The Three Domain System - Carl Woese

The Three Domain System - Carl Woese

• The Three Domain System, developed by Carl Woese, is a system for classifying biological organisms.
• In 1987, Carl Woese of University of Illinois (USA) summarized ten years of work and proposed a phylogenetic classification system for prokaryotic species based on the nucleotide sequence of 16S rRNA molecules, the RNA of small subunit of prokaryotic ribosome.

                              He concluded that 16S rRNA molecule sequences could not only be used for comparative analysis between different species of prokaryotes but also between prokaryotic and eukaryotic species to provide a tree of relatedness based on common ancestry or genealogy because both prokaryotic and eukaryotic cells contain small subunit rRNA (SSU rRNA).

The Three Domain System 

•  Under this system, organisms are classified into three domains and six kingdoms. The domains are 
  
  • Archaea,  
  • Bacteria,
  • Eukarya. 
  The kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, and Animalia.
• Woese (and many other scientists involved in this project) used the nucleotide sequence of Ribosomal rRNA (the small subunit) and other RNA and protein sequences as an “Evolutionary Chronometer” – an evolutionary time clock.
• What makes rRNA (or another sequence) a good ‘chronometer’?
  

  1. It is universally distributed across group chosen – all organisms have rRNA
  2. It is functionaly similar between organisms – rRNAs all participate in protein synthesis
  3. Its sequence changes slowly - good for looking across long periods of time
  4. The rRNA sequences can be aligned, or matched up, between 2 organisms

  Other sequences that can be used are the large rRNA subunit, or the gene for cytochrome c oxidase, ferredoxin.

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The Three domains - Some Characteristics: 

Domain Archaea

The Archaea possess the following characteristics:

1. Archaea are prokaryotic cells.
2. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of branched hydrocarbon chains (many also containing rings within the hydrocarbon chains) attached to glycerol by ether linkag
3. The cell walls of Archaea contain no peptidoglycan.
4. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukarya.
5. Archaea contain rRNA that is unique to the Archaea as indicated by the presence molecular regions distinctly different from the rRNA of Bacteria and Eukarya
6. Archaea often live in extreme environments and include methanogens, extreme halophiles, and hyperthermophiles. One reason for this is that the ether-containing linkages in the Archaea membranes is more stabile than the ester-containing linkages in the Bacteria and Eukarya and are better able to withstand higher temperatures and stronger acid concentrations
   
   EXAMPLE:  Methanogens( which produce the gas methane), Halophiles(live in very salty water),thermoacidophiles(thrive in acidic high temperature water)

Domain Bacteria (eubacteria)

Bacteria (also known as eubacteria or "true bacteria") are prokaryotic cells that are common in human daily life, encounter many more times than the archaebacteria. Eubacteria can be found almost everywhere and kill thousands upon thousands of people each year, but also serve as antibiotics producers and food digesters in our stomachs.  
The Bacteria possess the following characteristics:

1. Bacteria are prokaryotic cells.
2. Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages
3. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.
4. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya.
5. Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Eukarya.

EXAMPLE:Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria.

They are grouped into five main categories:

• Proteobacteria: This phylum contains the largest group of bacteria and includes E.coli, Salmonella, Heliobacter pylori, and Vibrio. bacteria.
• Cyanobacteria: These bacteria are capable of photosynthesis. They are also known as blue-green algae because of their color.
• Firmicutes: These gram-positive bacteria include Clostridium, Bacillus, and mycoplasmas (bacteria without cell walls).
• Chlamydiae: These parasitic bacteria reproduce inside their host's cells. Organisms include Chlamydia trachomatis (causes chlamydia STD) and Chlamydophila pneumoniae (causes pneumonia).
• Spirochetes: These corkscrew-shaped bacteria exhibit a unique twisting motion. Examples include Borrelia burgdorferi (cause Lyme disease) and Treponema pallidum (cause syphilis).

The Eukarya (eukaryotes)

The Eukarya (also spelled Eucarya) possess the following characteristics:

1. Eukarya have eukaryotic cells.
2. Like the Bacteria, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages
3. Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan.
4. Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics that affect eukaryotic cells.
5. Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Bacteria.

The Eukarya are subdivided into the following four kingdoms:

1. Protista Kingdom: Protista are simple, predominately unicellular eukaryotic organisms. Examples includes slime molds, euglenoids, algae, and protozoans.
2. Fungi Kingdom: Fungi are unicellular or multicellular organisms with eukaryotic cell types. The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis and obtain nutrients through absorption. Examples include sac fungi, club fungi, yeasts, and molds.
3. Plantae Kingdom: Plants are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering plants.
4. Animalia Kingdom: Animals are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and vertebrates.