The Bacteriophages, Softcover reprint of the original 1st ed. 1988
Volume 2
The Viruses Series

It has been 10 years since the Plenum Publishing Corporation printed a series of review articles on bacteriophages in Comprehensive Virology. Articles in that series contained physical-genetic maps but very little DNA sequence information. Now the complete DNA sequence is known for some phages, and others will soon follow. During the past 10 years, two phages have come into common use as reagents: A phage for cloning single copies of genes, and M13 for cloning and DNA sequencing by the dideoxy termination method. Also during this period the use of alter­ native sigma factors by RNA polymerase has become established for and T4. This seems to be a widely used mechanism in bacteria, SPO 1 since it has been implicated in sporulation, heat shock response, and regulation of nitrogen metabolism. The control of transcription by the binding of A phage CII protein to the -35 region of the promoter is a recent finding, and it is not known how widespread this mechanism may be. This rapid progress made me eager to solicit a new series of reviews. These chapters are of two types: each of the first type deals with an issue that is exemplified by many kinds of phages. Chapters of this type should be useful in teaching advanced courses. Chapters of the second type pro­ vide comprehensive pictures of individual phage families and should pro­ vide valuable information for use in planning experiments.

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.