2.20 Integrative and Conjugative Elements (ICE) 91
2.21 Integrons 93
2.22 Introns 96
2.23 Horizontal Gene Transfer 96
2.24 Distinguishing Self from Non-self 99
2.25 Distinguishing Self and Non-self: CRISPR-Cas Systems 99
2.26 Distinguishing Self and Non-self: Argonaute Proteins 102
2.27 Distinguishing Self and Non-self: Restriction Enzymes/Methylases 103
2.28 Distinguishing Self and Non-self: BREX 103
2.29 Self-sacrifice and Other Behaviours Involving Toxin—antitoxin Systems 104
2.30 Conservative Forces: DNA Repair and Homologous Recombination 104
2.31 The RecA Protein 105
2.32 RecA, LexA, and the SOS Response 106
2.33 Holliday Junction Resolution 108
2.34 Mismatch Repair 109
2.35 Non-homologous End Joining 110
3 Gene Control: Transcription and Its Regulation 113
3.1 Transcription: More Than Just Transcribing Genetic Information 113
3.2 RNA Polymerase 113
3.3 The Core Enzyme 114
3.4 The Sigma Factors (and Anti-Sigma Factors) 116
3.5 Promoter Architecture 120
3.6 Stringently Regulated Promoters 120
3.7 Transcription Factors and RNA Polymerase 121
3.8 Transcription Initiation 124
3.9 Transcription Elongation 125
3.10 Transcription Termination: Intrinsic and Rho-Dependent Terminators 127
3.11 Rho and Imported Genes 128
3.12 Rho, R-Loops, and DNA Supercoiling 128
3.13 Rho and Antisense Transcripts 128
3.14 Anti-Termination: Insights from Phage Studies 129
3.15 Transcription Occurs in Bursts 129
4 Gene Control: Regulation at the RNA Level 133
4.1 Antisense Transcripts and Gene Regulation in cis 134
4.2 RNA that Regulates in trans 134
4.3 DsrA and the RpoS/H-NS Link 138
4.4 sRNA Turnover 140
4.5 DEAD-box Proteins 140
4.6 RNA Chaperone Proteins 141
4.7 StpA, H-NS, and RNA Binding 142
4.8 Degradation of mRNA 143
4.9 RNA Folding and Gene Regulation 144
4.10 Transcription Attenuation 145
4.11 Riboswitches 145
4.12 RNA as a Structural Component in the Nucleoid 146
5 Gene Control: Regulation at the Protein Level 149
5.1 Control Beyond DNA and RNA 149
5.2 Translation Machinery and Control: tRNA and rRNA 149
5.3 Translation Machinery and Control: The Ribosome 150
5.4 Translation Initiation 152
5.5 Translation Elongation 154
5.6 Elongation Factor P (EF-P) 155
5.7 Translation Termination 156
5.8 Protein Secretion 157
5.9 Protein Secretion: The Sec Pathway 157
5.10 The Twin Arginine Translocation (Tat) Pathway of Protein Secretion 159
5.11 Type 1 Secretion Systems (T1SS) 160
5.12 Type 2 Secretion Systems (T2SS) 161
5.13 Type 3 Secretion Systems (T3SS) 162
5.14 Type 4 Secretion Systems (T4SS) 164
5.15 Type 5 Secretion Systems (T5SS): The Autotransporters 165
5.16 Type 6 Secretion Systems (T6SS) 166
5.17 Protein Secretion in Gram-Positive Bacteria: SecA1, SecA2, and SrtA 167
5.18 Type 7 Secretion Systems (T7SS) 168
5.19 Protein Modification: Acetylation 168
5.20 Protein Modification: Glycosylation 169
5.21 Protein Modification: Phosphorylation 169
5.22 Protein Splicing 171
5.23 Small Proteins 172
5.24 Selenocysteine and Pyrrolysine: The 21st and 22nd Amino Acids 173
6 Gene Control and Bacterial Physiology 175
6.1 The Bacterial Growth Cycle 175
6.2 Physiology Changes Throughout the Growth Cycle 176
6.3 Generating Physiological Variety from Genetic Homogeneity 178
6.4 Bacterial Economics – Some Basic Principles 179
6.5 Carbon Sources and Metabolism 180
6.6 Gene Control and Carbon Source Utilisation 183
6.7 Anaerobic Respiration 183
6.8 ArcA, Mobile Genetic Elements, and HGT 184
6.9 Stress and Stress Survival in Bacterial Life 185
6.10 Oxygen Stress 185
6.11 Iron Starvation 186
6.12 Siderophores and Iron Capture 188
6.13 TonB-Dependent Transporters 188
6.14 Gene Regulation and Iron Transport 190
6.15 Iron Storage and Homeostasis 191
6.16 Osmotic Stress andWater Relations in Bacteria 191
6.17 Signal Molecules and Stress 193
6.18 The Stringent Response 194
6.19 Regulation of the Acid Stress Response 196
6.20 Alkaline pH Stress Response 200
