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EcoSal Plus

image of EcoSal Plus
EISSN: 2324-6200

The cover image, "Salmonella typhi on Hep2," was provided courtesy of David Goulding, Genome Research Limited (http://www.sanger.ac.uk/).

EcoSal Plus is an authoritative online reference that publishes an ever-growing body of expert reviews covering virtually all aspects of E. coli, Salmonella, and other members of the family Enterobacteriaceae and their use as model microbes for biological explorations. This serial is intended primarily to serve the needs of the research community as a comprehensive and continuously updated archive of the entire corpus of knowledge about the enteric bacterial cell. All aspects of these organisms are covered, including physiology, metabolism, genetics, pathogenesis, ecology, genomics, systems biology, and history. These thoughtful reviews provide the integrated background needed for most microbiology investigations and are essential reading for research scientists. Features include: Articles contain links to K12 genes on the EcoCyc database site. Articles are available as downloadable PDF files. Images and tables are downloadable to PowerPoint files. For subscription information, see the Home page.

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About EcoSal Plus

EcoSal Plus is an authoritative online reference that publishes an ever-growing body of expert reviews covering virtually all aspects of E. coli, Salmonella, and other members of the family Enterobacteriaceae and their use as model microbes for biological explorations. This serial is intended primarily to serve the needs of the research community as a comprehensive and continuously updated archive of the entire corpus of knowledge about the enteric bacterial cell.  All aspects of these organisms are covered, including physiology, metabolism, genetics, pathogenesis, ecology, genomics, systems biology, and history. These thoughtful reviews provide the integrated background needed for most microbiology investigations and are essential reading for research scientists. Features include: Articles contain links to K12 genes on the EcoCyc database site. Articles are available as downloadable PDF files. Images and tables are downloadable to PowerPoint files. For subscription information, see the Home page.

[+] [–] Domain 1

Historical Perspectives

Editor: James B. Kaper
Escherichia coli and the French School of Molecular Biology
Escherichia coli and the Emergence of Molecular Biology
The Legacy of 20th Century Phage Research
Escherichia coli and Salmonella 2000: the View From Here

[+] [–] Domain 2 Cell Architecture and Growth

Editor: James M. Slauch
Fimbriae: Classification and Biochemistry
Regulation of Fimbrial Expression
Structure and Assembly of Escherichia coli Capsules
Outer Membrane Vesicles
The Nucleoid: an Overview
Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates

[+] [–] Domain 3

Metabolism

Editor: Valley Stewart

Introduction and Perspectives

Energy Generation/Redox Control

The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics
ATP Synthesis by Oxidative Phosphorylation
NADH as Donor
Respiration of Nitrate and Nitrite
Succinate as Donor; Fumarate as Acceptor
Oxygen as Acceptor
S- and N-Oxide Reductases

Solute and Ion Transport

Solute and Ion Transport: Outer Membrane Pores and Receptors
Bacterial Ion Channels
Ammonia Transport
Binding Protein-Dependent Uptake of Maltose into Cells via an ATP-Binding Cassette Transporter
Copper Homeostasis in Escherichia coli and Other Enterobacteriaceae
Magnesium Transport and Magnesium Homeostasis
Transition Metal Homeostasis

Pathways to Central Metabolism: Catabolism

Hexose/Pentose and Hexitol/Pentitol Metabolism
Catabolism of Hexuronides, Hexuronates, Aldonates, and Aldarates
Glycerol and Methylglyoxal Metabolism
Two-Carbon Compounds and Fatty Acids as Carbon Sources
C4-Dicarboxylate Degradation in Aerobic and Anaerobic Growth
Molecular Basis for Bacterial Growth on Citrate or Malonate
Catabolism of Amino Acids and Related Compounds

Central Metabolism

Glycolysis and Flux Control
Tricarboxylic Acid Cycle and Glyoxylate Bypass
Fermentative Pyruvate and Acetyl-Coenzyme A Metabolism
Anaerobic Formate and Hydrogen Metabolism

Biosynthesis

Amino Acid Metabolism and Fluxes
Selenocysteine
Selenocysteine Lyase
Selenophosphate Synthetase
Regulation of Serine, Glycine, and One-Carbon Biosynthesis
Biosynthesis of Glutamate, Aspartate, Asparagine, -Alanine, and -Alanine
Biosynthesis of Proline
Biosynthesis and Regulation of the Branched-Chain Amino Acids†
Regulation of Glutamine Synthetase Activity
Methionine
Biosynthesis of the Aromatic Amino Acids
Biosynthesis of Histidine
Biosynthesis of Arginine and Polyamines
Biosynthesis of Cysteine
Nucleotides, Nucleosides, and Nucleobases
Glycogen: Biosynthesis and Regulation
Biosynthesis of Membrane Lipids

Coenzymes, Cofactors and Prosthetic Groups

Biosynthesis of Riboflavin
Biosynthesis of Menaquinone (Vitamin K2) and Ubiquinone (Coenzyme Q)
Biosynthesis of Pantothenic Acid and Coenzyme A
Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation
Folate Biosynthesis, Reduction, and Polyglutamylation and the Interconversion of Folate Derivatives
Biosynthesis of Thiamin Pyrophosphate
Biosynthesis and Use of Cobalamin (B)
Biogenesis and Homeostasis of Nicotinamide Adenine Dinucleotide Cofactor
Biosynthesis of Hemes
Cytochrome Biogenesis
Biosynthesis and Insertion of the Molybdenum Cofactor
From Iron and Cysteine to Iron-Sulfur Clusters: the Biogenesis Protein Machineries

