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

11 8 An Integrated View of Genome Structure and Function8.1 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

14 End User License Agreement

1 Chapter 1 Table 1.1 The topoisomerases of E. coli .

2 Chapter 2Table 2.1 The members of the LexA regulon in E. coli .

3 Chapter 3Table 3.1 Subunit composition of Escherichia coli RNA polymerase holoenzyme (with...Table 3.2 RNA polymerase sigma factors (Escherichia coli ).

1 Chapter 1 Figure 1.1 The macrodomain structure of the E. coli chromosome. Shaded segment... Figure 1.2 Structure of oriC on the E. coli chromosome. The ATP‐dependent DnaA... Figure 1.3 Structure of the E. coli replisome in chromosome replication. The r... Figure 1.4 The structure of the DNA polymerase III subassembly (Pol III*). The... Figure 1.5 The control of DnaA production and activity. The SeqA and DnaA prot... Figure 1.6 The genetic neighbourhood of oriC in E. coli . Filled arrows represe... Figure 1.7 Termination of chromosome replication in E. coli . (a) The moving re... Figure 1.8 Resolution of a chromosome dimer by XerCD‐mediated recombination at... Figure 1.9 The choreography of chromosome movement in E. coli during the cell ... Figure 1.10 MukBEF structure and function. (a) The Dimeric MukB protein (inter... Figure 1.11 Spatiotemporal dispositions of chromosomes in model bacteria other... Figure 1.12 Theta model of plasmid replication. (a) The structure of the origi... Figure 1.13 Rolling circle plasmid replication. A circular plasmid using the r... Figure 1.14 The topological consequences of replisome activity. The replicatio... Figure 1.15 The topological consequences of transcription. This is the twin su... Figure 1.16 R‐loop formation. When RNA polymerase reads a G+C‐rich template, s... Figure 1.17 Integration of bacteriophage lambda at the lambda attachment site ... Figure 1.18 The interactions of the nucleoid‐associated proteins FIS, HU, and ... Figure 1.19 The multifaceted stringent response. A summary is shown of the pro... Figure 1.20 The stress and stationary phase sigma factor, RpoS. The rpoS gene ... Figure 1.21 The vast H‐NS regulon. The H‐NS protein controls the expression of... Figure 1.22 The dimerisation and oligomerisation of H‐NS. The amino‐terminal d... Figure 1.23 The DNA‐binding modes of H‐NS. The H‐NS monomer is shown as two li... Figure 1.24 The genetic switch controlling LEE virulence gene expression in EP...

2 Chapter 2 Figure 2.1 Simple sequence repeats (SSRs) and phase‐variable gene expression. ... Figure 2.2 The Hin invertasome and flagella phase variation in Salmonella . (a)... Figure 2.3 The structure of the composite transposon Tn 5 . This mobile element ... Figure 2.4 The structure of the composite transposon Tn 10 . Tn 10 is superficial...Figure 2.5 Formation of a hybrid promoter in the IS 911 circle transposition in...Figure 2.6 Control of transposase expression in insertion sequence IS 911 . The ...Figure 2.7 The replicative pathway of transposition. The transposon is represe...Figure 2.8 The structure of transposon Tn 3 and Tn 3‐ family member Tn 501 . ...Figure 2.9 Cointegrate resolution in Tn 3 transposition. The cointegrate circle...Figure 2.10 The cut‐and‐paste (or non‐replicative) pathway of transposition. T...Figure 2.11 Peel and paste transposition. (a) Structure of IS 200 showing the p...Figure 2.12 Transposon Tn 7 and att Tn 7 . The 14‐kb transposon Tn 7 has a left (L)...Figure 2.13 The CTnDOT Integrative Conjugative Element (ICE). (a) The rectangl...Figure 2.14 Integron structure. The basic platform of the integron consists of...Figure 2.15 CRISPR‐ cas structure. Summary structures are provided for class I ...Figure 2.16 RecBCD activity and Holliday junction resolution. (a) The RecBCD c...Figure 2.17 The SOS response. (a) DNA damage interrupts chromosome replication...Figure 2.18 DNA mismatch repair. (a) A mismatched base pair at position ‘X’ ca...Figure 2.19 Double‐stranded break repair. In a growing bacterium, when a doubl...

