Viruses

1 Biology of the Bacteriophage ?X174.- I. Introduction.- II. Background.- A. The Genomes.- B. The Genes.- C. Genetic Map.- D. Outline of the Infection Process.- E. Gene Expression.- III. Phage Structure.- A. The 114S Particle.- B. The 132S Particle.- IV. Infection.- A. Host Requirements.- B. Attachment.- C. Eclipse.- D. DNA Penetration.- V. DNA Synthesis and Packaging.- A. Stage I (SS ? RF).- B. Stage II (RF ? RF).- C. Stage III (RF ? SS/Phage).- D. Mechanism of Conversion from Stage II Replication to Stage III Replication.- E. Structure and Morphogenesis of Prohead.- VI. Gene Expression.- A. RNA Polymerase-Binding Sites of RF DNA.- B. Minicells.- C. Mutation at Ribosome-Binding Site.- D. Transcription Termination.- E. Mutations around the TJ Site.- F. Cloning of mRNA Stabilizing Sequences.- G. Expression of Overlapping Genes.- VII. Lysis.- VIII. Effects of ?X174 Genes on Host Bacterial Cells.- A. Gene A*.- B. Other Genes.- IX. Concluding Remarks.- References.- 2 The P2-like Phages and Their Parasite, P4.- I. Introduction.- A. Origin and Distribution of the P2-like Phages.- B. Phage P4.- C. Special Features.- D. Scope of This Review.- II. The Virions.- A. Morphology.- B. Virion Proteins.- C. Structure of the DNA.- D. Arrangement of DNA in the Particles.- III. The Genomes.- A. Deletions and Insertions.- B. Genetic Organization.- C. Hybrids, Plasmids, and Phasmids.- IV. Life Cycles of P2-like Phages.- A. Replication.- B. Morphogenesis, Packaging, and Lysis.- C. Regulation.- D. The Prophage.- E. Recombination.- V. The Life Cycle of Phage P4.- A. Replication.- B. Morphogenesis, Packaging, and Lysis.- C. Regulation.- D. P4 Effects on Helper.- E. Helper Effects on P4.- F. The Prophage.- G. Recombination.- H. P4 as a Cloning Vehicle.- VI. Appendixes.- A. Physical Maps of Selected Restriction Sites and Other Features of P2 and 186.- B. Selected Sequences.- References.- 3 Strategies of Bacteriophage DNA Replication.- I. Introduction.- A. Replication Control.- B. Temperate versus Lytic Bacteriophages.- C. Circular versus Linear Genomes.- D. DNA Modification.- E. Role of RNA Transcription.- F. Redundant Protein Functions.- G. One Gene, Two Polypeptides.- H. Cis-Acting Replication Proteins.- I. Conservation of Replication Proteins.- J. Building of "Replication Machines".- K. Multifunctional Proteins.- II. Replication of Single-Stranded DNA Molecule Bacteriophages M13, fd, fl, G4, and ?X174.- A. General Considerations.- B. Complementary Strand Synthesis.- C. DNA Structures at the Origin.- D. Nucleases Involved in Viral Strand Synthesis.- E. Viral Strand Synthesis.- F. DNA Sequences at the Origin.- III. Replication of Circular Double-Stranded Bacteriophages.- A. Bacteriophage ?.- B. Bacteriophage P1.- C. Bacteriophage P4.- IV. Replication of Double-Stranded Linear Bacteriophages.- A. Replication of DNA Molecules with Terminal Repeats and Internal Origins.- B. Replication through Initiation at the Ends.- C. Replication via Transposition in the Host Chromosome: Bacteriophage Mu.- References.- 4 Regulation of Phage Gene Expression by Termination and Antitermination of Transcription.- I. Introduction.- II. Coliphage Lambda.- A. A General Primer.- B. The Lambdoid Phages.- C. The N Antitermination Protein.- D. Host Factors.- E. The Nut Site.- F. A Model of N Action.- G. The Q Transcription Antitermination Function.- H. Retroregulation.- I. Contraantitermination.