Bacteriophages. Biology and Applns

Foreword......Page 6
Editors......Page 10
Acknowledgments......Page 12
Contributors......Page 14
Contents......Page 16
Introduction......Page 18
REFERENCES......Page 21
2.1. introduction......Page 22
2.2. Discovery of Bacteriophages......Page 23
2.3. Early Debate Regarding The Nature Of Bacteriophages......Page 24
2.4. First Practical Applications: Veterinary And Medicine......Page 26
2.5.2. Max Delbrück and the Development of Molecular Genetics......Page 29
2.5.3. Role of the Phage Community......Page 32
2.5.4. The Nature of the Gene and of Mutations......Page 33
References......Page 40
Basic Phage Biology......Page 46
3.1.1. The Nature of Bacteriophages......Page 47
3.1.2. Antigenic Properties of Phages......Page 49
3.1.3. Susceptibility of Phages to Chemical and Physical Agents......Page 50
3.2.2. Peptidoglycan......Page 55
3.2.4. Cellular Energetics......Page 57
3.3. General Overview of the Infection Process......Page 58
3.3.1. Adsorption......Page 59
3.3.3. Transition from Host to Phage-Directed Metabolism......Page 62
3.4. Lysogeny and its consequences......Page 63
3.6.1. Phages of Gram-Negative Bacteria......Page 66
3.6.2. Phages of Gram-Positive Bacteria......Page 70
3.6.2.1. Phages of Streptococci, Staphylococci, Listeria, and the Bacilli......Page 71
3.6.2.2. Phages of Lactic Acid Bacteria: The Dairy Phages......Page 72
3.6.4. Cyanophages......Page 74
3.7.1. RNA Phages......Page 75
3.7.2. Small DNA Phages......Page 76
3.7.3. Lipid-Containing Phages......Page 77
3.7.4. Phages of Mycoplasmas......Page 78
3.8. Archaephages......Page 79
References......Page 80
Ketevan Gachechiladze......Page 51
Bacteriophage Classification......Page 84
4.1.1. The Early Stage......Page 85
4.1.3. Purpose of Phage Classification......Page 86
4.2.1. Tailed Phages (Order Caudovirales)......Page 87
4.2.2.1. Polyhedral DNA Phages......Page 90
4.2.2.3. Filamentous Phages......Page 91
4.2.2.4. Pleomorphic Phages......Page 96
4.3.1. New Taxa and New Techniques......Page 98
4.3.2. The l-P22 Controversy......Page 99
4.3.3.2. Modular Classification......Page 100
4.4. LINKS BETWEEN PHAGES AND OTHER VIRUSES......Page 102
REFERENCES......Page 103
Genomics and Evolution of Tailed Phages......Page 108
5.1. INTRODUCTION......Page 109
5.2.2. Lambdoid Coliphages......Page 112
5.2.3.1. Overview......Page 113
5.2.3.2. Comparative Genomics of S. thermophilus Phages......Page 114
5.2.3.3. Genetic Relatedness among Sfi21-Like Siphoviridae......Page 117
5.2.4. l Supergroup of Siphoviridae: Synthesis of Data from Dairy and Lambdoid Phages......Page 118
5.2.5.2. P2 Phage Group......Page 120
5.2.5.5. Large Temperate Phages......Page 121
5.2.6. Prophage Genomics and Phage Evolution......Page 123
5.3.2.1. The T7 Group......Page 127
5.3.3.2. P. aeruginosa Bacteriophage FKZ......Page 128
5.3.3.3. Lactobacillus Phage LP65......Page 129
5.3.3.5. B. subtilis Phage SP01......Page 130
5.3.3.6. The T4-Like Phages......Page 131
5.4. EARLY EVOLUTION OF PHAGE METABOLIC ENZYMES......Page 134
5.5. Summary And Outlook......Page 137
REFERENCES......Page 139
Phage Ecology......Page 146
6.1. Introduction......Page 147
6.2.1. Phage Numbers in the Natural World......Page 148
6.2.2. Dynamic Phage-Host Relationships......Page 149
6.2.3. Co-Evolution of Phages and Their Host Bacteria......Page 152
6.2.4. Effects of Host Physiology and Nutritional Status......Page 153
6.2.5. Biofilms......Page 154
6.3.1. Marine Phage Impacts on the Food Web......Page 156
6.3.2.1. Cyanophages......Page 158
