18.03 Three Domains – Bacteria, Archaea, and Eukarya

Overview of the Three Domains

• Historical Perspective:
  • Previously, organisms were classified as prokaryotes (no nucleus) or eukaryotes (with nucleus).
• 1970s: Discovery of extremophiles (organisms thriving in extreme environments, e.g., hot springs, volcanic vents).
  • Extremophiles had genes coding for ribosomal RNA that resembled eukaryotic RNA.
  • Shared features with both bacteria and eukaryotes → led to rethinking of classification.
• Molecular Taxonomy:
  • Molecular biology studies revealed significant differences.
  • Introduced the domain as the highest taxonomic rank to reflect differences between typical bacteria and extremophiles.
  • Prokaryotes divided into two domains: Bacteria and Archaea.
  • All eukaryotes placed in the domain Eukarya.

Characteristic Features of Each Domain

1. Domain Bacteria

• General Characteristics:
  • Prokaryotic organisms (no nucleus or membrane-bound organelles).
  • Found in diverse environments (soil, water, human body).
  • Includes photosynthetic bacteria (e.g., cyanobacteria) and pathogenic bacteria.
• Key Features:
  • Cell Structure:
    • No nucleus; DNA exists as a circular chromosome.
    • DNA does not associate with histone proteins.
    • Plasmids (small circular DNA) often present.
    • No membrane-bound organelles (e.g., mitochondria, ER, Golgi).
  • Ribosomes:
    • 70S (smaller than eukaryotic ribosomes).
  • Cell Wall:
    • Always present; contains peptidoglycans (unique to bacteria).
  • Cell Division:
    • Reproduce asexually through binary fission, not mitosis.
  • Morphology:
    • Typically single cells or small groups.
  • Metabolism:
    • Diverse metabolic pathways (aerobic, anaerobic, photosynthetic).
• Examples:
  • Nostoc (filamentous cyanobacterium): fixes carbon dioxide via photosynthesis and nitrogen in specialized cells.

2. Domain Archaea

• General Characteristics:
  • Prokaryotic organisms.
  • Many are extremophiles, thriving in extreme environments like high-temperature hot springs, high-salinity lakes, and deep-sea hydrothermal vents.
  • Found in less extreme habitats (e.g., plankton in oceans).
• Key Features:
  • Cell Structure:
    • No nucleus; DNA exists as a circular chromosome.
    • DNA associates with histone proteins (similar to eukaryotes).
    • Plasmids often present.
    • No membrane-bound organelles.
  • Ribosomes:
    • 70S ribosomes with unique subunit features similar to eukaryotes.
    • rRNA sequences and ribosomal proteins resemble eukaryotic ribosomes more than bacterial ribosomes.
  • Membrane Composition:
    • Unique lipid composition (ether-linked lipids) not found in bacteria or eukarya.
  • Cell Wall:
    • Always present but lacks peptidoglycans.
  • Cell Division:
    • Reproduce asexually by binary fission.
  • Metabolism:
    • Can produce methane (methanogenesis).
    • Respire anaerobically, using sulfur instead of oxygen.
  • Examples:
    • Pyrococcus furiosus: thrives at near-boiling temperatures; freezes below 70°C.
  • Ecological Role:
    • Important in oceanic plankton and methane production.

3. Domain Eukarya

• General Characteristics:
  • Includes all eukaryotic organisms (cells with a nucleus and membrane-bound organelles).
  • Extremely diverse, ranging from unicellular protoctists to multicellular plants and animals.
• Key Features:
  • Cell Structure:
    • Nucleus: contains DNA organized into linear chromosomes with histone proteins.
    • Membrane-bound organelles (e.g., mitochondria, ER, chloroplasts).
  • Ribosomes:
    • 80S ribosomes in cytosol (larger than prokaryotic ribosomes).
    • Mitochondria and chloroplasts contain 70S ribosomes (similar to prokaryotes).
    • DNA in chloroplasts and mitochondria is circular.
  • Cell Wall:
    • Present in some eukaryotes (plants: cellulose; fungi: chitin).
  • Cell Division:
    • Reproduce by mitosis (asexual reproduction) and meiosis (sexual reproduction).
  • Morphology:
    • Unicellular, colonial, or multicellular forms.
  • Metabolism:
    • Great diversity; includes heterotrophic and autotrophic organisms.
  • Examples:
    • Plants (Hibiscus rosa-sinensis), animals (Loxodonta africana), protoctists, fungi.

Key Differences Between Bacteria, Archaea, and Eukarya

Distinctive Features of Archaeans Compared to Bacteria

1. Membrane Composition:

• Archaeans have unique ether-linked lipids, while bacteria have ester-linked lipids.

1. Ribosomal Structure:

• Archaeal ribosomes share similarities with eukaryotic ribosomes, particularly in rRNA sequences and ribosomal protein structures.

1. Cell Wall Composition:

• Archaeans lack peptidoglycans in their cell walls; their cell walls have unique structures.

1. Transcription Process:

• Archaeans use transcription machinery (RNA polymerase, transcription factors) that is more similar to eukaryotes.

Key Insights

• Archaea and Eukarya share a later evolutionary split, evidenced by genetic and molecular similarities.
• Bacteria and Archaea diverged early in evolutionary history.