Plant DNA Infectious Agents

1 The Molecular Biology of Cauliflower Mosaic Virus and Its Application as Plant Gene Vector.- I. Introduction.- II. The Biology of Cauliflower Mosaic Virus.- A. The Virus Particle.- B. The DNA of CaMV.- C. The Genetic Organisation of the CaMV.- 1. The Genes of CaMV.- 2. Transcripts of CaMV.- D. The Replication of CaMV.- E. Structural Homologies Between CaMV and Retroid Elements.- III. The Development of CaMV into a Plant Gene Vector.- A. Mutants of CaMV.- 1. Mutations in ORF II.- 2. Mutations in Other Regions of the CaMV Genome.- B. Translational Polarity.- C. Transducing Cauliflower Mosaic Virus Variants.- D. Defective Complementing Mutants of CaMV.- IV. Elements of CaMV as Tools in Plant Genetic Engineering.- V. Vector Based on Other Plant Viruses.- VI. Conclusion and Outlook.- VII. References.- 2 The Structure, Expression, Functions and Possible Exploitation of Geminivirus Genomes.- I. Introduction.- II. Genome Organisation.- A. Coding Regions.- B. Non-coding Regions.- III. Gene Expression.- IV. Gene Functions.- V. The Potential of Geminiviruses as Gene Vectors.- VI. References.- 3 cDNA Cloning of Plant RNA Viruses and Viroids.- I. General Introduction.- II. Construction of Full-Length cDNA Clones.- A. Introduction.- B. Synthesis of Double-Stranded cDNA.- C. Cloning Strategies.- D. Cloning in Transcription Vectors.- III. DNA Copies as Tools to Study the Molecular Biology of Plant RNA Viruses.- A. Introduction.- B. Infectivity of cDNA Clones.- i) Infectivity of DNA Copies.- ii) Infectivity of in vitro Transcripts from DNA Copies.- C. RNA Replication.- D. RNA Recombination.- E. Genetic Organisation and Gene Expression.- IV. Viroids and Satellites.- A. Introduction.- B. Molecular Cloning of Viroids.- C. Application of cDNA Clones.- i) Viroids.- ii) Satellite Viruses.- V. Diagnosis of Plant Diseases Using DNA Copies of Plant Viruses and Viroids.- A. Introduction.- B. Spot Hybridisation.- VI. Conclusions and Future Aspects.- VII. References.- 4 Agroinfection.- I. Introduction.- II. Potential Applications of Agroinfection.- A. Agrobacterium as an Organism for the Experimental Storage and Transmission of Plant Viruses.- 1. Storage and Safety.- 2. Efficiency and Flexibility.- 3. Release of Viral Genomes from the T-DNA.- 4. Analysis of T-DNA Transfer.- B. Transformation of Plant Cells with Viral Genetic Information.- 1. Transient Expression.- 2. Expression of Viral Genes in Host and Non-Host Plants.- 3. Transgenic Plants Containing Oligomers of Viral Genomes or Genome Components.- i) Complementation Between Different Components of a Multi-Component System.- ii) Analysis of in vitro Produced Mutant Viral Strains.- iii) Development of Proviral Vectors.- 4. Super-Infection of Plants Transgenic for Viral Sequences.- i) Cross-Protection.- ii) Complementation of Defective Viral Genes with Integrated Wild-Type-Genes; Development of Complementation Vectors.- III. Perspectives.- IV. References.- 5 The Mechanism of T-DNA Transfer from Agrobacterium tumefaciens to the Plant Cell.- I. General Introduction.- A. Scope of the Review.- B. Crown Gall Disease.- C. Molecular Basis of Neoplastic Transformation.- a) The Ti Plasmid and Its Organisation.- b) Functional Organisation of the T-DNA.- II. Early Events of Transformation.- A. Virulence Functions.- a) Chromosomal Virulence Region.- b) Organisation of the Virulence Region.- c) Regulation of vir Region Expression.- d) Nature of the Inducer.- B. T-DNA-Transfer.- a) The 25-bp Terminal Sequence.- b) Overdrive.- c) Analysis of the T-DNA/Plant DNA Junctions.- d) T-DNA Localisation and Structure Within the Plant Genome.- III. T-DNA Processing.- A. The Search of Processing Intermediates.- a) Genetic Assays.- b) Physical Assays.- c) Summary and Discussion.- B. Proteins Involved in T-DNA Processing.- a) Vir D Locus.- b) Vir C Locus.- c) Vir E Locus.- d) Vir F Locus.- IV. Conclusions.- V. References.- 6 Molecular Analysis of Root Induction by Agrobacterium rhizogenes.- I. Introduction.- II. Taxonomy.- III. Ri Plasmid Structure.- IV. Ri T-DNA Organization.- V. T-DNA of Ri Transformed Plants.- VI. Endogenous T-DNA of Plants.- VII. Conclusions and Further Speculations.- VIII. References.- 7 Pathways to Plant Genetic Manipulation Employing Agrobacterium.- I. Introduction.- II. Biology of Agrobacterium tumefaciens Ti Plasmid.- III. Strategies for Inserting Genes into T-DNA.- A. Homogenotization.- B. Cointegrating Intermediate Vectors.- C. Binary Vectors.- D. Disarming the T-DNA.- E. Specific Examples.- 1. Use of pMON200: A Cointegrating Vector.