Structure and Function of the Bacterial Genome

CHARLES J. DORMAN, PhD, ScD, MRIA has held the established chair of Microbiology at Trinity College Dublin, Ireland since 1994. Previously, he held a Royal Society University Research Fellowship at the Biochemistry Department in Dundee University, UK, where he was also a Lecturer in Biochemistry. Professor Dorman is a former Editor-in-Chief of Microbiology, is a Trustee and Council member of the Microbiology Society and has served as the Ambassador to Western Europe of the American Society for Microbiology. He is a founding member of the European Academy of Microbiology, a Fellow of the American Academy of Microbiology, a Fellow of the Royal Society of Biology and a Member of the Royal Irish Academy.

• Preface xiii1 The Bacterial Genome – Where the Genes are 11.1 Genome Philosophy 11.2 The Bacterial Chromosome 41.3 Chromosome Replication: Initiation 61.4 Chromosome Replication: Elongation 111.5 Chromosome Replication: Termination 121.6 Replication Produces Physically Connected Products 131.7 Decatenating the Sister Chromosomes 131.8 Resolving Chromosome Dimers 141.9 Segregating the Products of Chromosome Replication 151.10 Polar Tethering of Chromosome Origins 201.11 Some Bacterial Chromosomes are Linear 201.12 Some Bacteria Have More than One Chromosome 211.13 Plasmids 221.14 Plasmid Replication 221.15 Plasmid Segregation 261.16 The Nucleoid 281.17 The Chromosome Has Looped Domains 291.18 The Macrodomain Structure of the Chromosome 291.19 The Chromosome Displays Spatial Arrangement Within the Cell 301.20 SeqA and Nucleoid Organisation 311.21 MukB, a Condensin-Like Protein 321.22 MatP, the matS Site and Ter Organisation 331.23 MaoP and the maoS Site 341.24 SlmA and Nucleoid Occlusion 341.25 The Min System and Z Ring Localisation 341.26 DNA in the Bacterial Nucleoid 361.27 DNA Topology 361.28 DNA Topoisomerases: DNA Gyrase 381.29 DNA Topoisomerases: DNA Topoisomerase IV 401.30 DNA Topoisomerases: DNA Topoisomerase I 401.31 DNA Topoisomerases: DNA Topoisomerase III 411.32 DNA Replication and Transcription Alter Local DNA Topology 411.33 Transcription and Nucleoid Structure 411.34 Nucleoid-associated Proteins (NAPs) and Nucleoid Structure 431.35 DNA Bending Protein Integration Host Factor (IHF) 441.36 HU, a NAP with General DNA-binding Activity 461.37 The Very Versatile FIS Protein 471.38 FIS and the Early Exponential Phase of Growth 481.39 FIS and the Stringent Response 491.40 FIS and DNA Topology 491.41 Ferritin-Like Dps and the Curved-DNA-binding Protein CbpA 511.42 The H-NS Protein: A Silencer of Transcription 531.43 StpA: A Paralogue of H-NS 571.44 H-NS Orthologues Encoded by Plasmids and Phage 581.45 H-NSB/Hfp and H-NS2: H-NS Homologues of HGT Origin 581.46 A Truncated H-NS-Like Protein 591.47 Hha-like Proteins 591.48 Other H-NS Homologues: The Ler Protein from EPEC 601.49 H-NS Functional Homologues 621.50 H-NS Functional Homologues: Rok from Bacillus spp. 631.51 H-NS Functional Homologues: Lsr2 from Actinomycetes 631.52 H-NS Functional Homologues: MvaT from Pseudomonas spp. 631.53 The Leucine-responsive Regulatory Protein, LRP 641.54 Small, Acid-soluble Spore Proteins, SASPs 652 Conservation and Evolution of the Dynamic Genome 672.1 Disruptive Influences: Mutations 672.2 Repetitive Sequences in the Chromosome and Their Influence on Genetic Stability 692.3 Contingency Loci and the Generation of Microbial Variety 702.4 Rhs: Rearrangement Hotspots 712.5 REP Sequences 722.6 RIB/RIP, BIME-1, and BIME-2 Elements 732.7 ERIC Sequences 732.8 Repeat-Mediated Rearrangements: Mechanisms and Frequency 742.9 Site-specific Recombination and Phenotypic Variety 742.10 Site-Specific Recombination: Bacteriophage Lambda 752.11 The Lambda Lysis/Lysogeny Decision 762.12 Tyrosine Integrases 772.13 Serine Invertases 782.14 Large Serine Recombinases 792.15 Transposition and Transposable Elements 802.16 Pathways of Transposition 822.17 Peel-and-paste Transposition 852.18 Control of Transposition 882.19 Host Factors and Transposition 912.20 Integrative and Conjugative Elements (ICE) 912.21 Integrons 932.22 Introns 962.23 Horizontal Gene Transfer 962.24 Distinguishing Self from Non-self 992.25 Distinguishing Self and Non-self: CRISPR-Cas Systems 992.26 Distinguishing Self and Non-self: Argonaute Proteins 1022.27 Distinguishing Self and Non-self: Restriction Enzymes/Methylases 1032.28 Distinguishing Self and Non-self: BREX 1032.29 Self-sacrifice and Other Behaviours Involving Toxin—antitoxin Systems 1042.30 Conservative Forces: DNA Repair and Homologous Recombination 1042.31 The RecA Protein 1052.32 RecA, LexA, and the SOS Response 1062.33 Holliday Junction Resolution 1082.34 Mismatch Repair 1092.35 