The Bacteriophages: Volume 1

ISBN-13: 9781468454260 / Angielski / Miękka / 2012 / 614 str.

Richard Calendar

Opis

It has been 10 years since Plenum included a series of reviews on bacte riophages, in Comprehensive Virology. Chapters in that series contained physical-genetic maps but very little DNA sequence information. Now the complete DNA sequence is known for some phages, and the se quences for 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 Ml3 for cloning and DNA sequencing by the dideoxy termi nation method. Also during that period the use of alternative sigma fac tors by RNA polymerase has become established for SPOl and T4. This seems to be a widely used mechanism in bacteria, since it has been implicated in sporulation, heat shock response, and regulation of nitro gen 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 contributions 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 provide comprehensive pictures of individual phage families and should provide valuable information for use in planning experiments."

Spis treści

1 Phage Evolution and Speciation.- I. The Species Concept and Its Application to Phages.- II. Molecular Biology and the Origins of Phage.- III. The Gene Pool.- IV. Phage Genes Related to Host Genes.- V. Host Functions Replaceable by Phage-Derived Genes.- VI. Recombination in Natural Populations.- VII. Source and Distribution within the Genome of Recombinable Variation.- VIII. Reproductive Isolation in Nature.- References.- 2 Control Mechanisms in dsDNA Bacteriophage Assembly.- I. Introduction.- II. The Structure of dsDNA Phage Virions.- A. Head Structure.- B. Tail Structure.- C. Small Molecules in Phage.- III. The Nature of Phage Assembly Pathways.- IV. Current Problems in Phage Assembly and Structure.- A. Assembly Pathways.- B. Size Determination.- C. Nonequivalent Protein-Protein Interactions.- D. Structural Movements and Molecular Machines.- V. Genes and Morphogenesis.- A. Control of Gene Expression.- B. Gene Position.- VI. Prospects.- References.- 3 Changes in RNA Polymerase.- I. Introduction.- II. Covalent Modifications of RNA Polymerases.- III. Proteins Binding to the Bacterial RNA Polymerase Core.- A. Phage-Coded Initiation Proteins.- B. Other RNA Polymerase Core-Binding Proteins.- IV. DNA-Binding Proteins That Interact with, and Enhance the Activity of, RNA Polymerase.- V. Other RNA Polymerase-Binding Proteins and Other Phages.- VI. Concluding Comments.- References.- 4 The Single-Stranded RNA Bacteriophages.- I. Introduction.- II. Classification of RNA Phages.- A. RNA Coliphages.- B. RNA Phages of Other Genera.- III. Ecology of Coliphages.- IV. The Infection Process.- V. Virion Structure.- VI. Replication of Phage RNA.- A. Mature Phage RNA.- B. 6S RNA and Qß RNA Variants.- VII. Origin and Evolution of the 6S RNA Families.- VIII. Gene Expression.- A. The A Protein.- B. The Replicase (Subunit III.- C. The Coat Protein.- D. The Lysis Protein of Group A Phages.- E. The Lysis Protein of Group B Phages.- IX. Sequence Comparison between Group I, II, and III Phages.- A. The Maturation Protein.- B. The Replicase.- C. The Coat Protein.- D. The Lysis Protein.- E. The Noncoding Regions.- F. The Savings between MS2 and GA.- X. Phylogeny of RNA Phages.- XI. Concluding Remarks.- References.- 5 Phages with Protein Attached to the DNA Ends.- I. Introduction.- II. Characterization of the Terminal Protein at the DNA Ends of the Phage ?29, Cp-1, and PRD1 Families.- A. Phage ?29 and Related Phages.- B. Phage Cp-1 and Related Phages.- C. Phage PRD1 and Related Phages.- III. Linkage between the Terminal Protein and the DNA of Phages ?29, Cp-1, and PRD1.- IV. Nucleotide Sequence at the DNA Ends of the ?29, Cp-1, and PRD1 Families.- A. ?29 Family.- B. Cp-1 Family.- C. PRD1 Family.- V. Transcription of ?29 DNA.- VI. In Vivo Replication of ?29, Cp-1, and PRD1 DNAs.- A. Phage ?29.- B. Phage Cp-1.- C. Phage PRD1.- VII. In Vitro Replication of ?29, Cp-1, and PRD1 DNAs: Initiation Reaction.- A. Formation of a Covalent Complex between the Terminal Protein and 5’ dAMP in ?29 and M2.- B. Formation of a Covalent Complex between the Terminal Protein and 5’ dAMP in Phage Cp-1.- C. Formation of a Covalent Complex between the Terminal Protein and 5’ dGMP in Phage PRD 1.- VIII. Purification and Characterization of the ?29 Proteins p2, p3, p5, and p6, Involved in DNA Replication.