Dale_Molecular Genetics of Bacteria 4th ed
.pdfMolecular Genetics
of Bacteria
4th Edition
Molecular Genetics
of Bacteria
4th Edition
Jeremy W. Dale
Simon F. Park
University of Surrey, UK
Copyright # 2004 John Wiley & Sons Ltd,
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Library of Congress Cataloging-in-Publication Data
Dale, Jeremy.
Molecular genetics of bacteria / Jeremy W. Dale, Simon Park. — 4th ed. p.; cm.
Includes bibliographical references and index.
ISBN 0 470 85084 1 (Cloth) — ISBN 0 470 85085 X (Paper)
1. Bacterial genetics. 2. Microbial genetics. 3. Molecular genetics. 4. Genetic engineering. [DNLM: 1. Bacteria—genetics. 2. Genetic Engineering. 3. Molecular Biology. QW 51 D139m
2003] I. Park, Simon. II. Title. QH434 .D35 2003
572.80293—dc22
2003023103
British Library Cataloguing in Publication Data
A catalogue record for this book is available from the British Library
ISBN 0 470 85084 1 hardback 0 470 85085 X paperback
Typeset in 10.5/13pt Times by Kolam Information Services Pvt. Ltd, Pondicherry, India Printed and bound in Great Britain by TJ International Ltd, Padstow, Cornwall
This book is printed on acid-free paper responsibly manufactured from sustainable forestry in which at least two trees are planted for each one used for paper production.
Contents
1 Nucleic Acid Structure and Function |
1 |
||
1.1 |
Structure of nucleic acids |
1 |
|
|
1.1.1 |
DNA |
1 |
|
1.1.2 |
RNA |
3 |
|
1.1.3 |
Hydrophobic interactions |
3 |
|
1.1.4 Different forms of the double helix |
5 |
|
|
1.1.5 |
Supercoiling |
6 |
|
1.1.6 |
Denaturation and hybridization |
10 |
|
1.1.7 Orientation of nucleic acid strands |
11 |
|
1.2 |
Replication of DNA |
12 |
|
|
1.2.1 |
Unwinding and rewinding |
13 |
|
1.2.2 Fidelity of replication: proof-reading |
13 |
|
1.3 |
Chromosome replication and cell division |
14 |
|
1.4 |
DNA repair |
19 |
|
|
1.4.1 |
Mismatch repair |
19 |
|
1.4.2 |
Excision repair |
19 |
|
1.4.3 |
Recombination (post-replication) repair |
19 |
|
1.4.4 |
SOS repair |
20 |
1.5 |
Gene expression |
21 |
|
|
1.5.1 |
Transcription |
22 |
|
1.5.2 |
Translation |
26 |
|
1.5.3 |
Post-translational events |
32 |
1.6 |
Gene organization |
34 |
2 Mutation and Variation |
37 |
||
2.1 |
Variation and evolution |
37 |
|
|
2.1.1 |
Fluctuation test |
38 |
|
2.1.2 Directed mutation in bacteria? |
40 |
|
2.2 |
Types of mutations |
41 |
|
|
2.2.1 |
Point mutations |
41 |
|
2.2.2 |
Conditional mutants |
42 |
|
2.2.3 Variation due to larger scale DNA alterations |
44 |
|
|
2.2.4 Extrachromosomal agents and horizontal gene transfer |
44 |
|
2.3 |
Phenotypes |
45 |
Molecular Genetics of Bacteria, 4th Edition by Jeremy Dale and Simon F. |
Park |
# 2004 John Wiley & Sons, Ltd ISBN 0 470 85084 1 (cased) ISBN 0 |
470 85085 X (pbk) |
vi |
|
CONTENTS |
|
2.4 |
Restoration of phenotype |
47 |
|
|
2.4.1 |
Reversion and suppression |
47 |
|
2.4.2 |
Complementation |
49 |
2.5 |
Recombination |
49 |
|
2.6 |
Mechanisms of mutation |
50 |
|
|
2.6.1 |
Spontaneous mutation |
50 |
|
2.6.2 |
Chemical mutagens |
52 |
|
2.6.3 |
Ultraviolet irradiation |
54 |
2.7 |
Isolation and identification of mutants |
58 |
|
|
2.7.1 |
Mutation and selection |
58 |
|
2.7.2 |
Replica plating |
59 |
|
2.7.3 |
Penicillin enrichment |
61 |
|
2.7.4 Isolation of other mutants |
62 |
|
|
2.7.5 |
Molecular methods |
62 |
3 Regulation of Gene Expression |