- 2. Use of pMON505: A Binary Vector.- F. Border Sequences and Binary Vector T-DNA Structure.- IV. Practical Catalogue.- A. Survey of Binary Vectors.- B. Selectable Markers.- C. Expression Cassette Vectors.- V. Getting Genes into Plants.- VI. Novel Applications of Ti Transformation.- A. Gene Isolation by Complementation or Direct Selection.- B. T-DNA as a Transposon for Mutation and Promoter Probe.- VII. Prospects.- VIII. References.- 8 Plant Transposable Elements: Unique Structures for Gene Tagging and Gene Cloning.- I. Introduction.- II. Isolation and Characterization of a Transposable Element.- A. Recognition of a Transposable Element.- B. Genes Suitable for the Isolation of Transposable Elements.- C. Transposon Tagging of a Gene in Zea mays.- D. Genetical Analysis of the Tagged Mutants.- E. Frequency of Mutation.- III. Transposable Elements as Molecular Probes for Gene Isolation.- A. General Aspects.- B. Isolation of Mutants Induced by Autonomous Elements (Ac and En [Spm]).- C. Isolation of Clones Carrying Receptor Elements.- D. Identification of Gene-Specific Sequences.- IV. Conclusions.- V. References.- 9 Direct Gene Transfer to Plants.- I. Direct Gene Transfer.- A. Introduction.- B. A Representative Experiment.- C. Protocol and Transformation Frequency.- D. Electroporation.- E. No Hostrange Limitations.- F. Foreign Gene Mendelian Inheritance.- G. Stability of the Foreign Gene.- H. Instability of the Foreign Gene.- I. Molecular Proof for Transformation.- J. Gene Localization by in situ Hybridization.- K. Arrangement of Foreign DNA in the Host Genome.- L. Co-Transformation with Non-Selectable Genes.- M. Gene Transfer from Total Genomic DNA.- N. Limitations for Direct Gene Transfer.- II. Other Vectorless Gene Transfer Systems.- A. Liposome Fusion.- B. Spheroplast Fusion.- C. Microinjection.- III. Direct Gene Transfer in Theoretical and Applied Genetics.- A. Gene Isolation.- B. Gene Identification.- C. Replication.- D. Gene Replacement.- E. Gene Regulation.- F. Stability and Instability.- G. Gene Transfer to Chloroplasts and Mitochondria.- H. Gene Transfer into Cereals.- I. Gene Transfer into Potentially Totipotent Cells.- J. Gene Transfer Without Pre Cloning in Bacteria.- K. Gene Transfer into Organelles.- L. Tagging of Chromosomes.- M. Modulation of Expression.- N. Conclusions.- IV. References.- 10 Microinjection: An Experimental Tool for Studying and Modifying Plant Cells.- I. Introduction.- II. Recipient Cell Systems.- A. Cell Types.- B. Protoplasts.- C. Cell Culture Conditions.- III. Resolution of Intracellular Compartments.- A. Microscopy.- B. Fluorescent Stains.- IV. Microinjection Methodology.- A. Micromanipulation Techniques.- B. Equipment.- V. Genetic Transformation.- VI. Other Applications.- VII. Concluding Remarks.- VIII. References.- 11 Transformation of Chlamydomonas Reinhardtii.- I. Introduction.- II. Nuclear Transformation.- A. Selection.- i) ARG7 Locus.- ii) Resistance to Kanamycin.- iii) Other Selective Markers.- B. ARS Sequences of C. reinhardtii.- C. ARC Sequences.- D. Natural Plasmids.- E. Is Agrobacterium tumefaciens a Possible Transformation Vector for C. reinhardtii?.- III. Prospects of Chloroplast Transformation in C. reinhardtii.- IV. Conclusions.- V. References.- 12 Induction of Expression in and Stable Transformation of an Algal Cell by Nuclear Microinjection with Naked DNA.- I. Introduction.- II. Acetabularia.- III. Techniques.- IV. Expression of Genomic RNA.- V. Expression of Genomic DNA.- VI. Expression of Genes and Gene Constructions.- VII. Regulation of Expression.- VIII. Transformation.- IX. Genetics.- X. Discussion.- XI. References.- 13 Transient Expression of DNA in Plant Cells.- I. Overview of Transient Assay Applications.- II. Transient Assays in Plant Cells.- III. Transient Expression after Electroporation-Mediated Gene Transfer.- IV. Discussion.- V. References.- 14 Plastid Transformation: A Progress Report.- I. Introduction.- II. Construction of Vectors for the Transformation of Plastids.- III. General Conclusions.- IV. References.- 15 Targeting Nuclear Gene Products into Chloroplasts.- I. Introduction.- II. Binding of Precursors to the Outer Membrane of the Chloroplast.- III. Translocation of Polypeptides Across the Envelope Membranes.- IV. Processing of Precursors to the Nature Polypeptide.- V. The Transit Peptide Itself can Mediate Import of Foreign Polpeptides.- VI. Structural Analysis of Chloroplast Transit Peptides.- VII. Experimental Analysis of Transit Peptides.- VIII. Future Prospects.- IX. References.