[+] [–] Domain 4

Synthesis and Processing of Macromolecules

Editor: Susan T. Lovett

Protein

How We Got to Where We Are: the Ribosome in the 21st Century
An Introduction to the Structure and Function of the Ribosome
Assembly of the 30S Ribosomal Subunit
Structural Basis for the Decoding Mechanism
Modification of the Ribosome and the Translational Machinery during Reduced Growth Due to Environmental Stress
Antibiotic Resistance Mechanisms, with an Emphasis on Those Related to the Ribosome
Aminoacyl-tRNA Synthetases in the Bacterial World
Modified Nucleosides of Escherichia coli Ribosomal RNA
Transfer RNA Modification
Translation Initiation
The Tat Protein Export Pathway
Biogenesis and Membrane Targeting of Lipoproteins
Assembly of Outer Membrane β-Barrel Proteins: the Bam Complex
Type II Secretion in Escherichia coli
Type V Secretion: the Autotransporter and Two-Partner Secretion Pathways

DNA

Initiation of DNA Replication
Replisome Dynamics during Chromosome Duplication
DNA Methylation
The DNA Exonucleases of Escherichia coli
DNA Helicases
DNA Topoisomerases
Translesion DNA Synthesis
Stress-Induced Mutagenesis
Direct DNA Lesion Reversal and Excision Repair in Escherichia coli
DNA Mismatch Repair
Homologous Recombination—Experimental Systems, Analysis, and Significance
Homologous Recombination—Enzymes and Pathways

RNA

Promoter Escape by Escherichia coli RNA Polymerase
Nus Factors of Escherichia coli
Exoribonucleases and Endoribonucleases
Messenger RNA Decay

Complex Lipids and Carbohydrates

Peptidoglycan Recycling
Undecaprenyl Phosphate Synthesis

[+] [–] Domain 5

Responding to the Environment

Editor: James M. Slauch

The Cold Shock Response
The SOS Regulatory Network
Oxidative Stress
Osmotic Stress
Envelope Stress Responses
Stationary-Phase Gene Regulation in Escherichia coli §

[+] [–] Domain 6

Evolution and Genomics

Editor: David A. Rasko

The Influence of Ecological Factors on the Distribution and the Genetic Structure of Escherichia coli
Evolution and Ecology of Salmonella
The Ecology and Evolution of Microbial Defense Systems in Escherichia coli
The Origin of Mutants under Selection: Interactions of Mutation, Growth, and Selection

[+] [–] Domain 7

Genetics and Genetic Tools

Editor: James M. Slauch

Plasmids

The Cytology of Bacterial Conjugation

[+] [–] Domain 8

Pathogenesis

Editor: Michael S. Donnenberg

Adherence and Colonization

Adhesins of Enterotoxigenic Escherichia coli Strains That Infect Animals
Adhesins of Diffusely Adherent and Enteroaggregative Escherichia coli
Adhesins of Enterohemorrhagic Escherichia coli
Adhesins of Enteropathogenic Escherichia coli
Type 1 Fimbriae, Curli, and Antigen 43: Adhesion, Colonization, and Biofilm Formation

Toxins and Secretion Systems

The Escherichia coli Hemolysin
Autotransporter Proteins
Cytotoxic Necrotizing Factors: Rho-Activating Toxins from Escherichia coli
Heat-Labile Enterotoxins
Shiga Toxins: Potent Poisons, Pathogenicity Determinants, and Pharmacological Agents

Regulation of Virulence

Virulence Gene Regulation in Escherichia coli
Virulence Gene Regulation in Shigella

Interactions with the Host

NLRs: Nucleotide-Binding Domain and Leucine-Rich-Repeat-Containing Proteins
Salmonella and Enteropathogenic Escherichia coli Interactions with Host Cells: Signaling Pathways
Cytokines in Salmonellosis
Nitric Oxide in Salmonella and Escherichia coli Infections
Modulation of Iron Availability at the Host-Pathogen Interface in Phagocytic Cells
Adaptive Immune Responses during Salmonella Infection
Mucosal Immune Responses to Escherichia coli and Salmonella Infections
Salmonella as an Inducer of Autoimmunity
Vaccines against Infections Caused by Salmonella, Shigella, and Pathogenic Escherichia coli
Cytokines and Escherichia coli Sepsis
Intracellular Voyeurism: Examining the Modulation of Host Cell Activities by Salmonella enterica Serovar Typhimurium
Imaging Techniques for the Study of Escherichia coli and Salmonella Infections

Extraintestinal Infections

Meningitis-Associated Escherichia coli
Uropathogenic Escherichia coli
Molecular Epidemiology of Extraintestinal Pathogenic Escherichia coli
Salmonella Epidemiology and Pathogenesis in Food-Producing Animals
Invasive Salmonellosis in Humans

[+] [–] Domain 9 Life in Communities and the Environment

Editor: David Gordon

The Life of Commensal Escherichia coli in the Mammalian Intestine
Colonization of Abiotic Surfaces
Cell-to-Cell Signaling in Escherichia coli and Salmonella

[+] [–] Domain 10 Bioinformatics and Systems Biology

Editor: Peter D. Karp

Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide
The EcoCyc Database
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