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

2.10 Site‐Specific Recombination: Bacteriophage Lambda 2.11 The Lambda Lysis/Lysogeny Decision 2.12 Tyrosine Integrases 2.13 Serine Invertases 2.14 Large Serine Recombinases 2.15 Transposition and Transposable Elements 2.16 Pathways of Transposition 2.17 Peel‐and‐paste Transposition 2.18 Control of Transposition 2.19 Host Factors and Transposition 2.20 Integrative and Conjugative Elements (ICE) 2.21 Integrons 2.22 Introns 2.23 Horizontal Gene Transfer 2.24 Distinguishing Self from Non‐self 2.25 Distinguishing Self and Non‐self: CRISPR‐Cas Systems 2.26 Distinguishing Self and Non‐self: Argonaute Proteins 2.27 Distinguishing Self and Non‐self: Restriction Enzymes/Methylases 2.28 Distinguishing Self and Non‐self: BREX 2.29 Self‐sacrifice and Other Behaviours Involving Toxin—antitoxin Systems 2.30 Conservative Forces: DNA Repair and Homologous Recombination 2.31 The RecA Protein 2.32 RecA, LexA, and the SOS Response 2.33 Holliday Junction Resolution 2.34 Mismatch Repair 2.35 Non‐homologous End Joining

      6  3 Gene Control: Transcription and Its Regulation 3.1 Transcription: More Than Just Transcribing Genetic Information 3.2 RNA Polymerase 3.3 The Core Enzyme 3.4 The Sigma Factors (and Anti‐Sigma Factors) 3.5 Promoter Architecture 3.6 Stringently Regulated Promoters 3.7 Transcription Factors and RNA Polymerase 3.8 Transcription Initiation 3.9 Transcription Elongation 3.10 Transcription Termination: Intrinsic and Rho‐Dependent Terminators 3.11 Rho and Imported Genes 3.12 Rho, R‐Loops, and DNA Supercoiling 3.13 Rho and Antisense Transcripts 3.14 Anti‐Termination: Insights from Phage Studies 3.15 Transcription Occurs in Bursts

      7  4 Gene Control: Regulation at the RNA Level 4.1 Antisense Transcripts and Gene Regulation incis 4.2 RNA that Regulates intrans 4.3 DsrA and the RpoS/H‐NS Link 4.4 sRNA Turnover 4.5 DEAD‐box Proteins 4.6 RNA Chaperone Proteins 4.7 StpA, H‐NS, and RNA Binding 4.8 Degradation of mRNA 4.9 RNA Folding and Gene Regulation 4.10 Transcription Attenuation 4.11 Riboswitches 4.12 RNA as a Structural Component in the Nucleoid

      8  5 Gene Control: Regulation at the Protein Level 5.1 Control Beyond DNA and RNA 5.2 Translation Machinery and Control: tRNA and rRNA 5.3 Translation Machinery and Control: The Ribosome 5.4 Translation Initiation 5.5 Translation Elongation 5.6 Elongation Factor P (EF‐P) 5.7 Translation Termination 5.8 Protein Secretion 5.9 Protein Secretion: The Sec Pathway 5.10 The Twin Arginine Translocation (Tat) Pathway of Protein Secretion 5.11 Type 1 Secretion Systems (T1SS) 5.12 Type 2 Secretion Systems (T2SS) 5.13 Type 3 Secretion Systems (T3SS) 5.14 Type 4 Secretion Systems (T4SS) 5.15 Type 5 Secretion Systems (T5SS): The Autotransporters 5.16 Type 6 Secretion Systems

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