67 |
||
3.1 |
Gene copy number |
69 |
|
3.2 |
Transcriptional control |
70 |
|
|
3.2.1 |
Promoters |
70 |
|
3.2.2 Terminators, attenuators and anti-terminators |
77 |
|
|
3.2.3 Induction and repression: regulatory proteins |
79 |
|
|
3.2.4 |
Attenuation: trp operon |
87 |
|
3.2.5 |
Two-component regulatory systems |
92 |
|
3.2.6 |
Global regulatory systems |
94 |
|
3.2.7 Feast or famine and the RpoS regulon |
95 |
|
|
3.2.8 |
Quorum sensing |
95 |
3.3 |
Translational control |
99 |
|
|
3.3.1 |
Ribosome binding |
99 |
|
3.3.2 |
Codon usage |
101 |
|
3.3.3 |
Stringent response |
101 |
|
3.3.4 |
Regulatory RNA |
102 |
|
3.3.5 |
Phase variation |
102 |
4 Genetics of Bacteriophages |
103 |
||
4.1 |
Single-stranded DNA bacteriophages |
106 |
|
|
4.1.1 |
fX174 |
106 |
|
4.1.2 |
M13 |
109 |
4.2 |
RNA-containing phages: MS2 |
109 |
|
4.3 |
Double-stranded DNA phages |
110 |
|
|
4.3.1 |
Bacteriophage T4 |
110 |
|
4.3.2 |
Bacteriophage lambda |
113 |
|
4.3.3 Lytic and lysogenic regulation of bacteriophage lambda |
118 |
|
4.4 |
Restriction and modification |
125 |
|
4.5 |
Complementation and recombination |
128 |
|
4.6 |
Why are bacteriophages important? |
130 |
|
|
4.6.1 |
Phage typing |
131 |
|
|
|
CONTENTS |
vii |
|
|
4.6.2 |
Phage therapy |
131 |
|
|
4.6.3 |
Phage display |
132 |
|
|
4.6.4 Bacterial virulence and phage conversion |
133 |
|
5 |
Plasmids |
|
137 |
|
|
5.1 |
Some bacterial characteristics are determined by plasmids |
137 |
|
|
|
5.1.1 |
Antibiotic resistance |
137 |
|
|
5.1.2 |
Colicins and bacteriocins |
138 |
|
|
5.1.3 |
Virulence determinants |
138 |
|
|
5.1.4 Plasmids in plant-associated bacteria |
139 |
|
|
|
5.1.5 |
Metabolic activities |
139 |
|
5.2 |
Molecular properties of plasmids |
141 |
|
|
|
5.2.1 Plasmid replication and control |
143 |
|
|
5.3 |
Plasmid stability |
154 |
|
|
|
5.3.1 |
Plasmid integrity |
155 |
|
|
5.3.2 |
Partitioning |
157 |
|
|
5.3.3 |
Differential growth rate |
160 |
|
5.4 |
Methods for studying plasmids |
161 |
|
|
|
5.4.1 Associating a plasmid with a phenotype |
161 |
|
|
|
5.4.2 |
Classification of plasmids |
163 |
6 |
Gene Transfer |
165 |
||
|
6.1 |
Transformation |
166 |
|
|
6.2 |
Conjugation |
167 |
|
|
|
6.2.1 |
Mechanism of conjugation |
168 |
|
|
6.2.2 |
The F plasmid |
173 |
|
|
6.2.3 Conjugation in other bacteria |
174 |
|
|
6.3 |
Transduction |
178 |
|
|
|
6.3.1 |
Specialized transduction |
180 |
|
6.4 |
Recombination |
181 |
|
|
|
6.4.1 |
General (homologous) recombination |
181 |
|
|
6.4.2 Site-specific and non-homologous (illegitimate) recombination |
186 |
|
|
6.5 |
Mosaic genes and chromosome plasticity |
187 |
|
7 Genomic Plasticity: Movable Genes and Phase Variation |
189 |
|||
|
7.1 |
Insertion sequences |
189 |
|
|
|
7.1.1 Structure of insertion sequences |
189 |
|
|
|
7.1.2 Occurrence of insertion sequences |
190 |
|
|
7.2 |
Transposons |
192 |
|
|
|
7.2.1 |
Structure of transposons |
194 |
|
|
7.2.2 |
Integrons |
196 |
|
7.3 |
Mechanisms of transposition |
197 |
|
|
|
7.3.1 |
Replicative transposition |
197 |
|
|
7.3.2 |
Non-replicative (conservative) transposition |
200 |
|
|
7.3.3 |
Regulation of transposition |
201 |
|
|
7.3.4 Activation of genes by transposable elements |
203 |
viii |
|
CONTENTS |
|
|
7.3.5 Mu: a transposable bacteriophage |
204 |
|
|
7.3.6 Conjugative transposons and other transposable elements |
