Rhizobium Genetics and Plasmid Biology

6.

Plasmid Molecular Biology

6.1.

Plasmid Replication Systems

6.1.1.

Replication Origins (oriV)

6.1.1.1.

Origin structure

6.1.1.2.

6.1.1.3.

Initiator binding sites

6.1.1.4.

Replication timing

6.1.2.

RepABC Replication System

6.1.2.1.

RepA initiator function

6.1.2.2.

RepB partitioning role

6.1.2.3.

RepC regulatory activity

6.1.2.4.

Protein interactions

6.1.3.

Alternative Replication Systems

6.1.3.1.

6.1.3.2.

Rolling circle replication

6.1.3.3.

Theta replication

6.1.4.

Copy Number Control

6.1.4.1.

Negative regulation

6.1.4.2.

6.1.4.3.

Protein inhibitors

6.2.

Plasmid Partitioning and Stability

6.2.1.

Active Partitioning Systems

6.2.1.1.

6.2.1.2.

Type II systems

6.2.1.3.

Type III systems

6.2.1.4.

6.2.2.

Centromere-like Sequences

6.2.2.1.

6.2.2.2.

Protein binding

6.2.2.3.

Nucleoprotein complexes

6.2.3.

Segregation Mechanisms

6.2.3.1.

Chromosome attachment

6.2.3.2.

6.2.3.3.

Spatial organization

6.2.4.

Stability Maintenance

6.2.4.1.

Multimer resolution

6.2.4.2.

Post-segregational killing

6.2.4.3.

Addiction systems

6.3.

Plasmid Transfer Mechanisms

6.3.1.

Conjugative Transfer

6.3.1.1.

Mating pair formation

6.3.1.2.

6.3.1.3.

6.3.1.4.

Transfer replication

6.3.2.

Transfer Gene Organization

6.3.2.1.

tra gene clusters

6.3.2.2.

trb gene functions

6.3.2.3.

Regulatory elements

6.3.2.4.

Accessory factors

6.3.3.

Mobilization Systems

6.3.3.1.

Mobilizing plasmids

6.3.3.2.

Helper functions

6.3.3.3.

6.3.3.4.

Relaxase enzymes

6.3.4.

Transfer Regulation

6.3.4.1.

Quorum sensing control

6.3.4.2.

TraI/TraR systems

6.3.4.3.

Acyl-homoserine lactones

6.3.4.4.

Population density effects

6.4.

Plasmid Incompatibility

6.4.1.

Incompatibility Groups

6.4.1.1.

Classification systems

6.4.1.2.

Molecular basis

6.4.1.3.

Exclusion mechanisms

6.4.2.

Replication Incompatibility

6.4.2.1.

Origin competition

6.4.2.2.

Initiator titration

6.4.2.3.

Control circuit interference

6.4.3.

Entry Exclusion

6.4.3.1.

Surface exclusion

6.4.3.2.

Pilus retraction

6.4.3.3.

Immunity systems

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7. Plasmid Evolution and Horizontal Gene Transfer