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ARCHAIC GENOME

By 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 human pathogen.

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 Gary Olsen:

"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.


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