- III. P2 Phages and Satellite Phage P4.- A. P2.- B. Phage 186.- C. Satellite Phage P4.- IV. Conclusions.- References.- 5 DNA Packaging in dsDNA Bacteriophages.- I. Introduction.- II. Energetics and Mechanism of DNA Translocation.- A. Early Models of DNA Translocation.- B. Prohead Expansion in Packaging.- C. ATP-Driven DNA Translocation Models.- D. Functions of the Packaging Components.- E. Relationship of Packaging to DNA Ejection.- III. Structure of Packaged Phage DNA.- IV. Terminase and Headful Cutting of Concatemeric DNA in Packaging.- A. Phages with Unique Ends.- B. Phages with pac Site Cutting.- C. Phages with Non-Sequence-Specific Cutting of Concatemeric DNA.- D. Phages Packaging Nonconcatemeric dsDNA.- E. Common Features of DNA Maturation Processes.- V. Interactions of DNA Packaging with Other DNA Processes in Vivo, and DNA Structural Requirements for Packaging.- A. Interactions in Vivo.- B. DNA Structural Requirements for Packaging.- VI. Conclusions.- References.- 6 Filamentous Bacteriophage.- I. Introduction.- II. Genes and Proteins.- A. General.- B. Structural Genes and Proteins.- C. DNA Metabolism Genes and Proteins.- D. Morphogenetic Genes and Proteins.- III. Virion Structure.- A. Composition.- B. Properties.- C. Dissociation.- IV. Infection.- A. Adsorption.- B. Entry.- V. DNA Replication.- A. Complementary Strand Synthesis.- B. Synthesis of the (+) Strand.- C. In Vitro DNA Synthesis.- D. Single-Strand Synthesis.- E. Structure and Function of the (?) Strand Origin.- F. Structure and Function of the (+) Strand Origin.- VI. Expression of the f1 Genes.- A. Transcription.- B. Translation.- VII. Morphogenesis.- A. The Single-Stranded DNA-Gene V Protein Complex.- B. Membrane Association of Virion Proteins.- C. Assembly.- VIII. Genetics and Physiology.- A. Control of Gene Expression.- B. Restriction and Modification.- C. Recombination.- D. Defective Interfering Particles.- E. Lysogeny.- F. Filamentous Phages as Cloning Vectors.- IX. Other Reviews and Conclusions.- A. Other Reviews.- B. Conclusions.- References.- 7 Bacteriophage N4.- I. Introduction.- II. The Virion.- III. The Genome.- IV. N4 Adsorption.- V. N4 Growth Cycle.- A. Early Events.- B. Intermediate Events.- C. Late Events.- VI. N4 Transcription.- A. Early Transcription.- B. Middle Transcription.- C. Late Transcription.- VII. N4 Replication.- VIII. N4 Genetics.- IX. Prospects.- References.- 8 Lipid-Containing Bacteriophages.- I. Introduction.- II. Bacteriophage ?6.- A. Life Cycle.- B. Structure of the Virion.- C. Genetics and Molecular Cloning of the ?6 Genome.- D. Entry of Bacteriophage ?6.- E. Transcription and Replication of ?6 RNA.- III. PRD1-Type Phages.- A. Introduction.- B. Protein Localization and Particle Disruption.- C. Genetics and Cloning.- D. Assembly of PRD1.- IV. Morphogenetic Proteins in Phage Membrane Assembly.- References.- 9 Phage T4 Structure and Metabolism.- I. Introduction and Overview.- A. History.- B. The Genome.- C. The Life Cycle.- D. "Unnecessary" Complexities?.- II. Structure and Initiation of Infection.- III. Regulation of Transcription.- IV. Posttranscriptional Controls.- A. T4-Evoked Modifications of Ribosomes.- B. Translational Repressors.- C. Sequestering the Ribosome-Binding Site in Double-Stranded RNA.- D. RNA Processing.- E. RNA Degradation.- F. Introns in T4 Transcripts.- V. Modification and Restriction of T4 DNA.- VI. DNA Replication and Recombination.