Rhizobium Genetics and Plasmid Biology

  1. Plasmid Molecular Biology
    1. Plasmid Replication Systems
      1. Replication Origins (oriV)
        1. Origin structure
          1. DnaA boxes
            1. Initiator binding sites
              1. Replication timing
              2. RepABC Replication System
                1. RepA initiator function
                  1. RepB partitioning role
                    1. RepC regulatory activity
                      1. Protein interactions
                      2. Alternative Replication Systems
                        1. RepFIC family
                          1. Rolling circle replication
                            1. Theta replication
                            2. Copy Number Control
                              1. Negative regulation
                                1. Antisense RNAs
                                  1. Protein inhibitors
                                2. Plasmid Partitioning and Stability
                                  1. Active Partitioning Systems
                                    1. Type I systems
                                      1. Type II systems
                                        1. Type III systems
                                          1. ParAB proteins
                                          2. Centromere-like Sequences
                                            1. parS sites
                                              1. Protein binding
                                                1. Nucleoprotein complexes
                                                2. Segregation Mechanisms
                                                  1. Chromosome attachment
                                                    1. Motor proteins
                                                      1. Spatial organization
                                                      2. Stability Maintenance
                                                        1. Multimer resolution
                                                          1. Post-segregational killing
                                                            1. Addiction systems
                                                          2. Plasmid Transfer Mechanisms
                                                            1. Conjugative Transfer
                                                              1. Mating pair formation
                                                                1. Pilus assembly
                                                                  1. DNA processing
                                                                    1. Transfer replication
                                                                    2. Transfer Gene Organization
                                                                      1. tra gene clusters
                                                                        1. trb gene functions
                                                                          1. Regulatory elements
                                                                            1. Accessory factors
                                                                            2. Mobilization Systems
                                                                              1. Mobilizing plasmids
                                                                                1. Helper functions
                                                                                  1. oriT sequences
                                                                                    1. Relaxase enzymes
                                                                                    2. Transfer Regulation
                                                                                      1. Quorum sensing control
                                                                                        1. TraI/TraR systems
                                                                                          1. Acyl-homoserine lactones
                                                                                            1. Population density effects
                                                                                          2. Plasmid Incompatibility
                                                                                            1. Incompatibility Groups
                                                                                              1. Classification systems
                                                                                                1. Molecular basis
                                                                                                  1. Exclusion mechanisms
                                                                                                  2. Replication Incompatibility
                                                                                                    1. Origin competition
                                                                                                      1. Initiator titration
                                                                                                        1. Control circuit interference
                                                                                                        2. Entry Exclusion
                                                                                                          1. Surface exclusion
                                                                                                            1. Pilus retraction
                                                                                                              1. Immunity systems

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                                                                                                          5. Nitrogen Fixation Mechanisms

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                                                                                                          7. Plasmid Evolution and Horizontal Gene Transfer