6.3.3. Marine Phage Host Specificity and Horizontal Gene Transfer......Page 159
6.4. Soil and Plant-associated Phages......Page 161
6.5.1. Introduction......Page 162
6.5.2. Enteric Phages......Page 163
6.5.3. Other Phage Sites of Interest: Oral Cavity and Vagina......Page 166
6.6.1. Dairy Industry......Page 167
6.7. Outlook......Page 172
References......Page 173
Molecular Mechanisms of Phage Infection......Page 182
7.1. INTRODUCTION......Page 183
7.2. HOST RECOGNITION AND ADSORPTION OF TAILED PHAGES......Page 184
7.2.1. Phage Recognition of Gram-Negative Bacteria......Page 185
7.2.2. Phage Recognition of Gram-Positive Bacteria......Page 189
7.2.3. Host-Range Variation......Page 190
7.2.3.2. Adhesin Restructuring through Cross-Genus Recombination......Page 191
7.2.4. Summary......Page 193
7.3.2. Podovirus T7......Page 194
7.3.3. Myovirus T4......Page 196
7.3.4. Three Siphoviridae That All Use the FhuA Receptor but Have Very Different Mechanisms......Page 197
7.3.5. Phages PRD1 and PM2......Page 198
7.4.1. The Process of Replication......Page 199
7.4.2. DNA Repair, Recombination, and Mutagenesis......Page 202
7.4.3.2. Complex Phage-Encoded Replication, Recombination, and Repair Machinery: Phage T4......Page 203
7.4.3.4. Protein-Primed Replication Initiation: Phage f 29......Page 206
7.5.1. Overview......Page 207
7.5.2.1. Host Polymerase Used Early, Phage Enzyme Late: E. coli Podovirus T7......Page 210
7.5.2.2. A Capsid-Borne RNA Polymerase, and More: E. coli Podovirus N4......Page 211
7.5.2.3. Host Polymerase throughout, with Modifications: l, SPO1, and T4......Page 212
7.6.1. Structure and Efficiency of Ribosome Binding Sites......Page 214
7.6.2. Intron Ribozymes......Page 215
7.6.3. Translational Bypassing......Page 216
7.6.4. RNA-Based Regulatory Systems: Aptamers and SELEX......Page 217
7.7. MORPHOGENESIS AND DNA PACKAGING......Page 218
7.7.1. Head Formation......Page 219
7.7.2. DNA Packaging......Page 220
7.7.3. Tail Morphogenesis......Page 221
7.8.1. Overview......Page 223
7.8.2. The Single-Protein Lysis Systems of the Small Phages......Page 224
7.8.3. Holins, Endolysins, and Lysis Timing......Page 225
7.8.4. T-Even Phages: Lysis and Lysis Inhibition......Page 228
References......Page 230
Contents......Page 240
8.1. INTRODUCTION......Page 241
8.2.1. Extracellular Toxins......Page 244
8.2.1.1. Streptococcus and Staphylococcus......Page 245
8.2.1.2. E. coli......Page 246
8.2.1.3. V. cholerae......Page 248
8.2.2. Proteins Involved in Bacterial Attachment/Colonization......Page 251
8.2.3. Proteins Required for Host Immune Avoidance......Page 253
8.2.4. Proteins Essential for Bacterial Invasion of Host Cells......Page 255
8.2.6. Putative Virulence Proteins......Page 258
8.3.1. Imprecise Prophage Excision......Page 260
8.3.3. Integral Components of the Bacteriophage Genome......Page 261
8.4.1. Indirect Involvement of Bacteriophages......Page 262
8.4.2. Direct Involvement of Bacteriophages......Page 263
8.5. ROLES OF PHAGE-PHAGE INTERACTIONS IN BACTERIAL VIRULENCE......Page 264
8.5.1.1. V. cholerae CTXf Supplies Morphogenesis Genes for RS1f......Page 265
8.5.1.2. S. aureus f 80 Generalized Transduction of the tst Element......Page 266
8.5.1.4. V. cholerae CP-T1 Generalized Transduction of CTXf......Page 267
8.5.2. Helper Phage Source of Bacteriophage Host Receptor......Page 269
8.5.3.3. Interactions of S. enterica Gifsy-1 and Gifsy-2 Phages......Page 270
8.6. BACTERIOPHAGES AND PATHOGENICITY ISLANDS (PAIS)......Page 271
8.7. CONCLUSIONS......Page 274
REFERENCES......Page 275
9.1. Introduction......Page 284
