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| 30th Anniversary Of Third Domain Of Life: A "New Continent" |
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| SciMed - Horizons | |||
| TS-Si News Service | |||
| Friday, 19 October 2007 20:01 | |||
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Carl Woese had set out to map the evolutionary history of life
 Carl R. Woese is the world's greatest expert in the field of microbial taxonomy. As practiced for the previous hundred years, reductionist biology assumed that biological processes could be understood by studying genes and molecules. Woese discarded this approach as obsolete. Instead, he promoted a new synthetic biology based on emergent patterns of organization.
Woese set out to map the evolutionary history of life by comparing RNA sequences of a molecular sequence common to all living cells: the ribosome, which manufactures a cell’s proteins.
Each group of organisms contains sets of distinctive genetic sequences in their ribosomal RNA. These genetic “signatures” differentiate the groups. Woese’s analysis of a variety of organisms’ genetic signatures told a story that was different from the conventional wisdom.
Woese led the team in 1977 that identified the archaea as a unique domain of life, distinct from bacteria and other organisms. In doing this, Woese defined the large-scale structure of the primordial tree of life, with all living creatures descended from one of the three branches.
Prior to this finding, generations of evolutionary biologists and microbiologists believed that the microbes now called archaea were simply another taxon among bacteria. They had divided all living organisms into two broad superkingdoms, or domains: prokaryotes (which includes both the true bacteria and archaea); and eukaryotes (including all animals, plants, fungi and protists — a diverse group that includes protozoans, algae, slime molds and other organisms).
Many biologists were unwilling to accept the new classification scheme. They continued to see the archaea as a highly differentiated offshoot of the bacterial line. However, with the passage of time there has been continuing confirmation of the discovery. Their discovery – based on an analysis of ribosomal RNA, an ancient molecule essential to the replication of all cells — opened up a new field of study, and established a first draft of the evolutionary “tree of life.” The influence of this event has been pervasive and wide-ranging.
 Microbiology professor Carl Woese led the team in 1977 that identified the archaea as a unique domain of life, distinct from bacteria and other organisms. Prior to this finding, generations of evolutionary biologists and microbiologists believed that the microbes now called archaea were simply another taxon among bacteria. They had divided all living organisms into two broad superkingdoms, or domains. The prokaryotes included both the true bacteria and archaea. The eukaryotes included all animals, plants, fungi and protists (a diverse group that includes protozoans, algae, slime molds and other organisms). Some prominent biologists still hold to this classification scheme.
Woese set out to map the evolutionary history of life by comparing RNA sequences of a molecular sequence common to all living cells: the ribosome, which manufactures a cell’s proteins.
Each group of organisms contains sets of distinctive genetic sequences in their ribosomal RNA. These genetic “signatures” differentiate the groups. Woese’s analysis of a variety of organisms’ genetic signatures told a story that was different from the conventional wisdom, however.
This surprising discovery came when the researchers looked at the ribosomal RNA (rRNA) of a group of methane-generating microbes that had been classified as bacteria. Illinois microbiology professor Ralph Wolfe, an expert on these “methanogens,” was a member of Woese’s team, along with postdoctoral researcher George Fox, graduate student William Balch and lab technician Linda Magrum.
“Of all the numerous suggestions we had gotten for organisms to study, the one I solicited from my colleague, Ralph Wolfe, turned out to be the most important,” Woese wrote in an account of the discovery. “Ralph was in the process of working out the biochemistry of methanogenesis, which made it natural for him to suggest we characterize the methanogens.”
 Ralph Wolfe was one of only a handful of researchers studying methanogens in the mid-1970s. These organisms were notoriously difficult to grow in culture because they could survive only in an oxygen-free atmosphere that was rich in hydrogen and carbon dioxide. Balch, a graduate student in Wolfe’s lab, had found a way to create a sealed and pressurized atmosphere inside a test tube that would support these organisms, however. Using this technique, a methanogen now called M. bryantii, was grown in sufficient quantities for study.
Woese had already found a collection of rRNA sequences that were specific to bacteria, and another set of sequences unique to plants, animals and other eukarya. When he sequenced the ribosomal RNA of Wolfe’s methanogen, however, he found that it was strikingly different from that of eukarya and bacteria. Although it shared some universal sequences with the other organisms, it also carried its own unique set of sequences that did not fit with either group. It was “neither fish nor fowl,” Woese said.
The scientists were astonished, and quickly turned their attention to other methanogens. The genetic pattern held: The rRNA signatures of the methanogens were distinct from those of eukaryotes and bacteria. Woese concluded that the methanogens were not bacteria.
Wolfe recalled, “When Carl said they weren’t bacteria, I said: ‘Of course they are bacteria! They look like bacteria! They have this prokaryotic
 morphology and cell structure.’ ” But when Wolfe saw how the sequence data fell into discrete groups, with all the methanogens in a category of their own, “I became a believer,” he said. Their findings were published in the Proceedings of the National Academy of Sciences in October 1977 [Download below]. The paper’s three-sentence abstract stated simply that “the methanogens constitute a distinct phylogenetic group… only distantly related to bacteria.” A second PNAS paper, published the following month by Woese and Fox, outlined the evidence that there were three – rather than two – superkingdoms, or domains, of life.
“There was general amazement and feeling that something great had been discovered among the physical scientists,” Woese said.
However, many microbiologists and other life scientists were unwilling to accept the new classification scheme. They continued to see the archaea as a highly differentiated offshoot of the bacterial line.
In 2003, Woese won the Crafoord Prize in Biosciences for his discovery of this “third domain of life.” The prize, given by the Royal Swedish Academy of Sciences, marks accomplishments in scientific fields not covered by the Nobel Prizes in sciences, which the academy also selects.
Controversy over the work continued, however. Some scientists discounted the idea as a “fantastic”
hypothesis based on a limited and unreliable pool of data. To this day, many textbooks, dictionaries and other science reference materials include the “classical” and the Woese classification schemes. However, with the passage of time there has been continuing confirmation of the discovery. Now 79, Woese continues his work as a member of the “Biocomplexity” theme at the Institute for Genomic Biology. He works with collaborators in physics, chemistry, geology and microbiology in a continuing exploration of the genomic complexity of biological systems. He worries about what he sees as a general lack of interest in
evolution among microbiologists and other life scientists. And he hopes that a new generation of scientists will make full use of the genomic tools that he believes could revolutionize the study of the origins and evolution of life. Wolfe, 86, an emeritus professor of microbiology, continues his interest in the
physiology and biochemistry of the methanoarchaea. Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms. Carl R. Woese and George E. Fox. PNAS: November 1, 1977; vol. 74, no. 11, 5088-5090.
Abstract. A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
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