Rhizobium Genetics and Plasmid Biology

  1. Rhizobial Genome Organization
    1. General Genomic Architecture
      1. Genome Size Variation
        1. Range across genera
          1. Correlation with lifestyle
            1. Coding density
            2. Multipartite Genome Structure
              1. Chromosome-plasmid organization
                1. Replicon classification
                  1. Functional distribution
                  2. Genomic Complexity
                    1. Gene number variation
                      1. Repetitive elements
                        1. Horizontal gene transfer signatures
                      2. The Primary Chromosome
                        1. Essential Gene Content
                          1. DNA replication machinery
                            1. Transcription and translation
                              1. Cell division apparatus
                              2. Core Metabolic Pathways
                                1. Central carbon metabolism
                                  1. Amino acid biosynthesis
                                    1. Nucleotide metabolism
                                      1. Energy generation
                                      2. Housekeeping Functions
                                        1. Cell wall biosynthesis
                                          1. Protein folding and degradation
                                            1. Stress response systems
                                            2. Chromosomal Organization
                                              1. Gene clustering patterns
                                                1. Operon structure
                                                  1. Regulatory regions
                                                2. Extrachromosomal Elements
                                                  1. Plasmid Definition and Properties
                                                    1. Autonomous replication
                                                      1. Circular versus linear forms
                                                        1. Size range variation
                                                        2. Megaplasmids and Chromids
                                                          1. Large plasmid characteristics
                                                            1. Chromosome-like features
                                                              1. Essential gene content
                                                              2. Plasmid Classification Systems
                                                                1. Incompatibility groups
                                                                  1. Replication type
                                                                    1. Transfer capability
                                                                    2. Functional Categories
                                                                      1. Symbiotic plasmids
                                                                        1. Catabolic plasmids
                                                                          1. Resistance plasmids
                                                                            1. Cryptic plasmids

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                                                                        1. Introduction to Rhizobium and Nitrogen-Fixing Symbiosis

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                                                                        3. Symbiosis Plasmid Biology