Structure and Function of the Bacterial Genome. Charles J. Dorman
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rel="nofollow" href="#ulink_7c30e4db-2470-5511-95f4-9ed118f0427c">5.17 Protein Secretion in Gram‐Positive Bacteria: SecA1, SecA2, and SrtA 5.18 Type 7 Secretion Systems (T7SS) 5.19 Protein Modification: Acetylation 5.20 Protein Modification: Glycosylation 5.21 Protein Modification: Phosphorylation 5.22 Protein Splicing 5.23 Small Proteins 5.24 Selenocysteine and Pyrrolysine: The 21st and 22nd Amino Acids
9 6 Gene Control and Bacterial Physiology 6.1 The Bacterial Growth Cycle 6.2 Physiology Changes Throughout the Growth Cycle 6.3 Generating Physiological Variety from Genetic Homogeneity 6.4 Bacterial Economics – Some Basic Principles 6.5 Carbon Sources and Metabolism 6.6 Gene Control and Carbon Source Utilisation 6.7 Anaerobic Respiration 6.8 ArcA, Mobile Genetic Elements, and HGT 6.9 Stress and Stress Survival in Bacterial Life 6.10 Oxygen Stress 6.11 Iron Starvation 6.12 Siderophores and Iron Capture 6.13 TonB‐Dependent Transporters 6.14 Gene Regulation and Iron Transport 6.15 Iron Storage and Homeostasis 6.16 Osmotic Stress and Water Relations in Bacteria 6.17 Signal Molecules and Stress 6.18 The Stringent Response 6.19 Regulation of the Acid Stress Response 6.20 Alkaline pH Stress Response 6.21 Motility and Chemotaxis 6.22 Quorum Sensing 6.23 Biofilms 6.24 ‘Cheating’ as a Lifestyle Strategy 6.25 Thermal Regulation 6.26 Epigenomics and Phasevarions 6.27 Some Unifying Themes
10 7 Gene Control: Global Regulation by H‐NS 7.1 H‐NS Is a Global Regulator 7.2 H‐NS and Foreign DNA 7.3 H‐NS and Xenogenic Silencing: Three Case Studies 7.4 The H‐NS Virulence Regulon in Vibrio cholerae 7.5 HGT in V. cholerae: The CTXφ Phage and the VPI1 Island 7.6 The ToxRS, ToxT, TcpPH Regulatory Network 7.7 Control by VpsR, VpsT, and HapR 7.8 Quorum Sensing and Cholera 7.9 Chitin and HGT 7.10 The H‐NS Virulence Regulon in Shigella flexneri 7.11 Shigella Infection 7.12 The VirF AraC‐Like Transcription Factor 7.13 VirB: A Recruit from a Plasmid‐Partitioning System 7.14 The Shigella Virulence Plasmid 7.15 The Salmonella H‐NS Virulence Gene Regulon 7.16 Salmonella's Pathogenicity Islands (SPI) 7.17 SlyA, PhoP/Q, and SPI Gene Expression 7.18 Gene Control in SPI1 and SPI2
11 8 An Integrated View of Genome Structure and Function 8.1 Networks versus Hierarchies 8.2 Regulons, Stimulons, and Heterarchies/Netarchies 8.3 Transcription Burstiness and Regulatory Noise 8.4 The Significance of Gene Position 8.5 Messenger RNA May Not Be Free to Diffuse Far in Bacteria 8.6 RNA Polymerase Activity and Genome Organisation 8.7 Gene–Gene Interactions in the Folded Chromosome 8.8 DNA Supercoiling as a Global Regulator 8.9 Modelling the Nucleoid 8.10 Synthetic Biology
12 References
13 Index
List of Tables
1 Chapter 1Table 1.1 The topoisomerases ofE. coli.
2 Chapter 2Table 2.1 The members of the LexA regulon inE. coli.