Non-homologous End Joining 1103 Gene Control: Transcription and Its Regulation 1133.1 Transcription: More Than Just Transcribing Genetic Information 1133.2 RNA Polymerase 1133.3 The Core Enzyme 1143.4 The Sigma Factors (and Anti-Sigma Factors) 1163.5 Promoter Architecture 1203.6 Stringently Regulated Promoters 1203.7 Transcription Factors and RNA Polymerase 1213.8 Transcription Initiation 1243.9 Transcription Elongation 1253.10 Transcription Termination: Intrinsic and Rho-Dependent Terminators 1273.11 Rho and Imported Genes 1283.12 Rho, R-Loops, and DNA Supercoiling 1283.13 Rho and Antisense Transcripts 1283.14 Anti-Termination: Insights from Phage Studies 1293.15 Transcription Occurs in Bursts 1294 Gene Control: Regulation at the RNA Level 1334.1 Antisense Transcripts and Gene Regulation in cis 1344.2 RNA that Regulates in trans 1344.3 DsrA and the RpoS/H-NS Link 1384.4 sRNA Turnover 1404.5 DEAD-box Proteins 1404.6 RNA Chaperone Proteins 1414.7 StpA, H-NS, and RNA Binding 1424.8 Degradation of mRNA 1434.9 RNA Folding and Gene Regulation 1444.10 Transcription Attenuation 1454.11 Riboswitches 1454.12 RNA as a Structural Component in the Nucleoid 1465 Gene Control: Regulation at the Protein Level 1495.1 Control Beyond DNA and RNA 1495.2 Translation Machinery and Control: tRNA and rRNA 1495.3 Translation Machinery and Control: The Ribosome 1505.4 Translation Initiation 1525.5 Translation Elongation 1545.6 Elongation Factor P (EF-P) 1555.7 Translation Termination 1565.8 Protein Secretion 1575.9 Protein Secretion: The Sec Pathway 1575.10 The Twin Arginine Translocation (Tat) Pathway of Protein Secretion 1595.11 Type 1 Secretion Systems (T1SS) 1605.12 Type 2 Secretion Systems (T2SS) 1615.13 Type 3 Secretion Systems (T3SS) 1625.14 Type 4 Secretion Systems (T4SS) 1645.15 Type 5 Secretion Systems (T5SS): The Autotransporters 1655.16 Type 6 Secretion Systems (T6SS) 1665.17 Protein Secretion in Gram-Positive Bacteria: SecA1, SecA2, and SrtA 1675.18 Type 7 Secretion Systems (T7SS) 1685.19 Protein Modification: Acetylation 1685.20 Protein Modification: Glycosylation 1695.21 Protein Modification: Phosphorylation 1695.22 Protein Splicing 1715.23 Small Proteins 1725.24 Selenocysteine and Pyrrolysine: The 21st and 22nd Amino Acids 1736 Gene Control and Bacterial Physiology 1756.1 The Bacterial Growth Cycle 1756.2 Physiology Changes Throughout the Growth Cycle 1766.3 Generating Physiological Variety from Genetic Homogeneity 1786.4 Bacterial Economics – Some Basic Principles 1796.5 Carbon Sources and Metabolism 1806.6 Gene Control and Carbon Source Utilisation 1836.7 Anaerobic Respiration 1836.8 ArcA, Mobile Genetic Elements, and HGT 1846.9 Stress and Stress Survival in Bacterial Life 1856.10 Oxygen Stress 1856.11 Iron Starvation 1866.12 Siderophores and Iron Capture 1886.13 TonB-Dependent Transporters 1886.14 Gene Regulation and Iron Transport 1906.15 Iron Storage and Homeostasis 1916.16 Osmotic Stress andWater Relations in Bacteria 1916.17 Signal Molecules and Stress 1936.18 The Stringent Response 1946.19 Regulation of the Acid Stress Response 1966.20 Alkaline pH Stress Response 2006.21 Motility and Chemotaxis 2016.22 Quorum Sensing 2036.23 Biofilms 2056.24 ‘Cheating’ as a Lifestyle Strategy 2066.25 Thermal Regulation 2076.26 Epigenomics and Phasevarions 2096.27 Some Unifying Themes 2107 Gene Control: Global Regulation by H-NS 2117.1 H-NS is a Global Regulator 2117.2 H-NS and Foreign DNA 2117.3 H-NS and Xenogenic Silencing: Three Case Studies 2127.4 The H-NS Virulence Regulon in Vibrio cholerae 2127.5 HGT in V. cholerae: The CTXϕ Phage and the VPI1 Island 2137.6 The ToxRS, ToxT, TcpPH Regulatory Network 2157.7 Control by VpsR, VpsT, and HapR 2157.8 Quorum Sensing and Cholera 2177.9 Chitin and HGT 2177.10 The H-NS Virulence Regulon in Shigella flexneri 2197.11 Shigella Infection 2217.12 The VirF AraC-Like Transcription Factor 2227.13 VirB: A Recruit from a Plasmid-Partitioning System 2227.14 The Shigella Virulence Plasmid 2237.15 The Salmonella H-NS Virulence Gene Regulon 2237.16 Salmonella’s Pathogenicity Islands (SPI) 2247.17 SlyA, PhoP/Q, and SPI Gene Expression 2277.18 Gene Control in SPI1 and SPI2 2278 An Integrated View of Genome Structure and Function 2318.1 Networks versus Hierarchies 2318.2 Regulons, Stimulons, and Heterarchies/Netarchies 2328.3 Transcription Burstiness and Regulatory Noise 2338.4 The Significance of Gene Position 2348.5 Messenger RNA May Not Be Free to Diffuse Far in Bacteria 2368.6 RNA Polymerase Activity and Genome Organisation 2378.7 Gene–Gene Interactions in the Folded Chromosome 2398.8 DNA Supercoiling as a Global Regulator 2408.9 Modelling the Nucleoid 2438.10 Synthetic Biology 243References 247Index 379