Structure and Function of the Bacterial Genome. Charles J. Dorman

      1  Cover

      2  Dedication

      3  Preface

      4  1 The Bacterial Genome – Where the Genes Are 1.1 Genome Philosophy 1.2 The Bacterial Chromosome 1.3 Chromosome Replication: Initiation 1.4 Chromosome Replication: Elongation 1.5 Chromosome Replication: Termination 1.6 Replication Produces Physically Connected Products 1.7 Decatenating the Sister Chromosomes 1.8 Resolving Chromosome Dimers 1.9 Segregating the Products of Chromosome Replication 1.10 Polar Tethering of Chromosome Origins 1.11 Some Bacterial Chromosomes Are Linear 1.12 Some Bacteria Have More than One Chromosome 1.13 Plasmids 1.14 Plasmid Replication 1.15 Plasmid Segregation 1.16 The Nucleoid 1.17 The Chromosome Has Looped Domains 1.18 The Macrodomain Structure of the Chromosome 1.19 The Chromosome Displays Spatial Arrangement Within the Cell 1.20 SeqA and Nucleoid Organisation 1.21 MukB, a Condensin‐Like Protein 1.22 MatP, the matS Site and Ter Organisation 1.23 MaoP and the maoS Site 1.24 SlmA and Nucleoid Occlusion 1.25 The Min System and Z Ring Localisation 1.26 DNA in the Bacterial Nucleoid 1.27 DNA Topology 1.28 DNA Topoisomerases: DNA Gyrase 1.29 DNA Topoisomerases: DNA Topoisomerase IV 1.30 DNA Topoisomerases: DNA Topoisomerase I 1.31 DNA Topoisomerases: DNA Topoisomerase III 1.32 DNA Replication and Transcription Alter Local DNA Topology 1.33 Transcription and Nucleoid Structure 1.34 Nucleoid‐associated Proteins (NAPs) and Nucleoid Structure 1.35 DNA Bending Protein Integration Host Factor (IHF) 1.36 HU, a NAP with General DNA‐binding Activity 1.37 The Very Versatile FIS Protein 1.38 FIS and the Early Exponential Phase of Growth 1.39 FIS and the Stringent Response 1.40 FIS and DNA Topology 1.41 Ferritin‐Like Dps and the Curved‐DNA‐binding Protein CbpA 1.42 The H‐NS Protein: A Silencer of Transcription 1.43 StpA: A Paralogue of H‐NS 1.44 H‐NS Orthologues Encoded by Plasmids and Phage 1.45 H‐NSB/Hfp and H‐NS2: H‐NS Homologues of HGT Origin 1.46 A Truncated H‐NS‐Like Protein 1.47 Hha‐like Proteins 1.48 Other H‐NS Homologues: The Ler Protein from EPEC 1.49 H‐NS Functional Homologues 1.50 H‐NS Functional Homologues: Rok from Bacillus spp. 1.51 H‐NS Functional Homologues: Lsr2 from Actinomycetes 1.52 H‐NS Functional Homologues: MvaT from Pseudomonas spp. 1.53 The Leucine‐responsive Regulatory Protein, LRP 1.54 Small, Acid‐soluble Spore Proteins, SASPs

      5  2 Conservation and Evolution of the Dynamic Genome 2.1 Disruptive Influences: Mutations 2.2 Repetitive Sequences in the Chromosome and Their Influence on Genetic Stability 2.3 Contingency Loci and the Generation of Microbial Variety 2.4 Rhs: Rearrangement Hotspots 2.5 REP Sequences 2.6 RIB/RIP, BIME‐1, and BIME‐2 Elements 2.7 ERIC Sequences 2.8 Repeat‐Mediated Rearrangements: Mechanisms and Frequency 2.9 Site‐specific