Molecular Genetics of Bacteria

• Authors: Larry Snyder, Joseph E. Peters, Tina M. Hekin, Wendy Champness
• Fourth Edition, 2013

Introduction

Three Domains of Life (p. 3-5)

• Why three domains?
  • “Sequence data show that Homo sapiens differ from chimpanzees by only about 2% of DNA sequence while 25-50% of the genes in a typical bacterium are unique to the species.” (p. 3)
  • Also, while mammals diverged from each other in the ~100mya, bacterial lineages diverged on the order of billions of years ago.
  • p.6 - Patrick Forterre suggested in 2006 that all three domains lived in RNA world and all three independently developed DNA as the archival medium from three distinct infections from three different DNA viruses.
• Note, spp. refers to “several different unknown species under a known genus”.
• Domain 1: Bacteria (p. 3)
  • Challenging to use traditional phenetics to classify bacteria based on their shapes, sizes, and appearances even though there is great diversity here. Better to use 16s of rRNA.
  • Cyanobacteria were originally confused for plants (deprecated name: blue-green algae) because they have chlorophyll and are often filamentous. In fact filamentous cyanobacteria are multicellular.
  • Streptomyces are gram-positive and are the largest genus of Actinobacteria. Appearance-wise, they form hyphae and stalks of spores which make them look like fungi.
  • Caulobacter spp. are gram-negative and have both free-swimming and sessile forms that attach to surfaces through a holdfast structure.
  • Myxococcus are a type of gram-negative myxobacteria that are similar to slime molds in that they can change from free-living single-celled organisms into aggregations of fruiting bodies.
  • Gram-staining
    • The primary stain is crystal violet which accumulates in petidoglycan. Petidoglycan is a polymer of sugar and amino acids and forms aa thick mesh-like material outside the plasma membrane of bacteria.
      • Petidoglyocan contributes 50-90% to the cell envelope for Gram-positive bacteria but only ~10% of the cell envelope for Gram-negative bacteria.
      • After washing out excess crystal violet, only the Gram+ bacteria retain the stain, turning purple/violet.
      • The Gram-negative bacteria are counterstained with safranin and turn pink.
  • Gram-positive species turn purple after stain
    • High G+C percentage in DNA branch: actinomycetes, Mycobacterium
      • Streptomyces the most important genus of Actinobacteria. Streptomyces spp are an attractive alternative to E. coli when producing industrial quantities of biotech materials. Streptomyces produce over two-thirds of clinically useful antibiotics of natural origin.
    • Low G+C percentage in DNA branch include Actinobacteria and Firmicutes (Bacillus, clostridia, lactic acid bacteria, mycoplasms)
  • Gram-negative species turn pink after sstain
    • Proteobacteria, e.g., E. coli, Psudomonas, Rhizobium
    • Caulobacter spp. which are free-living and sessile
    • Myxococcus spp. such as Myxococcus xanthus
• Domain 2: Archaea (p. 3-5)
  • Most extremophiles are archaea, but archaea are also live in many non-extreme environmments (p.5)
  • Two primary phyla:
    • Euryarchaeota which include methanogens, halophiles, and hyperthermophiles
    • Crenarchaeota which include sulfur-dependent thermophiles and perhaps the most well-studied archeaon Sulfolobus solfataricus
• Domain 3: Eukaryotes (p. 5)
  • Includes all nucleus- and organelle-bearing species such as plants, animals, fungi, as well as all single-celled eukaryotes (e.g., yeast and all other protists).
  • From a cladistic perspective, Protista is paraphyletic.
  • “In spite of widely diverse appearances, lifestyles, and relative complexity, all eukaryotes are remarkably similar at the biochemical level, particularly in their pathways for macromolecular synthesis.”
  • Endosymbiotic Theory posits that mitochondria are descended from Alphaproteobacteria while chloroplasts are derived from ancestral Cyanobacteria.

Bacteriology Techniques and Advantages (p. 6-8)

• Bacteria are haploid
• Short generation times (20 minutes for E. coli)
• Asexual reproduction
• Colony growth on agar plates
• Colony purification (p. 7) and selection (p. 8)
• Serial dilutions
• Storing stocks of bacterial strains
• Genetic Exchange

Phage Genetics

A Brief History of Bacterial Molecular Genetics (p. 9)

• Three types of lateral genetic transfer (LGT) aka horizontal genetic transfer (HGT):
  1. Transformation – asynchronous absorption of DNA without viral vector
  2. Conjugation – sex between 2 connected bacteria via pilli
  3. Transduction – asynchronous transmission of DNA via viral vector

Papers to read

• 2006 Patrick Forterre, *Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain
• Genome Taxonomy Database (GTDB) based in Australia
  • 2020 Parks, Chuvochina, Chaumeil, Rinke, Mussig and Hugenholtz A complete domain-to-species taxonomy for Bacteria and Archaea