Mesoplasma florum:Physiology

From White

• Structure and function

• Growth and cell division

• Membrane bioenergetics: the proton potential

• Electron transport

• Regulation of the metabolic pathways

• Bioenergetics in the cytosol

• Central metabolic pathways

• Metabolism of lipids

• Metabolism of Nucleotides

• Metabolism of amino acieds

• DNA synthesis

• RNA synthesis

• Protein synthesis

• Inorganic metabolism

• Fermentation

• Homeostasis

• Membrane transport

• Protein transport

• Physiologic response to environment and stress

From Neidhardt

• Composition and organization of the bacterial cell

• Structure and function of the bacterrial cell parts

• assembly and polymerization: the bacterial interior

• Assembly and polymerization: the bacterial envelope

• Biosynthesis and fueling

• Quest for food

• Growth of cells and populations

• Effects of temperature, pressure and pH

• Genetic adaptation: the genome and its plasticity

• Genetic adaptation: genetic exchange and recombination

• Coordination of metabolic reactions

• Regulation of gene expression: individual operons

• Regulation of gene expression: multigene systems and global regulation

• Cell cycle

• Growth rate as a variable

From Schumann

• Structure of a bacterial cell
  • cytoplasm compartment
  • cytoplasmic membrane compartment
  • extracellular matrices
  • appendages

• Organization of the bacterial chromosome
  • structure of the chromosome
  • principles to compact the bacterial chromosome
  • superhelicity
  • histone like proteins in E. coli
  • ogranization of the bacterial chromosome into genes and repetitive sequences
  • genes
  • repetitive sequences
  • large rearrangements within the chromosome
  • duplications
  • deletions
  • inversions

• The bacterial cell cycle: Replication of the chromosome, partitioning, and cell divison
  • replication of circular chromosomes
  • partitioning of daughter chromosomes
  • cell division

• Recombination
  • homologous recombination
  • the RecBCD pathway of homologous recombination
  • The RecF pathway of homologous recombination
  • additional homologous recombination functions
  • recovery of replication at a blocking DNA lesion
  • sequence specific recombination
  • integration/excision systems
  • resolvase systems
  • inversion systems
  • shufflons
  • integrons
  • homing endonucleases
  • illegitimate recombination
  • insertion sequence elements
  • transposons
  • transposing bacteriophages
  • mechanisms of transposition
  • conjugative and integrative elements
  • nonhomologous endjoining (NHEJ)

• Origin of Mutations and Repair of DNA lesions
  • Classes of mutations
  • Origin of mutations
  • Spontaneous mutations
  • Induced mutations
  • Detection systems for mutations
  • Adaptive mutations
  • Repeair of DNA lesions
  • The methyl-mediated mismatch repair system
  • Very short patch repair
  • The nucleotide excision repair systems
  • Pathways of base excision repair
  • Repair of oxidized nucleotides
  • Photoreactivation of cyclobutane dimers
  • Transcription coupled nucleotide excision repair
  • The adaptive response
  • The SOS response
  • Replication and repair
  • Repair of interstrand crosslinks in DNA
  • Deinococcus radiodurans

• Principles of Gene Regulation
  • Regulation at the level of DNA
  • Alterations of the structure of the DNA
  • GATC methylation and gene expression
  • Programmed DNA rearrangements within the chromoosome
  • Transcriptional silencing and cryptic genes
  • Regulation at the level of transcription
  • The DNA dependent RNA polymerase
  • Regions of the promoter
  • Initiation of transcription
  • Elongation of transcription
  • Termination of transcription
  • Anti-sigma factors
  • Anti-termination/Attenuation of termination
  • Regulatiors of the DNA dependent RNA polymerase
  • Post-transcriptional regulation
  • Protein mediated regulation
  • Riboregulation
  • Riboswitches
  • mRNA decay
  • Introns
  • RNA binding proteins
  • Rgulation at the level of translation
  • Initiation of translation
  • Elongation of translation
  • Termination of translation
  • Ribosome recycling
  • Translational control
  • The 21 and 22 amino acids selenocysteine and pyrrolysine
  • Mechanisms to create multiple gene products from a single cistron
  • Post-translational regulation
  • Proteolysis
  • Protein splicing
  • Protein glycosylation
  • Circular polypeptides

• Protein quality control through chaperones, protein folding catalysts and ATP-dependent proteases
  • Introduction
  • Molecular chaparones
  • Folder chaparones
  • Holder chaparones
  • Disaggregating chaparones
  • Intramolecular chaparones
  • Folding of nascent polypeptide chains
  • Protein-folding catalysis
  • Peptidyl-prolyl isomerases
  • Disulfide bond formation
  • Proteases
  • ATP-dependent proteases
  • ATP-independent proteases

• Secretion of proteins
  • Introduction
  • Protein sorting signals for subcellular localization
  • Cytosolic targeting factors
  • Translocases move mewly made proteins into or across membranes
  • The Sec pathway of protein translocation through the inner membrane
  • The Tat pathway of secretion proteins through the inner membrane
  • Insertion proteins into the inner membrane
  • Anchoring of lipoproteins into the outer membranes
  • Protein translocation pathways through both membranes of gram-negative bacteria
  • The type I secretion pathway
  • The type II secretion pathway
  • The type III secretion pathway
  • The type IV secretion pathway
  • The type V secretion pathway (Autotransporter)
  • Vesicle-mediated export
  • Cell wal anchored surface proteins
  • S-layers

• Stress genes and their regulation
  • The stress response pathway
  • The heat shock response
  • The cold shock response
  • The osmotic shock response
  • The hyperosmotic shock response
  • The hyposomotic shock response
  • The oxidative shock response
  • The OxyR regulon
  • The SoxRS regulon
  • pH regulated genes
  • Acid stress
  • Alkaline stress
  • Metabolic stress: the stringent response
  • Nutrient limitations (starvation stress)
  • Envelope stress response

• Exchange of genes: transformation, conjugation and transduction
  • Transformation
  • Transformation of gram-positive bacteria
  • Transformation of gram-negative bacteria
  • Cojugation
  • Gram-negative bacteria
  • Gram-positive bacteria
  • Conjugative transposons
  • Transduction
  • Generalized transduction
  • Specialized transduction
  • Horizontal gene transfer

Organizational ideas

• Structure & composition
• Information and control
• Transport systems
• Degradation pathways
• Fermentation and energy production
• Synthetic pathways
  • DNA replication
  • RNA transcription
  • Protein production
  • Cell division