3 Chapter 3Figure 3.1 RNA polymerase and transcription initiation. (a) This gives a summa...Figure 3.2 Structures of an RpoD‐dependent transcription promoter and of the R...Figure 3.3 Domain structure of RpoN (σ N, σ 54, sigma‐54). The 477‐amino‐acid σ 5...Figure 3.4 Transcription regulation at initiation, elongation, termination. (a...Figure 3.5 Backtracking of RNA polymerase during transcript elongation. The RN...

4 Chapter 4Figure 4.1 Gene control at the RNA level. (a) Cleavage of a polycistronic mRNA...Figure 4.2 CsrA regulon. The CsrA RNA binding protein co‐purifies with hundred...Figure 4.3 Envelope stress, the RpoE sigma factor and sRNAs. The RpoE sigma fa...

5 Chapter 5Figure 5.1 Translation initiation. Clockwise, from top left: Initiation factor...Figure 5.2 Translation elongation. Clockwise, from the top: the 70S ribosome w...Figure 5.3 SecA‐SecYEG‐dependent protein secretion. The SecYEG complex in the ...Figure 5.4 SRP‐SecYEG‐dependent protein secretion. (a) The signal recognition ...Figure 5.5 The twin arginine translocation (Tat) pathway. The Gram‐negative ve...Figure 5.6 Type 1 secretion system (T1SS). The system has three components: an...Figure 5.7 Type 2 secretion system (T2SS). The Gsp protein names refer to the ...Figure 5.8 Type 3 secretion system. The proteins are given the names of counte...Figure 5.9 Type 4 secretion system. (a) A summary of the structure of the T4SS...Figure 5.10 Type 5 secretion system (T5SS). The unfolded autotransporter prote...Figure 5.11 Type 6 secretion system (T6SS). The system consists of a contracti...

6 Chapter 6Figure 6.1 The bacterial growth cycle. The graph shows an idealised growth cur...Figure 6.2 Generation of proton motive force and the operation of the F 1F 0ATP...Figure 6.3 A simple chemiosmotic circuit. The cytoplasmic membrane is impervio...Figure 6.4 Iron‐mediated gene regulation via the RyhB sRNA. In iron‐restricted...Figure 6.5 TonB‐dependent transport systems. The TonB dimer contra‐rotates wit...Figure 6.6 Operation of the osmotic stress response during upshock. The bacter...Figure 6.7 Operation of the ProU uptake system in osmotically stressed bacteri...Figure 6.8 Synthesis of the alarmone (p)ppGpp. In nutrient‐poor conditions, Re...Figure 6.9 The Acid Fitness Island (AFI) of Escherichia coli . The locations, o...

7 Chapter 7Figure 7.1 The H‐NS regulon of V. cholerae . (a) The genes involved in the colo...Figure 7.2 The infection of the small intestinal epithelium by Vibrio cholerae Figure 7.3 The control of virulence, motility, and biofilm expression in V. ch ...Figure 7.4 Chitin influences DNA uptake by V. cholera . The dns gene encodes th...Figure 7.5 Invasion of the human large intestinal epithelium by Shigella flexn ...Figure 7.6 The H‐NS regulon of Shigella flexneri . The Entry Region of the larg...Figure 7.7 The macrodomain structure of the Salmonella chromosome ( S. enterica Figure 7.8 The H‐NS virulence regulon of Salmonella enterica serovar Typhimuri...

8 Chapter 8Figure 8.1 Evolutionarily co‐located genes in the E. coli chromosome. The chro...