Plastids: Methods and Protocols

Preface...

Table of Contents...

Contributing Authors...

Part I Plastid Evolution, Plasticity, Structural, and Functional Diversity 

1.Primary Endosymbioses: Emergence of the Primary Chloroplast and the Chromatophore, Two Independent Events 

Eric Maréchal

2.Complex Endosymbioses I: From Primary to Complex Plastids, Multiple Independent Events 

Zoltán Füssy and Miroslav Oborník

3.Complex Endosymbiosis II: The Non-Photosynthetic Plastid of Apicomplexa Parasites (The Apicoplast) and Its Integrated Metabolism 

Cyrille Y. Botté and Yoshiki Yamaryo- Botté

4.Diversity and Plasticity of Plastids in Land Plants 

Katalin Solymosi, Johanna Lethin, and Henrik Aronsson

5.The Main Functions of Plastids 

Norbert Rolland, Imen Bouchnak, Lucas Moyet, Daniel Sali, and Marcel Kuntz

6.Plastid Transient and Stable Interactions with Other Cell Compartments 

Stefanie J. Mueller-Schuessele and Morane Michaud

Part II Laboratory Protocols

7.Imaging Plastids in 2D and 3D: Confocal and Electron Microscopy 

Serena Flori, Pierre-Henri Jouneau, Benoit Gallet, Leandro F. Estrozi, Christine Moriscot, Guy Schoehn, Giovanni Finazzi, and Denis Falconet

8.Purification of Chloroplasts and Chloroplast Subfractions: Envelope, Thylakoids, and Stroma - From Spinach, Pea, and Arabidopsis thaliana 

Maryse A. Block and Catherine Albrieux

9.Isolation of Inner and Outer Membranes of the Chloroplast Envelope from Spinach and Pea 

Maryse A. Block

10.Purification of Non-Green Plastids (Proplastids and Amyloplasts) from Angiosperms, and Isolation of Their Envelope Membranes 

Claude Alban and Etienne-Pascal Journet

11.In Vitro Protein Import into Isolated Chloroplasts  

Maryse A. Block

12.Analysis of the MTL Super-Complex at Contact Sites between Mitochondria and Plastids 

Morgane Michaud

13.Isolation of Plastid-Fractions from the Diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum 

14.Isolating the Plasmodium falciparum Apicoplast using Magnetic Beads 

Cyrille Y. Botté, Geoffrey I. McFadden, and Yoshiki Yamaryo-Botté

15.Extraction and Quantification of Lipids from Plant or Algae

16.Quantitative Assessment of the Chloroplast Lipidome

Valérie Gros and Juliette Jouhet

17.Determination of the DNA/RNA-Associated Sub-Proteome from Chloroplasts and Other Plastid Types 

Maha Chieb, Monique Liebers, Fabien Chevalier, Silva Lerbs-Mache, Robert Blanvillain, and Thomas Pfannschmidt

18.Mapping Plastid Transcript Population by Circular Reverse Transcription-Polymerase Chain Reaction 

Florence Courtois and Livia Merendino

19.Bioinformatic Analysis of Chloroplast Gene Expression and RNA Post-Transcriptional Maturations using RNA Sequencing 

Bastien Malbert, Guillen Rigaill, Veronique Brunaud, Claire Lurin, and Etienne Delannoy

20.A Guide to the Chloroplast Transcriptome Analysis using RNA-Seq 

Elena J.S. Michel, Amber M. Hotto, Susan R. Strickler, David B. Stern, and Benoît Castandet

21.A Toolkit for the Characterization of the Photoprotective Capacity of Green Algae 

Águila Ruiz-Sola and Dimitris Petroutsos

22.Rescue of Deletion Mutants to Isolate Plastid Transformants in Higher Plants 

Mohammad El Hajj, Mohd Fahdli Bin Hamdan, Elena Martin Avila, and Anil Day

23.Genetic Analysis of Chloroplast Biogenesis, and Function and Mutant Collections  

Sho Fujii, Hajime Wada, and Koichi Kobayashi

24.Generation of Mutants of Nuclear-Encoded Plastid Proteins Using CRISPR/Cas9 in the Diatom Phaeodactylum tricornutum

Guillaume Allorent, Erika Guglielmino, Cécile Giustini, and Florence Courtois

Part III In Silico Tools

Daniel Moog

26.AT_CHLORO - The First Step When Looking for Information about Subplastidial Localization of Proteins 

Daniel Salvi, Sylvain Bournais, Lucas Moyet, Imen Bouchnak, Marcel Kuntz, Christophe Bruley, and Norbert Rolland