- A. Purification of Protein p2: Characterization of DNA Polymerase and 3’ ? p 5’ Exonuclease Activities.- B. Purification of Protein p3.- C. Activity of Purified Proteins p2 and p3 in the Formation of the p3-dAMP Initiation Complex and Its Further Elongation.- D. Effect of Aphidicolin and Nucleotide Analogues on the ?29 DNA Polymerase.- E. Isolation of Mutants of Protein p3 by in VitroMutagenesis of Gene 3: Effect of the Mutations on the in Vitro Formation of the Initiation Complex.- F. Purification and Characterization of Protein p6.- G. Purification and Characterization of Protein p5.- IX. Template Requirements for the Formation of the Initiation Complex.- X. Possible Role of the Inverted Terminal Repeat in the Replication of ?29, Cp-1, and PRD1 DNAs.- XI. Model for the Protein-Primed Replication of ?29.- XII. Role of the Parental Terminal Protein in ?29 DNA Packaging.- XIII. Protein-Primed Initiation of Replication: A General Mechanism.- References.- 6 Phage Mu.- I. Introduction.- II. Virion Morphology.- III. Physical and Genetic Structure of Mu DNA.- A. The ? Region.- B. The G Segment.- C. The ? Region.- IV. Life Cycle.- A. Infection/Integration.- B. Lysis—Lysogeny Decision.- C. Lytic Growth.- V. Transposition.- VI. Excision.- VII. G Inversion.- VIII. The mom Gene.- IX. Mu-like Phages.- X. Perspectives.- References.- 7 Bacteriophage T1.- I. Background.- II. Basic Characteristics and Methods of Study.- III. The Virus Particle.- IV. The T1 Map.- V. Phage Development.- A. Adsorption.- B. DNA Replication.- C. Protein and mRNA Synthesis.- D. Maturation.- VI. Miscellaneous.- A. Restriction and Modification.- B. Coinfection and Exclusion.- C. Transduction.- VII. Summary.- References.- 8 The T7 Group.- I. Introduction.- II. The T7 Prototype.- A. The T7 ViriQn.- B. The T7 Growth Cycle.- III. The T7 Relatives.- A. T7 Relatives Growing on E. coli B.- B. T7 Relatives Growing on E. coli Strains Other Than B.- C. T7-Related Phages with Non-E. coli Enterobacterial Hosts.- D. T7-Related Phages for Nonenterobacterial Strains.- IV. Further Comparisons and General Remarks.- References.- 9 Bacteriophage P1.- I. Introduction.- II. Physical and Genetic Structure.- A. Phage Particles.- 1. Morphology.- 2. Buoyant Density.- 3. Viral Proteins.- 4. Viral DNA.- B. Transducing Particles.- C. Prophages.- 1. Size and Copy Number.- 2. Localization: Plasmid and Integrated States.- 3. Genome Organization.- III. Adsorption and Injection.- A. The Receptor.- B. Host Range Extension.- C. Recombinational Control of Host Range: The cix-cin System.- 1. Organization of cix-cin and Homologies with Other Systems.- 2. Enhancer-Mediated Bacterial Control of Inversion.- 3. Potential Autoregulatory Circuits in Inversion.- 4. A Physiological Consequence of the Frequency of C and G Segment Inversion.- D. Injection.- IV. Cyclization.- A. The Need for Cyclization.- B. lox-cre-Mediated Site-Specific Recombination.- 1. Organization of the lox-cre System.- 2. Mechanism of lox-cre Recombination.- 3. Role of lox-cre Recombination in the Cyclization of P1 DNA.- C. Alternative Modes of Cyclizing P1 DNA.- V. Restriction-Modification.- A. Organization and Function of the Restriction-Modification Genes.- B. The P1 Restriction and Modification Enzyme and Its Mode of Action.- C. Timing of Restriction and Modification following P1 Infection.- D. Defense against Restriction (darA and darB)..- VI. Lysogenization versus Lytic Growth. Immunity and Virulence.- A. Physiological Influences on the Decision Process.- B. The Bipartite Nature of the Immunity System.- C. The Tripartite Nature of the Immunity System.- D. A Closer Look at immC.- 1. A Multiplicity of cl Protein-Binding Sites in the P1 Genome.- 2. Genes and Regulatory Elements in immC.- 3. The Regulation of cl Repressor.- E. A Closer Look at immI.- F. Bacterial Functions Implicated in Lysogenization.- VII. The Prophage State.- A. General Considerations.- 1. The Extent of Prophage Genome Expression.- 2. Relation of Plasmid Incompatibility to Mechanisms of Maintenance.- 3. Localization of P1 inc Determinants.- B. Plasmid Replication and Its Control.- 1. Organization of the R Replicon.- 2. Replication Control.- 3. Alternative Replicons.- 4. Host Participation in Plasmid Replication.- 5. Plasmid Participation in Control of Its Host.- C. Plasmid Partition and Its Control.