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Structure and Function of the Bacterial Genome

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Structure and Function of the Bacterial Genome

Charles J. Dorman

ISBN: 978-1-119-30879-9 April 2020 Wiley-Blackwell

Hardcover
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Description

Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis

This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe.

Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function. 

  • Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics
  • Offers a 'DNA-centric' approach to considering transcription control
  • Views horizontal gene transfer from a gene regulation perspective
  • Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones

Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.

Preface

CHAPTER 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 The products of replication are physically connected

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 organization

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 Truncated H-NS-like proteins

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

CHAPTER 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 BIME elements

2.7 RIB/RIP elements

2.8 ERIC sequences

2.9 Site-specific recombination and phenotypic variety

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 and 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

CHAPTER 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

CHAPTER 4 GENE CONTROL: REGULATION AT THE RNA LEVEL

4.1 Antisense transcripts and gene regulation in cis

4.2 RNA that regulates in trans

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

CHAPTER 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 (T6SS)

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 The 21st and 22nd amino acids

CHAPTER 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 genetical 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

CHAPTER 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 xenogeneic silencing: three case studies

7.4 The H-NS virulence regulon in Vibrio cholerae

7.5 HGT in V. cholerae: the CTX 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 Salmonella's pathogenicity islands (SPI)

7.16 The Salmonella H-NS virulence gene regulon

7.17 SlyA, PhoP/Q and SPI gene expression

7.18 Gene control in SPI1 and SPI2

CHAPTER 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 organization

8.7 Gene-gene communication in the folded chromosome

8.8 DNA supercoiling as a global regulator

8.9 Modelling the nucleoid

8.10 Synthetic biology

References

Index