6.21 Motility and Chemotaxis 201
6.22 Quorum Sensing 203
6.23 Biofilms 205
6.24 ‘Cheating’ as a Lifestyle Strategy 206
6.25 Thermal Regulation 207
6.26 Epigenomics and Phasevarions 209
6.27 Some Unifying Themes 210
7 Gene Control: Global Regulation by H-NS 211
7.1 H-NS is a Global Regulator 211
7.2 H-NS and Foreign DNA 211
7.3 H-NS and Xenogenic Silencing: Three Case Studies 212
7.4 The H-NS Virulence Regulon in Vibrio cholerae 212
7.5 HGT in V. cholerae: The CTXϕ Phage and the VPI1 Island 213
7.6 The ToxRS, ToxT, TcpPH Regulatory Network 215
7.7 Control by VpsR, VpsT, and HapR 215
7.8 Quorum Sensing and Cholera 217
7.9 Chitin and HGT 217
7.10 The H-NS Virulence Regulon in Shigella flexneri 219
7.11 Shigella Infection 221
7.12 The VirF AraC-Like Transcription Factor 222
7.13 VirB: A Recruit from a Plasmid-Partitioning System 222
7.14 The Shigella Virulence Plasmid 223
7.15 The Salmonella H-NS Virulence Gene Regulon 223
7.16 Salmonella’s Pathogenicity Islands (SPI) 224
7.17 SlyA, PhoP/Q, and SPI Gene Expression 227
7.18 Gene Control in SPI1 and SPI2 227
8 An Integrated View of Genome Structure and Function 231
8.1 Networks versus Hierarchies 231
8.2 Regulons, Stimulons, and Heterarchies/Netarchies 232
8.3 Transcription Burstiness and Regulatory Noise 233
8.4 The Significance of Gene Position 234
8.5 Messenger RNA May Not Be Free to Diffuse Far in Bacteria 236
8.6 RNA Polymerase Activity and Genome Organisation 237
8.7 Gene–Gene Interactions in the Folded Chromosome 239
8.8 DNA Supercoiling as a Global Regulator 240
8.9 Modelling the Nucleoid 243
8.10 Synthetic Biology 243
References 247
Index 379
"The book aims to integrate information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling and gene expression control with well-known gene regulation paradigms from model organisms to give the reader a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe. The general public is aware that bacteria can come in benign forms and forms that pose threats to health. This book will explore the governance of the expression of the genes that make a bacterium what it is: a friend or foe to the human/animal/plant host. The reader will learn that the factors that govern the expression of genes by turning them on or off often contribute to the organization of the genetic material within the cell. Our understanding of the architecture of the genome has advanced rapidly in recent years and we are learning more and more about the forces that work to keep genomes the way they are, to change them and the consequences of change for the life of the evolving bacterium. These conservative and disruptive forces will be described, together with their influence on gene expression. The book will also review the basics of gene expression control, bringing the topic up-to-date with information about small RNAs, RNAs that sense chemical signals and the role of DNA as a regulatory factor as well as a carrier of genetic information and will consider where these genes are placed in the core genome and how they are regulated using a combination of imported control proteins and pre-existing ones. The reader will also gain a clearer understanding of the rules that govern microbial cells and how we can exploit this knowledge to enhance the benefits offered by benign microbes, limit the damage caused by malign ones and begin the process of synthesizing artificial ones to meet needs in human society"--Provided by publisher. DESCRIPTION Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis
This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe.
Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function.
Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics Offers a 'DNA-centric' approach to considering transcription control Views horizontal gene transfer from a gene regulation perspective Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.