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RIP Carl Woese, of three-domains fame

by lpetrich
Tags: carl, fame, threedomains, woese
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lpetrich
#1
Feb8-13, 04:06 AM
P: 530
Carl R. Woese: 1928 – 2012 | The Institute for Genomic Biology

His greatest discovery was a major revision of the overall tree of life.

When he started to get to work on that question in the mid-1970's, he and his colleagues believed that the biggest distinction was between prokaryotes and eukaryotes. But he wanted to learn more. He looked for some biological molecule that might be ubiquitous and convenient to sequence, and he decided on small-subunit ribosomal RNA (SSU rRNA). Back then, it was difficult to sequence a whole strand, so he cut it up with an enzyme and then sequenced the fragments. But that proved good enough.

Typical sizes of ribosomal-RNA strands:
Escherichia coli bacterium: small: 1542 nt, large: 2906 nt
Human: small: 1869 nt, large: 5070 nt, some extras: 121 nt, 156 nt
nt = nucleotides

He put a lot of organisms' SSU rRNA through his sequencing setup, and he compared the sequences that he found.


He made a remarkable discovery, which he published in 1977. There was a deep split in the prokaryotes, a split so deep that it was comparable to the split with the eukaryotes that he also found.

On one side were most of the more familiar prokaryotes, like disease organisms. On the other side was a motley collection of mostly free-living organisms that are often averse to oxygen, and that sometimes inhabit extreme conditions like great heat and acidity. That other side seemed to CW to be the sort of organisms that would do well in the early Earth before the emergence of oxygen-releasing photosynthesis. He decided to named them "archaebacteria" or Archaea. The more familiar ones he named Eubacteria or Bacteria.

So he came up with a classification featuring three side-by-side domains: Eubacteria, Archaea, and Eukarya (eukaryotes).


At first, CW's split of the prokaryotes did not seem very well-supported to some biologists -- the Eubacteria and Archaea seemed more alike than different. However, subsequent research found other gene sequences and various phenotypic features that are consistent with this early split, and by the late 1980's, Woese's three-domain system had become generally accepted. Features like:
  • DNA-polymerase structure - that's the enzyme that replicates the DNA in the genome
  • Membrane-lipid structure
    • Opposite asymmetries of the glycerol's central carbon
    • Fatty acids -- A: isoprene polymer (branched-chain), B: straight chain
    • Fatty acids to glycerol -- A: ether-linked, B: ester-linked
    • Some Archaea have membrane lipids that extend across the cell membrane
  • Initial amino acid of a protein -- A: methionine, B: formylmethionine
  • Resistance to various antibiotics, diphtheria toxin, etc.

But over the last decade or so, a challenge has emerged to CW's three-domain system: the status of Eukarya. By the late 1980's, the endosymbiotic origin of mitochondria and chloroplasts had become well-established, but what about the rest of the cell?

As far as can be determined, the informational systems of Eukarya are much like those of Archaea, while many metabolic enzymes are closer to Eubacteria. So was the ancestral eukaryote an archaeon-eubacterium symbiosis?

Even more difficult for CW's three-domain system is where the eukaryote informational systems branched off from. The three-domain system would picture branching off before the diversification of the ancestors of the present-day Archaea. But there are some studies that claim that those systems branched off from inside Archaea. So we go from 3 to 2 taxa in the highest-level branching of the Tree of Life.

Let's see what's happened over the centuries.
  • Aristotle ~350 BCE, Carolus Linnaeus 1735: Plantae, Animalia
  • Ernst Haeckel 1966: Protista, Plantae, Animalia
  • Herbert F. Copeland 1938: Monera, Protista, Plantae, Animalia (Monera = prokaryotes)
  • Édouard Chatton, Stanier, van Niel 1960's: Prokaryota (Monera), Eukaryota (Protista, Plantae, Animalia)
  • Robert Whittaker 1969: Prokaryota (Monera), Eukaryota (Protista, Plantae, Fungi, Animalia)
  • Carl Woese 1977: Eubacteria / Bacteria, Archaebacteria / Archaea, Eukarya
  • James Lake 1984: Bacteria, Archaea (including Eukarya: the eocyte hypothesis)
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atyy
#2
Feb8-13, 07:44 AM
Sci Advisor
P: 8,665
Maths and physics undergrad.


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