Carl Woese In Forefront Of Bacterial Evolution Revolution
By Lisa Holland
For the better part of this century, microbiologists have largely ignored evolutionary
relationships among bacteria. But a revolution has occurred in microbiology with the
advent of nucleic sequencing: Today, new phylogenetic relationships can be
determined in far more detail and depth than was ever thought possible.
Carl R. Woese, 62, of the department of microbiology at the University of Illinois in
Urbana, is widely considered the leader of this revolution. His 1987 review, "Bacterial
evolution," published in Microbiological Reviews (51:221-71, 1987),
comprehensively summarizes work done over the previous 10 years on the new
phylogenetic
categorization in microbiology. With more than 300 citations already (as tabulated
from the Institute for Scientific Information's Science Citation Index), this review
stands as the most cited microbiology paper of those published in the last three years
(see accompanying chart).
Woese's paper discusses past failed attempts at developing a bacterial phylogeny.
Stymied by technical difficulties, early micro- biologists gave up and discounted the
area as unnecessary to the advancement of their field. But Woese argues in his review
that without credible evolutionary guidelines, the theory that divides all organisms
into either eukaryotes or prokaryotes rests on a shaky foundation. In his paper, he
outlines the eubacterial and archaebacterial phylogenies that have been defined using
sequencing data.
The importance of the new bacterial phylogeny goes far beyond a rewritten taxonomy,
however. A detailed, accurate phylogenetic tree will help scientists understand
bacteria not only in terms of their morphologies and biochemistries but also according
to their relationships to other bacteria. This understanding will have a profound
effect on the design and interpretation of experiments. Furthermore, sequencing
information has extended the scope of evolutionary knowledge nearly tenfold. "It shows
the evolutionist an intimacy between the evolution of the planet and the life forms
thereon that he has never before experienced," says Woese.
Trained as a biophysicist, Woese characterizes his switch from biophysics to
evolutionary problems as "an evolutionary process." His early studies of translation and
the
nature of ribosomal RNA eventually focused on the genetic code as an evolutionary
problem. He began using nucleic sequencing technology, developed in the early
1960s, to determine ribosomal RNA sequences. Scientists consider these molecules to
be the best historical chronometers because they occur in all organisms. Also, the
different positions in their sequences change at different rates, making it possible to
use these molecules to measure both close and the most distant phylogenetic
relationships.
In the early days, reverse transcrip-tase had not yet been discovered, so it was not
possible to determine complete ribosomal RNA sequences. By comparing ribosomal
RNA fragments, however, researchers were able to identify phylogenetic groupings at
many levels.
In 1977, Woese used this method, called oligonucleotide cataloging, to determine that
the extreme halophiles, methanogens, and extreme thermophiles, now called the
archaebacteria, are a distinct kingdom and not as closely related to the eubacteria
(such as cyanobacteria or purple bacteria) as was previously thought (C.R. Woese et
al., PNAS, 74:5088-90, 1977).
"Woese had to overcome a lot of initial resistance in getting the science community to
accept that it is possible to establish phylogenetic trees for bacteria,"
microbiologist Roy A. Jensen of the University of Florida in Gainesville tells The
Scientist. "Many scientists didn't trust the conclusions drawn from the sequence data."
Today most microbiologists have accepted nucleic sequencing as a valid tool to
determine bacterial evolution. There is still a debate, however, over the best way to
analyze sequence data to produce phylogenetic relationships. The two main and
conflicting methods - those of Woese and of James A. Lake of the Molecular Biology
Institute of the University of California at Los Angeles - were compared last year (see
M. Gouy and W.-H. Li, Nature, 339:145-7, 1989), and evidence was found, by these
reviewers, in support of Woese's arguments.
Still, the discrepancies produced by both Woese's and Lake's methodologies have yet
to be reconciled. But until a verifiable analytic method is defined, Woese argues
that "phylogenies derived from sequence analysis have to be accepted for what they
minimally are: hypotheses, to be tested and either strengthened or rejected on the
basis of other kinds of data."
Meanwhile, scientists are using the newly developed bacterial phylogenetics as a
springboard for further experiments. For example, Jensen is studying the evolutionary
biochemical pathways in organisms. When phylogenetic divergence of bacteria occurs
relatively close in time, ascertaining the exact order of the tiny branching in a
tree is difficult with nucleic sequencing. But once a credible phylogenetic tree is
available, scientists can track a biochemical feature, such as gene fusions that produce
multifunctional proteins, through history to fine-tune the branching order
(Biosciences, 38:99-103, 1988). Scientists in other fields also use this methodology. For
example, Norman Pace, of the Institute of Molecular and Cellular Biology at Indiana
University in Bloomington, uses the new branching orders to study how related
organisms interact on an ecological level.
Woese tells The Scientist that he is now concentrating on fleshing out the entire
bacterial tree and identifying the branching subgroups. Ultimately, he hopes to unravel
the identity of the universal ancestor, from which all organisms have descended.
Before this will happen, he says, the entire bacterial genome must be identified.
"Understanding the bacterial genome is necessary to open many doors throughout the
entire field of biology and evolutionary study," says Woese. "Unfortunately, the
thrust today is unraveling genomes in the medical arena, but this is like putting the
cart before the horse. People who think that the medical genome project will have
more impact are wasting their money."
Lisa Holland is a freelance science writer based in New York City.