Rhizobium Genetics and Plasmid Biology

  1. Nitrogen Fixation Mechanisms
    1. Nodule Development and Structure
      1. Nodule Morphology Types
        1. Determinate nodule characteristics
          1. Spherical structure
            1. Limited growth
              1. Uniform bacteroid population
              2. Indeterminate nodule features
                1. Cylindrical shape
                  1. Persistent meristem
                    1. Developmental zones
                  2. Nodule Anatomy
                    1. Outer cortex
                      1. Inner cortex
                        1. Infected zone
                          1. Vascular bundles
                          2. Cellular Organization
                            1. Infected cells
                              1. Uninfected cells
                                1. Vascular elements
                                  1. Gas-filled spaces
                                2. Bacteroid Development
                                  1. Symbiosome Formation
                                    1. Endocytosis process
                                      1. Membrane biogenesis
                                        1. Compartment establishment
                                        2. Peribacteroid Membrane
                                          1. Membrane composition
                                            1. Transport functions
                                              1. Metabolite exchange
                                              2. Bacteroid Differentiation
                                                1. Morphological changes
                                                  1. Metabolic reprogramming
                                                    1. Gene expression alterations
                                                    2. Terminal versus Reversible Differentiation
                                                      1. Irreversible changes
                                                        1. Cell cycle arrest
                                                          1. Polyploidy development
                                                        2. Nitrogenase Enzyme System
                                                          1. Enzyme Complex Structure
                                                            1. Component I (MoFe protein)
                                                              1. Component II (Fe protein)
                                                                1. Cofactor composition
                                                                  1. Protein interactions
                                                                  2. Catalytic Mechanism
                                                                    1. Substrate binding
                                                                      1. Electron transfer
                                                                        1. ATP hydrolysis
                                                                          1. Product formation
                                                                          2. Cofactor Biosynthesis
                                                                            1. FeMo-cofactor assembly
                                                                              1. Iron-sulfur cluster formation
                                                                                1. Molybdenum incorporation
                                                                              2. Nitrogen Fixation Genetics
                                                                                1. nif Gene Organization
                                                                                  1. nifH encoding
                                                                                    1. nifD and nifK functions
                                                                                      1. nifE and nifN roles
                                                                                        1. Cofactor synthesis genes
                                                                                        2. fix Gene Functions
                                                                                          1. Symbiosis-specific requirements
                                                                                            1. Electron transport components
                                                                                              1. Metabolic adaptations
                                                                                                1. fixABCX operon
                                                                                                  1. fixNOQP cluster
                                                                                                  2. Regulatory Networks
                                                                                                    1. NifA transcriptional activator
                                                                                                      1. FixLJ two-component system
                                                                                                        1. Oxygen sensing mechanisms
                                                                                                          1. Metabolic integration
                                                                                                        2. Oxygen Management
                                                                                                          1. Oxygen Sensitivity Problem
                                                                                                            1. Nitrogenase inactivation
                                                                                                              1. Oxidative damage
                                                                                                                1. Metabolic constraints
                                                                                                                2. Nodule Oxygen Control
                                                                                                                  1. Diffusion barriers
                                                                                                                    1. Oxygen gradients
                                                                                                                      1. Microaerobic zones
                                                                                                                      2. Leghemoglobin Function
                                                                                                                        1. Oxygen buffering
                                                                                                                          1. Facilitated diffusion
                                                                                                                            1. Respiratory support
                                                                                                                            2. Protective Mechanisms
                                                                                                                              1. Antioxidant systems
                                                                                                                                1. Repair mechanisms
                                                                                                                                  1. Metabolic adjustments

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                                                                                                                              4. Molecular Communication and Nodulation

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                                                                                                                              6. Plasmid Molecular Biology