Tuesday, July 15, 2008

Carl Woese Changed the Tree of Life (The Giant's Shoulders carnival)

Prior to 1977 the tree of life was composed of two branches, prokaryotes and eukaryotes. However, that changed when the Carl Woese lab published the classic paper Classification of Methanogeic bacteria by 16S ribosomal RNA Characterization. This paper introduced a new domain of life, archae (referred to at the time of publication as archaebacteria), and simultaneously created a new paradigm for understanding the origins of life on earth. Furthermore, this paper underscored the importance and power of classifying organisms using genetic relationships instead of morphological similarities.
When Woese began his academic career, the current dogma was that microbes could not be organized phylogenetically, a conclusion based largely on several failed attempts at classifying bacteria by utilizing shape and metabolism. Woese chose to utilize ribosomal RNA (rRNA), an abundant, well-conserved nucleic acid found in all living organisms. Woese successfully used rRNA sequence to unravel the relatedness of several diverse bacteria as well as mitochondria and chloroplasts. His technique of choice was to reconstruct the sequence of the 16S rRNA using oligonucleotide cataloging. Briefly, this method involves digesting the nucleic acid with T1 RNAse, which cuts after every guanine residue, followed by another digestion with an enzyme that cuts after the adenine, cytosine or uracil residues.
Later, Woese began investigating an unclassified, poorly characterized, morphologically diverse group of organisms that exhibited similar biochemistry. The methanogens, as they were called, shared the common ability to grow anaerobically by oxidizing hydrogen and reducing carbon dioxide to methane. The result of this analysis described the relatedness of these organisms to other bacteria and each other.
The paper, Classification of Methanogeic bacteria by 16S ribosomal RNA Characterization, was published in PNAS in 1977, but was not fully appreciated or accepted until several years later.
Fox et al. utilizes oligonucleotide cataloging of 16S rRNA to show that methanogens are a distinct, phylogenetic group. In the discussion, the authors present additional evidence that supports their finding, including, but not limited to: (a) the inability to detect cytochromes within the methanogens; (b) the fact that the cell walls of methanogens do not contain peptidoglycan; (c) the 23S rRNA sequence is also divergent from typical bacteria.
Finally the authors concluded that the “mathanogens ultimately [had] to be classified as a group distinct from other bacteria.” They also discussed the likely possibility that the methanogens represent ancient organisms that might have “existed at a time when an anaerobic atmosphere, rich in carbon dioxide and hydrogen, enveloped the planet and, if so, could have played a pivotal role in this planet’s evolution.”

Although his finding was not embraced by microbiolgists at the time of publication, Woese has since been recognized and awarded for the profound impact he had on microbiology and evolutionary biology. His awards include a MacArthur Fellowship in 1984, election to the National Academy of Sciences in 1988, the Leeuwenhoek Medal in 1992, the National Medal of Science in 2000, the Crafoord Prize from the Royal Swedish Academy of Sciences in 2003 and in 2006 he became a foreign member of the Royal Society.

Fox, G., Magrum, L., Balch, W., Wolfe, R., Woese, C. (1977) “Classification of methanogenic bacteria by 16S ribosomal RNA characterization” Proc Natl Acad Sci U S A 74 (10): 4537–41.
Woese, C., Kandler, O., Wheelis, M. (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.". Proc Natl Acad Sci U S A 87 (12): 4576–9.
Morell, V. (1997) Microbiology's scarred revolutionary. Science 276, 699-702


chall said...

that is one of my favorite papers... maaybe even more so since I read it before I even started my undergrad ( :) ) so I didn't have to relearn too much of the old school vs new school.

..although we did have arguments in the Department about which would go where :)

microbiologist xx said...

Thanks for your comment. When I decided to participate in this carnival, I knew I would pick this paper.
Furthermore, what amazes me is that there is one results section and one figure. Can you believe it?
On a side note, I can't imagine looking at all those films. Yikes.