Plant Functional Genomics

• About the Editor
  
• Contributors
  
• Preface. Definition and Origin of Plant Functional Genomics
  
• Abbreviations
  
• SECTION I: BREAKTHROUGH TECHNIQUES
  
• Chapter 1. Full-Length cDNAs for the Discovery and Annotation of Genes in Arabidopsis thaliana (Motoaki Seki, Mari Narusaka, Masakazu Satou, Miki Fujita, Tetsuya Sakurai, Youko Oono, Kenji Akiyama, Kazuko Yamaguchi-Shinozaki, Kei Iida, Piero Carninci, Junko Ishida, Jun Kawai, Maiko Nakajima, Yoshihide Hayashizaki, Akiko Enju, and Kazuo Shinozaki)
  
• Introduction
  
• Collection of Arabidopsis Full-Length cDNAs
  
• Application of Full-Length cDNAs to Genome Annotation
  
• Application of Full-Length cDNAs to Functional Analysis
  
• Conclusions and Perspectives
  
• Chapter 2. T-DNA Mutagenesis: From Tagging to Insertion Sequence Databases (Allen Sessions)
  
• Crown Galls, Neoplasia, and Agrobacterium
  
• Agrobacteria As Friend Not Foe
  
• Development of Transformation Protocols for the Efficient Generation of T-DNA Insertion Mutants
  
• Even Faster and More Efficient Transformation
  
• From a Population of T-DNA Insertion Mutants to a File of T-DNA Flanking Sequence Tags
  
• Amplification of T-DNA Borders and the Distribution of Predicted Insertions
  
• Chapter 3. Novel Reverse Genetics Tools in Plant Functional Genomics (Xin Li and Yuelin Zhang)
  
• Introduction
  
• Deleteagene
  
• TILLING
  
• Combinatorial Gene Slicing
  
• Chapter 4. Transcriptomics in Plants: From Expression to Gene Function (Laurent Zimmerli and Shauna Somerville)
  
• Introduction
  
• The Technologies
  
• Experimental Design
  
• Analysis
  
• Data Verification and Quality Checks
  
• Limitations
  
• Perspective
  
• Chapter 5. Metabolite Profiling in Plants (Richard N. Trethewey)
  
• Introduction
  
• Background and Fundamentals of Metabolite Profiling
  
• Metabolite-Profiling Technologies
  
• Applications of Metabolite Profiling to Plants
  
• Outlook for Metabolite Profiling
  
• Chapter 6. Large-Scale Yeast Two-Hybrid Analysis (Barry Causier, John Graham, and Brendan Davies)
  
• Introduction
  
• The Basis of the Yeast Two-Hybrid System
  
• Large-Scale Yeast Two-Hybrid Studies: A Brief History
  
• High-Throughput Yeast Two-Hybrid Methodologies
  
• Applications of Large-Scale Yeast Two-Hybrid Screening
  
• The Caveat
  
• SECTION II: SPECIES EXAMPLES
  
• Chapter 7. Functional Genomics of a Cyanobacterium, Synechocystis sp. PCC 6803 (Takakazu Kaneko, Shusei Sato, and Satoshi Tabata)
  
• Introduction
  
• A Large-Scale Gene Disruption
  
• Transcriptome Analysis
  
• Proteome Analysis
  
• Analysis of Protein Interactions with the Yeast Two-Hybrid System
  
• Genome Databases
  
• Conclusions and Future Perspectives
  
• Chapter 8. Chlamydomonas Genomics: New Approaches for a Classical Model System (Heidi K. Ledford, Rachel M. Dent, and Krishna K. Niyogi)
  
• Introduction
  
• The Chloroplast Genome
  
• The Mitochondrial Genome
  
• The Nuclear Genome
  
• Functional Genomics
  
• Transcriptomics
  
• Proteomics and Metabolomics
  
• Tying It All Together: Databases for the Chlamydomonas Community
  
• Closing Thoughts and Future Directions
  
• Chapter 9. Functional Genomics in Physcomitrella (Wolfgang Frank, Hauke Holtorf, and Ralf Reski)
  
• Introduction
  
• Mass Production of Standardized Moss Material
  
• Production of a Physcomitrella EST Collection
  
• In Vivo Transposon Mutagenesis of cDNA Libraries
  
• Fast-Forward Production of Single Knockout Constructs
  
• High-Throughput Transformation Protocol
  
• Mutant Quality Control
  
• Screening for Mutant Phenotypes
  
• Molecular Analysis of Mutants
  
• Conclusion
  
• Chapter 10. Arabidopsis Functional Genomics Tools: An Overview (Koen Dekker)
  
• Introduction
  
• Curriculum Vitae of a Model
  
• Functional Genomics Tools
  
• Tools for Reverse Genetics
  
• Tools for Forward Screening
  
• Tools for Studying Mechanisms
  
• Weaknesses
  
• Threats to Continued Impact
  
• Opportunities
  
• Chapter 11. Rice Functional Genomics: From Nucleotide Sequence to Gene Function (Takuji Sasaki)
  
• Introduction
  
• Functional Genomics Based on Forward Genetics
  
• Functional Genomics Based on Reverse Genetics
  
• Functional Genomics Based on Activation Tagging
  
• Conclusion
  
• Chapter 12. Maize Genomics (Joachim Messing)
  
• Maize As a Crop
  
• Genome Size
  
• Genome Expansion
  
• Clone Maps
  
• Genetic Maps
  
• Gene Tagging
  
• Gene-Enrichment Procedures
  
• ESTs
  
• Microarrays
  
• Genomic Sequences
  
• Rice/Maize Clone Maps
  
• Chapter 13. Prospects for Functional Genomics in a New Model Grass (Glyn Jenkins, Luis A. J. Mur, Pauline Bablak , Robert Hasterok, and John Draper)
  
• Why a New Model Grass?
  
