The singular quest for a universal tree of life

Abstract

Carl Woese developed a unique research program, based on rRNA, for discerning bacterial relationships and constructing a universal tree of life. Woese's interest in the evolution of the genetic code led to him to investigate the deep roots of evolution, develop the concept of the progenote, and conceive of the Archaea. In so doing, he and his colleagues at the University of Illinois in Urbana revolutionized microbiology and brought the classification of microbes into an evolutionary framework. Woese also provided definitive evidence for the role of symbiosis in the evolution of the eukaryotic cell while underscoring the importance of lateral gene transfer in microbial evolution. Woese and colleagues' proposal of three fundamental domains of life was brought forward in direct conflict with the prokaryote-eukaryote dichotomy. Together with several colleagues and associates, he brought together diverse evidence to support the rRNA evidence for the fundamentally tripartite nature of life. This paper aims to provide insight into his accomplishments, how he achieved them, and his place in the history of biology.

Photograph of Carl working on a fingerprint, circa 1976. (Courtesy of Ken Luehrsen.)

Fig 1

The fingerprint produced by ribosome T₁ digestion of E. coli 16S rRNA is shown. Each spot contains one or more individual digestion products. They congregate in groups based on uracil content that are referred to as isopliths. Within each isoplith, the spots are further separated by the number of residues they contain. Thus, spot 24d is one of several tetramers with 2 uracil residues and 18b is an 8-mer with one uracil. The spots labeled 05x and 05y (in red) contain posttranscriptionally modified nucleotides that cause them to have aberrant mobility. The absence of these highly characteristic spots on the methanogen 16S rRNA fingerprints was the first indication of the uniqueness of the Archaea. (Adapted from reference with permission of the publisher.)

Carl at a light table with various fingerprints in the background. (Courtesy of the Institute for Genomic Biology, University of Illinois at Urbana-Champaign.)

Fig 2

The E. coli RNase T₁ oligomers ≥6 residues in length are mapped onto the secondary structure of 16S rRNA. It is immediately seen that they are an extremely good sample of the entire sequence. In addition to being distributed throughout the RNA, they frequently cover only one side of helical regions. (Adapted from reference with permission from Elsevier.)

Cropped color photograph of Carl taken by Tom Roberts in July 2002. (Courtesy of the Institute for Genomic Biology, University of Illinois at Urbana-Champaign.)