Bacterial Genetics and Genomics

Mechanisms of Genetic Variation and Adaptation

3.1.

3.1.1.

3.1.1.1.

3.1.1.1.1.

3.1.1.1.1.1.

3.1.1.1.1.2.

3.1.1.1.2.

3.1.1.1.2.1.

3.1.1.1.2.2.

3.1.1.1.2.3.

3.1.1.2.

Insertion and Deletion Mutations

3.1.1.2.1.

Small Indels

3.1.1.2.2.

Frameshift Effects

3.1.1.2.3.

Reading Frame Restoration

3.1.1.3.

Large-Scale Chromosomal Changes

3.1.1.3.1.

Inversions

3.1.1.3.1.1.

Paracentric Inversions

3.1.1.3.1.2.

Pericentric Inversions

3.1.1.3.2.

Duplications

3.1.1.3.2.1.

Tandem Duplications

3.1.1.3.2.2.

Dispersed Duplications

3.1.1.3.3.

3.1.1.3.3.1.

3.1.1.3.3.2.

3.1.1.3.4.

3.1.2.

3.1.2.1.

Spontaneous Mutations

3.1.2.1.1.

DNA Replication Errors

3.1.2.1.1.1.

Polymerase Slippage

3.1.2.1.1.2.

Proofreading Failures

3.1.2.1.2.

Spontaneous DNA Damage

3.1.2.1.2.1.

3.1.2.1.2.2.

3.1.2.1.2.3.

3.1.2.2.

3.1.2.2.1.

3.1.2.2.1.1.

3.1.2.2.1.1.1.

3.1.2.2.1.1.2.

3.1.2.2.1.2.

3.1.2.2.1.2.1.

Methyl Methanesulfonate

3.1.2.2.1.2.2.

Ethyl Methanesulfonate

3.1.2.2.1.3.

3.1.2.2.1.3.1.

3.1.2.2.1.3.2.

3.1.2.2.2.

3.1.2.2.2.1.

3.1.2.2.2.1.1.

Pyrimidine Dimer Formation

3.1.2.2.2.1.2.

DNA Crosslinking

3.1.2.2.2.2.

Ionizing Radiation

3.1.2.2.2.2.1.

Free Radical Formation

3.1.2.2.2.2.2.

3.1.3.

3.1.3.1.

3.1.3.1.1.

3.1.3.1.1.1.

3.1.3.1.1.2.

Light-Dependent Repair

3.1.3.1.2.

Alkyl Transfer Repair

3.1.3.1.2.1.

3.1.3.2.

3.1.3.2.1.

3.1.3.2.1.1.

3.1.3.2.1.2.

3.1.3.2.1.3.

3.1.3.2.1.4.

3.1.3.2.2.

Nucleotide Excision Repair

3.1.3.2.2.1.

UvrABC Excinuclease

3.1.3.2.2.2.

Damage Recognition

3.1.3.2.2.3.

Excision and Repair Synthesis

3.1.3.3.

Mismatch Repair

3.1.3.3.1.

MutS Protein Function

3.1.3.3.2.

MutL Protein Function

3.1.3.3.3.

MutH Endonuclease

3.1.3.3.4.

Dam Methylation Role

3.1.3.4.

Recombinational Repair

3.1.3.4.1.

Homologous Recombination

3.1.3.4.2.

RecA Protein Function

3.1.3.4.3.

Holiday Junction Resolution

3.1.3.5.

SOS Response

3.1.3.5.1.

LexA Repressor

3.1.3.5.2.

RecA Coprotease Activity

3.1.3.5.3.

Error-Prone Repair

3.1.3.5.4.

Translesion Synthesis Polymerases

3.2.

Horizontal Gene Transfer

3.2.1.

Transformation

3.2.1.1.

Natural Competence

3.2.1.1.1.

Competence Development

3.2.1.1.2.

Competence Factors

3.2.1.1.3.

Environmental Triggers

3.2.1.1.4.

Species Variation

3.2.1.2.

DNA Uptake Mechanisms

3.2.1.2.1.

3.2.1.2.2.

3.2.1.2.3.

3.2.1.2.4.

3.2.1.3.

3.2.1.3.1.

Homologous Recombination

3.2.1.3.2.

Illegitimate Recombination

3.2.1.3.3.

Recombination Frequency

3.2.1.4.

Artificial Transformation

3.2.1.4.1.

Chemical Methods

3.2.1.4.1.1.

Calcium Chloride Treatment

3.2.1.4.1.2.

Competent Cell Preparation

3.2.1.4.2.