9.2.1. Luciferase Reporter Phage (LRP)......Page 285
9.2.2. Other Reporter Phage......Page 289
9.3. Phage Display......Page 290
9.4. Dual Phage......Page 292
9.5. Phage Amplification Assays......Page 294
9.6. Detection via Phage-mediated cell lysis......Page 296
9.7. Use of phage and phage products as binding reagents......Page 297
References......Page 298
10.1. INTRODUCTION......Page 302
10.2.1. Overview......Page 304
10.2.2. Phage Detection......Page 305
10.2.3. Sources of Phage Contamination......Page 306
10.3.1. Controlling Phage Proliferation......Page 307
10.3.3. Development/Selection of Bacteriophage-Insensitive Bacterial Mutants......Page 308
10.3.4. Genetically Engineering Phage-Resistant Bacterial Strains......Page 310
Acknowledgments......Page 311
References......Page 312
11.1. INTRODUCTION......Page 314
11.2.1. The Ff Class of Bacteriophages......Page 315
11.2.3. Helper Phages......Page 316
11.3.1. Lambda Cloning Vectors......Page 318
11.3.2. Selection of Recombinant Genomes......Page 320
11.3.3. Lambda Vector System Applications......Page 321
11.4.1. P1 Cloning System and Methods......Page 322
11.4.2. P1-Based Artificial Chromosomes......Page 324
11.4.3. P1 Phagemid System for Delivery of DNA to Gram-Negative Bacteria......Page 325
11.5. PHAGES AS LETHAL AGENT DELIVERY VEHICLES......Page 326
11.6. PHAGE VECTORS FOR TARGETED GENE DELIVERY TO MAMMALIAN CELLS......Page 328
REFERENCES......Page 330
12.1. INTRODUCTION......Page 338
12.2.1. Enzyme Structure......Page 339
12.2.2. Mode of Action......Page 341
12.2.4. Synergistic Effects......Page 342
12.3.2. Control of Sepsis and Bacteremia......Page 344
12.3.3. Killing Biowarfare Bacteria......Page 345
12.4.1. Immune Response to the Enzymes......Page 347
12.4.2. Bacterial Resistance to the Enzymes......Page 348
12.5. CONCLUDING REMARKS......Page 349
REFERENCES......Page 350
Phage Therapy in Animals and Agribusiness......Page 352
13.2.1. The First Known Use of Phages to Treat Bacterial Diseases of Animals......Page 353
13.2.2. Early Studies Examining the Efficacy of Bacteriophages for Preventing and Treating Animal Infections......Page 354
13.2.3.1. Salmonella Infections......Page 355
13.2.3.2. Escherichia coli Infections......Page 356
13.2.3.3. Enterococcus faecium Infections......Page 360
13.2.3.4. Vibrio cholerae Infections......Page 361
13.2.3.5. Clostridium difficile Infections......Page 363
13.2.3.6. Acinetobacter baumanii, Pseudomonas aeruginosa, and Staphylococcus aureus Infections......Page 364
13.2.4. Bacteriophages As a Potential Tool for Reducing Antibiotic Usage in Agribusiness......Page 365
13.3.1. Plant Infections......Page 367
13.3.2. Infections of Aquacultured Fish......Page 369
13.4.1. Using Phages to Produce Bacterial Vaccines......Page 370
13.4.2. Using Phage-Generated Bacterial Lysates to Prevent and Treat Animal Infections......Page 371
13.4.3. Phages and “Bacterial Ghost” Vaccines......Page 372
13.4.5. Using Phage-Encoded Enzymes As Antibacterial Agents......Page 375
13.5.1. General Considerations......Page 376
13.5.2. Using Phages to Reduce Contamination of Livestock with Foodborne Pathogens......Page 377
13.5.3. Using Phages to Reduce Contamination of Raw Foods with Foodborne Pathogens......Page 378
13.5.4. Using Phages to Reduce Contamination of Ready-to-Eat Foods with Foodborne Pathogens......Page 380
13.5.5. Prevalence of Bacteriophages in Foods and Other Parts of the Environment......Page 382
13.5.6. Food Spoilage and Bacteriophages......Page 385
REFERENCES......Page 388
Bacteriophage Therapy in Humans......Page 398