- 1. Organization of the par Region.- 2. Mode of Action and Control of the par Region.- 3. A Role for Site-Specific Recombination.- 4. Host Participation in Plasmid Partitioning.- VIII. Vegetative Growth.- A. Organization of the Genes for Vegetative Functions.- 1. Early Genes.- 2. Late Genes.- B. Vegetative Replication.- 1. The Nature of Vegetative Replication.- 2. The Nature of the Lytic Replicon(s).- 3. Host Functions and Their P1-Determined Analogues in Vegetative Replication.- C. Regulation and Timing of Gene Expression.- 1. Expression of Vegetative Functions in the Prophage State.- 2. Replicative Induction of Early Vegetative Functions: A Model.- 3. Control of Late Vegetative Functions.- D. Morphogenesis.- 1. Head Morphogenesis.- 2. Tail Morphogenesis.- E. DNA Packaging and Cleavage of the P1 pac Site.- 1. Processive Headful Packaging.- 2. Localization of pac and pac-Cleavage Functions.- 3. Regulation of pac Cleavage.- IX. Transduction.- A. Specialized Transduction.- 1. Modes of Integrative Recombination.- 2. IS1-Mediated Generation of a Specialized Transducing Phage: P1 argF.- B. Generalized Transduction.- 1. Formation of Generalized Transducing Particles.- 2. Alternative Fates of Transducing DNA in the Recipient.- 3. The Physiology of Bacterial Recipients of Transducing DNA.- X. Comparative Biology.- A. Pl, the Plasmid.- B. P1, the Phage.- C. P1, the Pastiche.- D. Coda.- References.- 10 Bacteriophage T5 and Related Phages.- I. Introduction.- A. Phage Structure.- B. DNA Structure.- C. The Replication Cycle.- II. The Genetic and Physical Map.- A. Pre-Early Genes.- B. Early Genes.- C. Late Genes.- III. Phage Attachment and DNA Injection.- A. Adsorption to Host Cells.- B. Injection of Parental DNA.- IV. Transcription.- A. Temporal Pattern of Transcription.- B. Transcription Maps.- C. Promoters.- D. Coupled Transcription and Replication.- V. Effects on Host Metabolism.- A. Host DNA Degradation.- B. Synthesis of Host Macromolecules.- C. Inhibition of Host Enzymes.- VI. Nucleotide Metabolism.- A. Induction of New Enzymes.- B. 5’-Deoxyribonucleotidase.- C. Reduction of Ribonucleotides.- D. Synthesis of dTTP.- VII. DNA Replication.- References.- 11 Bacteriophage SPO1.- I. Introduction.- II. The Virion.- III. Other hmUra-Containing B. subtilis Phages.- IV. Maps of the SPO1 Genome.- V. Regulation of SPO1 Gene Action.- A. Sequential Modifications of RNA Polymerase.- B. Additional Complexities in the Regulation of Gene Action.- VI. Shutoff of Host Activities.- A. Introduction.- B. Host DNA Synthesis.- C. Host RNA and Protein Synthesis.- D. Shutoff Genes.- VII. SPO1 DNA Replication.- A. Gene Products Involved in Replication.- B. Structure of Replicating DNA.- C. Regulation of Replication.- D. Two Clusters of Replication Genes.- E. 2C Replication.- VIII. Late Functions.- A. Lysis.- B. Morphogenesis.- IX. Miscellaneous Functions.- A. Adsorption and Penetration.- B. Transfection.- C. Recombination.- X. Summary.- References.- 12 Viruses of Archaebacteria.- I. Introduction.- II. Viruses of Extremely Halophilic and Methanogenic Archaebacteria.- A. Origin.- B. Morphology.- C. DNA.- D. Proteins.- E. Ion Requirements.- F. Phage-Host Relationships.- G. Molecular Biology of Halobacteriophage ?H.- H. Evolution of Phages of Halobacteria and Methanogens.- I. Viruslike Particle from Methanococcus sp..- III. Viruses of Extremely Thermophilic, Sulfur-Dependent Archaebacteria.- A. Viruslike Particle of Pyrococcus woesei.- B. The Thermoproteus tenax Viruses TTV 1, 2, 3, and 4.- C. Viruses of Sulfolobales.- References.- 13 Temperate Bacteriophages of Bacillus subtilis.- I. Introduction.- II. Group I Phages: ?105, ?6, ?10, ?14.- A. General Description.- B. The Lytic Cycle.- C. ?105 “Repressor” Activity.- D. In vivo Specialized Transduction by ?105.- E. ?105 and ?14 as Cloning Vehicles.- III. Group II Phage: SPO2.- A. Relationship to ?105.- B. Characteristics of SPO2.- IV. Group III Phages: ?3T, SP?, pll, SPR, Z, IG1, IG3, IG4, and H2.- A. General Description.- B. Isolation.- C. Phage Immunity; Chromosome Attachment Sites.- D. Host Range and Serology.- E. Betacin Production.- F. Thymidylate Synthetase.- G. Other Mutations of Group III Phages.- H. DNA Methyltransferases.- I. Specialized Transduction.- J. Cloning in Group III Phages.- V. Group IV Phage: SP16.- VI. Group V Defective Phages: PBSX, PBSZ, et al..- References.