205 |
|
7.4 |
Phase variation |
205 |
|
|
7.4.1 Variation mediated by simple DNA inversion. |
207 |
|
|
7.4.2 Variation mediated by nested DNA inversion |
208 |
|
|
7.4.3 Antigenic variation in the gonococcus |
208 |
|
|
7.4.4 Phase variation by slipped strand mispairing |
211 |
|
|
7.4.5 Phase variation mediated by differential DNA methylation |
214 |
|
8 Genetic Modification: Exploiting the Potential of Bacteria |
215 |
||
8.1 |
Strain development |
215 |
|
|
8.1.1 |
Generation of variation |
215 |
|
8.1.2 Selection of desired variants |
216 |
|
8.2 |
Overproduction of primary metabolites |
216 |
|
|
8.2.1 |
Simple pathways |
217 |
|
8.2.2 |
Branched pathways |
218 |
8.3 |
Overproduction of secondary metabolites |
220 |
|
8.4 |
Gene cloning |
221 |
|
|
8.4.1 Cutting and joining DNA |
222 |
|
|
8.4.2 |
Plasmid vectors |
223 |
|
8.4.3 |
Transformation |
225 |
|
8.4.4 |
Bacteriophage lambda vectors |
225 |
|
8.4.5 |
Cloning larger fragments |
227 |
|
8.4.6 |
Bacteriophage M13 vectors |
229 |
8.5 |
Gene libraries |
229 |
|
|
8.5.1 Construction of genomic libraries |
229 |
|
|
8.5.2 Screening a gene library |
231 |
|
|
8.5.3 Construction of a cDNA library |
233 |
|
8.6 |
Products from cloned genes |
234 |
|
|
8.6.1 |
Expression vectors |
234 |
|
8.6.2 |
Making new genes |
236 |
|
8.6.3 |
Other bacterial hosts |
239 |
|
8.6.4 |
Novel vaccines |
241 |
8.7 |
Other uses of gene technology |
242 |
|
9 Genetic Methods for Investigating Bacteria |
245 |
||
9.1 |
Metabolic pathways |
245 |
|
|
9.1.1 |
Complementation |
246 |
|
9.1.2 |
Cross-feeding |
246 |
9.2 |
Microbial physiology |
247 |
|
|
9.2.1 |
Reporter genes |
249 |
|
9.2.2 |
Lysogeny |
250 |
|
9.2.3 |
Cell division |
251 |
|
9.2.4 |
Motility and chemotaxis |
252 |
|
9.2.5 |
Cell differentiation |
253 |
|
|
CONTENTS |
ix |
9.3 |
Bacterial virulence |
257 |
|
|
9.3.1 Wide range mechanisms of bacterial pathogenesis |
257 |
|
|
9.3.2 Detection of virulence genes |
259 |
|
9.4 |
Specific mutagenesis |
262 |
|
|
9.4.1 |
Gene replacement |
262 |
|
9.4.2 |
Antisense RNA |
264 |
9.5 Taxonomy, evolution and epidemiology |
264 |
||
|
9.5.1 |
Molecular taxonomy |
264 |
|
9.5.2 Diagnostic use of PCR |
267 |
|
|
9.5.3 |
Molecular epidemiology |
267 |
10 Gene Mapping to Genomics |
273 |
||
10.1 |
Gene mapping |
273 |
|
|
10.1.1 |
Conjugational analysis |
273 |
|
10.1.2 |
Co-transformation and co-transduction |
276 |
|
10.1.3 Molecular techniques for gene mapping |
277 |
|
10.2 |
Gene sequencing |
279 |
|
|
10.2.1 |
DNA sequence determination |
281 |
|
10.2.2 |
Genome sequencing |
282 |
|
10.2.3 |
Comparative genomics |
285 |
|
10.2.4 |
Bioinformatics |
288 |
10.3 Physical and genetic maps |
289 |
||
|
10.3.1 |
Deletions and insertions |
290 |
|
10.3.2 |
Transposon mutagenesis |
290 |
|
10.3.3 |
Gene replacement |
292 |
|
10.3.4 |
Site-directed mutagenesis |
292 |
10.4 Analysis of gene expression |
292 |
||
|
10.4.1 |
Transcriptional analysis |
293 |
|
10.4.2 |
Translational analysis |
296 |
|
10.4.3 Systematic analysis of gene function |
300 |
|
10.5 |
Conclusion |
300 |
|
Appendix A |
Further Reading |
301 |
|
Appendix B |
Abbreviations |
305 |
|
Appendix C |
Glossary |
309 |
|
Appendix D |
Enzymes |
323 |
|
Appendix E |
Genes |
327 |
|
Appendix F Standard Genetic Code |
331 |
||
Appendix G |
Bacterial Species |
333 |
Index |
337 |