The Bacteriophages (The Viruses) de Richard Calendar

The Bacteriophages: Volume 1: The Viruses

Richard Calendar

en Limba Engleză Paperback – 28 mar 2012

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.

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Cuprins

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.- III. The Nature of Phage Assembly Pathways.- IV. Current Problems in Phage Assembly and Structure.- V. Genes and Morphogenesis.- 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.- 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.- III. Ecology of Coliphages.- IV. The Infection Process.- V. Virion Structure.- VI. Replication of Phage RNA.- VII. Origin and Evolution of the 6S RNA Families.- VIII. Gene Expression.- IX. Sequence Comparison between Group I, II, and III Phages.- 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.- 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.- V.Transcription of ?29 DNA.- VI. In Vivo Replication of ?29, Cp-1, and PRD1 DNAs.- VII. In Vitro Replication of ?29, Cp-1, and PRD1 DNAs: Initiation Reaction.- VIII. Purification and Characterization of the ?29 Proteins p2, p3, p5, and p6, Involved in DNA Replication.- 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.- IV. Life Cycle.- 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.- VI. Miscellaneous.- VII. Summary.- References.- 8 The T7 Group.- I. Introduction.- II. The T7 Prototype.- III. The T7 Relatives.- IV. Further Comparisons and General Remarks.- References.- 9 Bacteriophage P1.- I. Introduction.- II. Physical and Genetic Structure.- III. Adsorption and Injection.- IV. Cyclization.- V. Restriction-Modification.- VI. Lysogenization versus Lytic Growth. Immunity and Virulence.- VII. The Prophage State.- VIII. Vegetative Growth.- IX. Transduction.- X. Comparative Biology.- References.- 10 Bacteriophage T5 and Related Phages.- I. Introduction.- II. The Genetic and Physical Map.- III. Phage Attachment and DNA Injection.- IV. Transcription.- V. Effects on Host Metabolism.- VI. Nucleotide Metabolism.- VII. DNAReplication.- 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.- VI. Shutoff of Host Activities.- VII. SPO1 DNA Replication.- VIII. Late Functions.- IX. Miscellaneous Functions.- X. Summary.- References.- 12 Viruses of Archaebacteria.- I. Introduction.- II. Viruses of Extremely Halophilic and Methanogenic Archaebacteria.- I. Viruslike Particle from Methanococcus sp..- III. Viruses of Extremely Thermophilic, Sulfur-Dependent Archaebacteria.- References.- 13 Temperate Bacteriophages of Bacillus subtilis.- I. Introduction.- II. Group I Phages: ?105, ?6, ?10, ?14.- III. Group II Phage: SPO2.- IV. Group III Phages: ?3T, SP?, pll, SPR, Z, IG1, IG3, IG4, and H2.- V. Group IV Phage: SP16.- VI. Group V Defective Phages: PBSX, PBSZ, et al..- References.