ARCHAIC GENOME |
Sean Henahan, Access Excellence
CHAMPAIGN, Ill (Aug. 23, '96)
The sequencing of the genome of ancient organisms found in inhospitable climates deep in thermal vents under the sea should greatly advance understanding of the evolution of life on Earth.
The microorganisms known as the archaea are neither eukaryotes nor prokaryotes. Their discovery in 1977 upset the dogma of the time that all life on Earth belonged to one or the other of these groups. The discovery also launched a debate on the genetic origins of the novel life forms.
Researchers at the University of Illinois have now described the entire genome of an archaeon known as Methanococcus janaschii. The organism was found near a hydrothermal
vent 2,600 meters below the surface of the Pacific Ocean. The anaerobic life form lives at temperatures approaching the boiling
point of water and generates energy by converting carbon
dioxide and hydrogen to methane.
The researchers report that the organism's genome consists of a main circular chromosome and two smaller, circular, extra-chromosomal
elements. The complete nucleotide sequence of all of
these elements was determined using the same technology
used to sequence the first complete genome of
a cellular organism, Haemophilus influenzae, a
Unlike most eukaryotes, the genes of M. jannaschii are
densely packed with little noncoding DNA between them.
The proteins coded by the M. janaschii genes, however,
show many structural similarities to eukaryotic
proteins. The transcription apparatus (which
synthesizes RNA in the cell) is quite different from
that of bacteria and seems to be a simpler version of
that found in eukaryotes. The proteins that replicate
DNA also have no counterparts in bacteria, more
closely resembling those found in eukaryotes.
These findings support the idea that the archaea are
more closely related to the eukaryotes than to bacteria,
the researchers said.
"The data confirm what we've long suspected, that the
archaea are related to us, to the eukaryotes; they are
descendants of the microorganisms that gave rise to the
eukaryotic cell billions of years ago," said Carl Woese, a
U. of I. professor of microbiology. It was Woese who first discovered the archaea 20 years ago.
The research suggests the archaea may be related to the
missing link between eukaryotes and earlier life forms.
"The image that has been kicking around in biology ever
since the cellular organization of a eukaryote was
identified is that there had to have been a simple
cell type before the eukaryotes, notes colleague
"The question has been: Who are the present day
cousins of that ancestor? Who is the closest living
relative that is not a eukaryote? The only attempts
to pin that down have been superficial, and it seems
that here it is," Olsen said. "The way the archaea
express their genes is fundamentally different from
the way a typical bacterium does it. In fact, the
archaeal system is structurally like the eukaryotic
system. It has the same componentry."
The discovery of the archaea has changed the way biology is taught, adds Charles G. Miller, head of the
U. of I. microbiology department: "Many beginning
microbiology texts show Woese's universal tree of
life inside the front cover of the book.
Even the way biology is taught to high school
students will change as a result of Woese's work.
We used to learn that 'higher' bacteria evolved into
fungi and protozoa and fungi and protozoa became
plants and animals," Miller said. "Carl's insight
has totally changed this way of thinking. New
generations of biology students will be learning
about Woese's universal tree of life instead."
The project to sequence M. jannaschii is part of
the Department of Energy's Microbial Genome Program,
which was launched in 1994 as a spinoff from the
DOE's Human Genome Program to provide a complete
analysis of the DNA of several microorganisms.
Knowledge gained from studying the archaea -- each
of which has about 2 million base pairs in its genetic
makeup, compared to some 3 billion base pairs in a
human being -- could have payoffs in producing
improved industrial biocatalysts, in cleaning up
pollution through bioremediation, in sewage treatment
and in the development of alternative energy sources.
In terms of microbiology, Woese and Olsen said,
microbial genomics will help to make sense of
microbial diversity, providing an understanding of
the microbial underpinnings of the biosphere that
are essential to the maintenance of all life on Earth.
Woese's development of the use of ribosomal RNA
sequence comparisons has revolutionized the
process of identifying life forms, Olsen said.
"It has given us quantitative measures of diversity
and the ability to look at things and say, 'Wow, this
thing is like nothing we've seen before.' This has
become one of the dominant methods for studying
the diversity of life on Earth, particularly
microbial life," he said.
"Most of the organisms of the ocean have not
been cultivated in a laboratory; in most cases
they are not even closely related to anything
that has been cultivated in a laboratory. We are
clueless as to what these things are doing,"
Olsen said. "It's incredible that we're almost
completely ignorant about some of the most
fundamental processes that underlie the
ecology of the planet."
The current research appears in the Aug. 23, 1996 issue of the journal Science.