14.1. INTRODUCTION......Page 399
14.2.1. First Therapeutic Applications......Page 400
14.2.2. The “Bacteriophage Inquiry”......Page 401
14.2.3. Phage Therapy in Europe, Canada, and the United States During the 1920s to 1940s......Page 405
14.3.1. Credibility Problems Caused by a Lack of Quality Control and of Properly Controlled Studies......Page 410
14.3.2. Conflicting Reports about the Efficacy of Phage Therapy......Page 412
14.3.3. Development of Antimicrobials: Broad-Spectrum Antibiotics vs. Narrow-Spectrum Phages......Page 413
14.4.1. Phage Therapy in Western Europe, Africa, and the United States......Page 414
14.4.2. Phage Therapy in the Former Soviet Union......Page 416
14.4.3. Phage Therapy in Georgia......Page 423
14.4.4. Phage Therapy Centers in Russia......Page 428
14.4.5. Phage Therapy in Poland......Page 429
14.5.1. Mode of Therapeutic Action of Phages......Page 430
14.5.2.1. Phage Movement between Biological Compartments......Page 431
14.5.2.2. Nonspecific Mechanisms That Clear Phages from the Bloodstream......Page 433
14.5.2.3. The Development of Phage-Neutralizing Antibodies......Page 434
14.5.2.4. Emergence of Bacterial Strains Resistant to Particular Phages......Page 436
14.5.3. Safety Considerations......Page 437
14.5.4. Comparison of Phages and Antibiotics: Advantages and Limitations of Phage-Based Therapies......Page 440
REFERENCES......Page 443
Appendix: Working with Bacteriophages: Common Techniques and Methodological Approaches......Page 454
A.2.1. Equipment......Page 456
A.2.3. Phage Stocks......Page 457
A.2.4.2. Preparing Bacterial Cultures for Phage Infection......Page 458
A.2.4.3. Determination of Bacterial Titers......Page 459
A.2.5.1. General Considerations......Page 460
A.2.5.2. Solid Media......Page 462
A.2.5.3. Media for Anaerobic Growth......Page 464
A.2.5.4. Recipes for Commonly Used Bacteriologic Media and Reagents......Page 465
A.3.1. General Considerations......Page 466
A.3.3.1. Concentration by Ultrafiltration......Page 467
A.3.4. Enrichment of Phages in the Source Material......Page 468
A.3.4.2. Multiple Enrichment......Page 469
A.3.6. Isolation of Phages from Bacteria That Do Not Form Lawns on Solid Media......Page 470
A.4.1. Plaque Assays......Page 472
A.4.1.1. Serial Dilutions......Page 473
A.4.1.2. Agar Overlay Methods......Page 474
A.4.1.3. Killer Titer......Page 477
A.4.2. Most Probable Number (MPN) Assays......Page 478
A.5.1. General Considerations......Page 479
A.5.2.1. Standard Liquid Culture......Page 480
A.5.2.2. Plate Lysate......Page 481
A.5.4.1. Concentration by Centrifugation......Page 483
A.5.4.3. Purification by Centrifugation in CsCl Gradients......Page 484
A.5.5. Storage of Phage......Page 487
A.6.1.1. Isolation of Phage DNA......Page 488
A.6.1.2. Digestion of Phage DNA with Restriction Endonucleases......Page 489
A.6.1.3. Agarose and Polyacrylamide Gel Electrophoresis of Phage DNA......Page 490
Procedure......Page 491
A.6.1.4. Pulsed Field Gel Electrophoresis of Large Phage Genomes......Page 492
A.6.2.1. Analysis of the Phage Infection Process......Page 493
Materials......Page 495
Procedure......Page 496
Processing of Samples......Page 497
A.6.2.2. Single Step Growth......Page 498
A.6.3. Radiolabeling and Analysis of Phage Proteins by Polyacrylamide Gel Electrophoresis......Page 499
A.6.3.1. Radiolabeling of Phage Proteins......Page 500
Materials......Page 501
Procedure......Page 502
A.6.3.2. SDS-PAGE of Phage Proteins......Page 504
Preparation......Page 505
Dos and Do nots......Page 506
REFERENCES......Page 507
Index......Page 512