Molecular Genetics of Bacteria

Molecular Genetics of Bacteria 4th Edition......Page 4
Contents......Page 8
Preface......Page 14
1.1.1 DNA......Page 16
1.1.3 Hydrophobic interactions......Page 18
1.1.4 Different forms of the double helix......Page 20
1.1.5 Supercoiling......Page 21
1.1.6 Denaturation and hybridization......Page 25
1.1.7 Orientation of nucleic acid strands......Page 26
1.2 Replication of DNA......Page 27
1.2.2 Fidelity of replication: proof-reading......Page 28
1.3 Chromosome replication and cell division......Page 29
1.4.3 Recombination (post-replication) repair......Page 34
1.4.4 SOS repair......Page 35
1.5 Gene expression......Page 36
1.5.1 Transcription......Page 37
1.5.2 Translation......Page 41
1.5.3 Post-translational events......Page 47
1.6 Gene organization......Page 49
2.1 Variation and evolution......Page 52
2.1.1 Fluctuation test......Page 53
2.1.2 Directed mutation in bacteria?......Page 55
2.2.1 Point mutations......Page 56
2.2.2 Conditional mutants......Page 57
2.2.4 Extrachromosomal agents and horizontal gene transfer......Page 59
2.3 Phenotypes......Page 60
2.4.1 Reversion and suppression......Page 62
2.5 Recombination......Page 64
2.6.1 Spontaneous mutation......Page 65
2.6.2 Chemical mutagens......Page 67
2.6.3 Ultraviolet irradiation......Page 69
2.7.1 Mutation and selection......Page 73
2.7.2 Replica plating......Page 74
2.7.3 Penicillin enrichment......Page 76
2.7.5 Molecular methods......Page 77
3 Regulation of Gene Expression......Page 82
3.1 Gene copy number......Page 84
3.2.1 Promoters......Page 85
3.2.2 Terminators, attenuators and anti-terminators......Page 92
3.2.3 Induction and repression: regulatory proteins......Page 94
3.2.4 Attenuation: trp operon......Page 102
3.2.5 Two-component regulatory systems......Page 107
3.2.6 Global regulatory systems......Page 109
3.2.8 Quorum sensing......Page 110
3.3.1 Ribosome binding......Page 114
3.3.3 Stringent response......Page 116
3.3.5 Phase variation......Page 117
4 Genetics of Bacteriophages......Page 118
4.1.1 fX174......Page 121
4.2 RNA-containing phages: MS2......Page 124
4.3.1 Bacteriophage T4......Page 125
4.3.2 Bacteriophage lambda......Page 128
4.3.3 Lytic and lysogenic regulation of bacteriophage lambda......Page 133
4.4 Restriction and modification......Page 140
4.5 Complementation and recombination......Page 143
4.6 Why are bacteriophages important?......Page 145
4.6.2 Phage therapy......Page 146
4.6.3 Phage display......Page 147
4.6.4 Bacterial virulence and phage conversion......Page 148
5.1.1 Antibiotic resistance......Page 152
5.1.3 Virulence determinants......Page 153
5.1.5 Metabolic activities......Page 154
5.2 Molecular properties of plasmids......Page 156
5.2.1 Plasmid replication and control......Page 158
5.3 Plasmid stability......Page 169
5.3.1 Plasmid integrity......Page 170
5.3.2 Partitioning......Page 172
5.3.3 Differential growth rate......Page 175
5.4.1 Associating a plasmid with a phenotype......Page 176
5.4.2 Classification of plasmids......Page 178
6 Gene Transfer......Page 180
6.1 Transformation......Page 181
6.2 Conjugation......Page 182
6.2.1 Mechanism of conjugation......Page 183
6.2.2 The F plasmid......Page 188
6.2.3 Conjugation in other bacteria......Page 189
6.3 Transduction......Page 193
6.3.1 Specialized transduction......Page 195
6.4.1 General (homologous) recombination......Page 196
6.4.2 Site-specific and non-homologous (illegitimate) recombination......Page 201
6.5 Mosaic genes and chromosome plasticity......Page 202
7.1.1 Structure of insertion sequences......Page 204
7.1.2 Occurrence of insertion sequences......Page 205
7.2 Transposons......Page 207
7.2.1 Structure of transposons......Page 209
7.2.2 Integrons......Page 211
7.3.1 Replicative transposition......Page 212
7.3.2 Non-replicative (conservative) transposition......Page 215
7.3.3 Regulation of transposition......Page 216
7.3.4 Activation of genes by transposable elements......Page 218
7.3.5 Mu: a transposable bacteriophage......Page 219
7.4 Phase variation......Page 220
7.4.1 Variation mediated by simple DNA inversion.......Page 222
7.4.3 Antigenic variation in the gonococcus......Page 223
7.4.4 Phase variation by slipped strand mispairing......Page 226
7.4.5 Phase variation mediated by differential DNA methylation......Page 229
8.1.1 Generation of variation......Page 230
8.2 Overproduction of primary metabolites......Page 231
8.2.1 Simple pathways......Page 232
8.2.2 Branched pathways......Page 233
8.3 Overproduction of secondary metabolites......Page 235
8.4 Gene cloning......Page 236
8.4.1 Cutting and joining DNA......Page 237
8.4.2 Plasmid vectors......Page 238
8.4.4 Bacteriophage lambda vectors......Page 240
8.4.5 Cloning larger fragments......Page 242
8.5.1 Construction of genomic libraries......Page 244
8.5.2 Screening a gene library......Page 246
8.5.3 Construction of a cDNA library......Page 248
8.6.1 Expression vectors......Page 249
8.6.2 Making new genes......Page 251
8.6.3 Other bacterial hosts......Page 254
8.6.4 Novel vaccines......Page 256
8.7 Other uses of gene technology......Page 257
9.1 Metabolic pathways......Page 260
9.1.2 Cross-feeding......Page 261
9.2 Microbial physiology......Page 262
9.2.1 Reporter genes......Page 264
9.2.2 Lysogeny......Page 265
9.2.3 Cell division......Page 266
9.2.4 Motility and chemotaxis......Page 267
9.2.5 Cell differentiation......Page 268
9.3.1 Wide range mechanisms of bacterial pathogenesis......Page 272
9.3.2 Detection of virulence genes......Page 274
9.4.1 Gene replacement......Page 277
9.5.1 Molecular taxonomy......Page 279
9.5.3 Molecular epidemiology......Page 282
10.1.1 Conjugational analysis......Page 288
10.1.2 Co-transformation and co-transduction......Page 291
10.1.3 Molecular techniques for gene mapping......Page 292
10.2 Gene sequencing......Page 294
10.2.1 DNA sequence determination......Page 296
10.2.2 Genome sequencing......Page 297
10.2.3 Comparative genomics......Page 300
10.2.4 Bioinformatics......Page 303
10.3 Physical and genetic maps......Page 304
10.3.2 Transposon mutagenesis......Page 305
10.4 Analysis of gene expression......Page 307
10.4.1 Transcriptional analysis......Page 308
10.4.2 Translational analysis......Page 311
10.5 Conclusion......Page 315
Appendix A Further Reading......Page 316
Appendix B Abbreviations......Page 320
Appendix C Glossary......Page 324
Appendix D Enzymes......Page 338
Appendix E Genes......Page 342
Appendix F Standard Genetic Code......Page 346
Appendix G Bacterial Species......Page 348
Index......Page 352