. Regressive Evolution of Photosynthesis in the Roseobacter Clade

Abstract

1 Introduction

2 Photosynthesis Gene Cluster

3 The Mode of Evolution

4 Horizontal Gene Transfer

5 When did Roseobacters Evolve?

6 Evolutionary Scenario

7 Conclusions

Acknowledgements

References

Color Plates

Index