- A. Overview of Replication in Vivo.- B. Genetics of "Primary" Origin Initiation.- C. Physiology of Tertiary Initiation.- D. Genetics of Recombination-Dependent (Secondary) Initiation.- E. Biochemistry of Replication Proteins.- VII. DNA Packaging.- VIII. Virion Structure and Assembly.- A. Head Structure and Assembly.- B. Size Determination.- C. In Vitro Assembly.- D. Tail Structure and Assembly.- E. The Baseplate and Tube: Structure and Assembly.- F. Tail Fiber Structure and Assembly.- IX. Outlook.- References.- 10 Phages of Cyanobacteria.- I. Introduction.- II. Genetics.- A. Nucleic Acids and Their Synthesis in Cyanophage-Infected Cells.- B. Lysogeny with Emphasis on Filamentous Cyanobacteria.- C. Mutagenic Agents.- III. Physiology.- A. Cation Requirements and the Adsorption of Cyanophages to Host Cells.- B. Metabolite Incorporation.- C. Host Metabolism and Cyanophage Replication.- IV. Ecology.- A. Cyanophage Control of Cyanobacterial Blooms.- B. Cyanobacterial-Cyanophage Interactions in Continuous Culture.- C. Use of Cyanobacterial-Cyanophage Systems to Bioassay Pesticides.- V. Concluding Remarks.- References.- 11 Bacteriophage P22.- I. Introduction.- II. Life Cycle.- A. Lytic Growth.- B. Lysogeny.- C. Genetic Plasticity.- III. Genetic Structure and Function.- A. Site-Specific Recombination System.- B. Homologous Recombination Functions.- C. Other PL Operon Genes.- D. Early Transcriptional Regulation.- E. Repressor and Its Control.- F. Cro.- G. cl.- H. DNA Replication Genes.- I. Late-Transcriptional Regulation.- J. Lysis Genes.- K. DNA Packaging Initiation Site (pac).- L. Head Genes.- M. imml Genes.- N. Tail Gene.- References.- 12 Bacteriophage Gene Products That Cause Human Disease.- I. Introduction.- II. Diphtheria Toxin.- A. Diphtheria.- B. Bacterial Host.- C. Corynephage ?.- D. Other Corynephages.- E. Regulation of tox Expression.- F. Diphtheria Toxin Structure and Function.- G. Targeting Diphtheria Toxin-Related Hybrid Proteins to Cancer Cells.- III. Botulinum Toxin.- A. Botulism.- B. Bacterial Host.- C. Converting Bacteriophages of C. botulinum.- D. Botulinum Toxin Structure and Function.- IV. Streptococcal Pyrogenic Exotoxins.- A. Scarlet Fever.- B. Streptococcus pyogenes and Its Toxins.- C. SPE-Converting Bacteriophages.- D. Structure and Function of the SPEs.- V. Staphylococcal Enterotoxins.- A. Staphylococcal Food Poisoning.- B. Staphylococcus aureus and Its Toxins.- C. SE-Converting Bacteriophages.- D. Structure and Function of the SEs.- VI. Shigalike Toxins of Escherichia coli.- A. E. coli-Induced Enteric Diseases.- B. SLT-Converting Coliphages.- C. Regulation of Toxin Expression.- D. Structure and Function of the SLTs.- VII. Concluding Remarks.- References.- 13 Structure and Function of the Transcription Activator Protein cII and Its Regulatory Signals.- I. Introduction.- II. cII-Regulated Promoter Signals.- III. Physical, Chemical, and Functional Characterization of Purified cII Protein.- IV. Sequence-Specific DNA Binding.- V. Domain Analysis of cII Protein.- A. The Amino-Terminal Domain: Amino Acid Residues 2-8.- B. The Oligomerization Domains: Amino Acid Residues 9-25 and 46-71.- C. The DNA-Binding Domain: Amino Acid Residues 26-45.- D. The Carboxyterminal Domain: Amino Acid Residues 72-97.- VI. Cross-Reactivity of ? cII and P22 Cl Proteins on Promoter Signals from ?, P22, and i21 Phages.- VII. Control of cII Degradation.- References.