• Understanding the Plant
  
• Understanding the Genome
  
• Toward Functional Genomics of Pathogenic Interactions
  
• SECTION III: ORGANELLES
  
• Chapter 14. Chloroplast Proteomics (Klaas J. van Wijk)
  
• The Dynamic Nature of the Plastid and Its Proteome
  
• The Scope of This Chapter
  
• Prediction of the Plastid Proteome
  
• Prediction of Proteomes of Nonphotosynthetic Plastids
  
• Systematic Experimental Identification and Characterization of the Plastid Proteome
  
• Posttranslational Modifications of the Chloroplast Proteome
  
• Plastid-Localized Protein Complexes and Protein-Protein Interactions
  
• Conclusions and Future Perspectives
  
• Chapter 15. Plant Mitochondrial Proteomics (A. Harvey Millar and Joshua L. Heazlewood)
  
• Defining the Plant Mitochondrial Proteome
  
• Technology Issues
  
• Science Issues
  
• Future Directions
  
• SECTION IV: PATHWAYS AND PROCESSES
  
• Chapter 16. Functional Characterization of the Photosynthetic Apparatus in Arabidopsis thaliana (Henrik Vibe Scheller, Christina Lunde, Anna Haldrup, and Poul Erik Jensen)
  
• Introduction
  
• Overview of Electron Transport
  
• Photosystem II
  
• The Cytochrome b/f Complex
  
• Photosystem I
  
• Accessory Electron Transport Systems
  
• Elements Involved in Nonphotochemical Quenching
  
• The ATP Synthase
  
• Conclusion
  
• Chapter 17. Functional Genomics of Plant Nitrogen Metabolism (Mathilde Orsel, Anne Krapp, Karine Boivin, Françoise Daniel-Vedele, Hélène Roussel, Christian Meyer, and Christelle Thibault)
  
• Introduction
  
• Functional Genomics of Nitrate Transport in Arabidopsis
  
• Transcriptome Analysis in Relation to Variations in Nitrogen Supply
  
• Conclusion
  
• Chapter 18. Functional Genomics of Plant Salinity (Hans J. Bohnert)
  
• Salinity Tolerance in Context
  
• Problems Plants Face in High Salinity
  
• The Genomics Tool Kit Applied to Salinity Stress Research
  
• Mutants and Mutant Phenotypes in Salinity Stress Tolerance
  
• ESTs and cDNAs from Salt-Stressed Plants
  
• Salinity-Induced Changes of the Transcriptome
  
• Salinity-Dependent Signal Transduction
  
• Salinity Stress Engineering
  
• Future Developments
  
• Chapter 19. Functional Genomics Applied to Plant Fatty Acid Biosynthesis (Sari A. Ruuska and John B. Ohlrogge)
  
• Introduction
  
• Directed Gene Discovery: Approach
  
• Large-Scale DNA Sequencing and Gene-Expression Analysis
  
• Summary and Future Prospects
  
• Chapter 20. Genetic and Molecular Control of Seed Development in Arabidopsis (Loïc Lepiniec, Martine Devic, and Frédéric Berger)
  
• Introduction
  
• From Genetic to Molecular Bases of Seed Development
  
• Ovule Development
  
• Endosperm Development
  
• Embryogenesis
  
• Limitations of the Genetic Approach and New Prospects
  
• SECTION V: PROTEIN FAMILIES
  
• Chapter 21. Plant Transporters (Marcelo Desimone, Reinhard Kunze, Ulf-Ingo Flügge, and Wolf B. Frommer)
  
• Introduction
  
• Identification of Novel Transporters by Heterologous Expression
  
• Gene Expression
  
• Subcellular Localization
  
• Protein Interactions
  
• Analysis of Loss-of-Fuction (“Knockout”) Mutants and “Knockdown” Mutants
  
• The ARAMEMNON Database: A Novel Bioinformatics Tool for Sequence Interpretation
  and Data Mining on Transporters and Membrane Proteins
  
• Connecting Arabidopsis Functional Genomics Resources with Crop Plant Research
  
• Chapter 22. Functional Genomics of the Cytochrome P450 Gene Superfamily in Arabidopsis thaliana (David W. Galbraith and Søren Bak)
  
• What are Cytochrome P450s?
  
• Comparative Genome Analysis
  
• A Small Proportion of the Arabidopsis P450s Have Been Assigned a Specific Cellular
  Function
  
• A Variety of New Methods Are Becoming Increasingly Available to Assign Function
  to P450 Family Members
  
• Conclusions and Perspectives
  
• Chapter 23. Functional Genomics of Protein Phosphorylation in Arabidopsis thaliana (Claudia Hass, Stefan Weinl, Klaus Harter, and Jörg Kudla)
  
• Introduction
  
• Protein Kinases and Phosphatases Encoded in the Arabidopsis Genome
  
• Histidine Kinases and Two-Component Signaling System
  
• Early Steps in Plant Histidine Kinase Signaling
  
• Conclusion
  
• Index
  
• Reference Notes Included
  

Biography

Dario Leister