3.2.1.4.2.1.

3.2.1.4.2.2.

3.2.2.

3.2.2.1.

3.2.2.1.1.

3.2.2.1.2.

tra Gene Organization

3.2.2.1.3.

Pilus Structure and Function

3.2.2.1.4.

3.2.2.2.

3.2.2.2.1.

3.2.2.2.2.

3.2.2.2.3.

3.2.2.2.3.1.

F Plasmid Integration

3.2.2.2.3.2.

Chromosomal Transfer

3.2.2.2.3.3.

Mapping by Interrupted Mating

3.2.2.2.4.

3.2.2.2.4.1.

3.2.2.2.4.2.

3.2.2.3.

3.2.2.3.1.

3.2.2.3.2.

3.2.2.3.3.

DNA Nicking and Transfer

3.2.2.3.4.

Complementary Strand Synthesis

3.2.2.4.

Gram-Positive Conjugation

3.2.2.4.1.

Pheromone Systems

3.2.2.4.2.

Aggregation Substances

3.2.2.4.3.

Plasmid Transfer Mechanisms

3.2.3.

Transduction

3.2.3.1.

Bacteriophage Biology

3.2.3.1.1.

Phage Structure

3.2.3.1.2.

Host Range Determination

3.2.3.1.3.

3.2.3.2.

3.2.3.2.1.

3.2.3.2.2.

3.2.3.2.3.

Replication and Transcription

3.2.3.2.4.

3.2.3.3.

3.2.3.3.1.

3.2.3.3.2.

3.2.3.3.3.

3.2.3.4.

Generalized Transduction

3.2.3.4.1.

Random DNA Packaging

3.2.3.4.2.

Pac Site Recognition

3.2.3.4.3.

Transducing Particle Formation

3.2.3.4.4.

Recipient Cell Infection

3.2.3.5.

Specialized Transduction

3.2.3.5.1.

Site-Specific Integration

3.2.3.5.2.

Imprecise Excision

3.2.3.5.3.

Adjacent Gene Transfer

3.2.3.5.4.

Lambda Phage System

3.3.

Mobile Genetic Elements

3.3.1.

Insertion Sequences

3.3.1.1.

IS Element Structure

3.3.1.1.1.

Terminal Inverted Repeats

3.3.1.1.2.

Transposase Gene

3.3.1.1.3.

Target Site Duplication

3.3.1.2.

Transposition Mechanisms

3.3.1.2.1.

Conservative Transposition

3.3.1.2.2.

Replicative Transposition

3.3.1.2.3.

Target Site Selection

3.3.1.3.

3.3.1.3.1.

3.3.1.3.2.

3.3.1.3.3.

3.3.1.3.4.

3.3.2.

3.3.2.1.

Composite Transposons

3.3.2.1.1.

Structure Organization

3.3.2.1.2.

Flanking IS Elements

3.3.2.1.3.

Central Region Genes

3.3.2.1.4.

Antibiotic Resistance Carriage

3.3.2.2.

Complex Transposons

3.3.2.2.1.

Tn3 Family

3.3.2.2.2.

Transposition Mechanism

3.3.2.2.3.

Resolution Process

3.3.2.2.4.

Cointegrate Formation

3.3.2.3.

Conjugative Transposons

3.3.2.3.1.

Self-Transfer Ability

3.3.2.3.2.

Integration Mechanisms

3.3.2.3.3.

Excision and Circularization

3.3.3.

3.3.3.1.

3.3.3.1.1.

3.3.3.1.2.

3.3.3.1.3.

3.3.3.2.

3.3.3.2.1.

3.3.3.2.2.

Site-Specific Recombination

3.3.3.2.3.

Cassette Arrays

3.3.3.3.

Role in Antibiotic Resistance

3.3.3.3.1.

Resistance Gene Capture

3.3.3.3.2.

Expression from Common Promoter

3.3.4.

Genomic Islands

3.3.4.1.

Pathogenicity Islands

3.3.4.1.1.

Virulence Gene Clusters

3.3.4.1.2.

Horizontal Acquisition

3.3.4.1.3.

Integration Sites

3.3.4.1.4.

Mobility Elements

3.3.4.2.

Symbiosis Islands

3.3.4.2.1.

Nitrogen Fixation Genes

3.3.4.2.2.

Host Interaction Genes

3.3.4.3.

Metabolic Islands

3.3.4.3.1.

Catabolic Pathways

3.3.4.3.2.

Environmental Adaptation

2. Core Genetic Processes in Bacteria

Go to top

4. Bacterial Genomics and Bioinformatics