By David N. Leff

For the 21st time since it all began in 1995, another fruit hanging on the evolutionary Tree of Life has had its genome sequenced. This latest member to join the genomic club, a bacterium called Thermotoga maritima, is the oddest ball of them all.

TIGR - The Institute For Genomic Research in Rockville, Md.- published the microorganism's complete sequence in today's Nature, dated May 27, 1999. Its title is, "Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima." This announcement marked the eighth time since 1995 that TIGR has been there, done that - i.e., sequenced a bacterial genome.

It was back in 1986 that field microbiologists reported isolating T. maritima from geothermal heated marine sediments, near the aptly named town of Vulcano in southern Italy. Thermatoga, too, was aptly named: It grows best at temperatures around 80 degrees Celsius, or 176 degrees Fahrenheit, which is just 24 degrees below the boiling point of water.

The 29 TIGR co-authors it took to scope T. maritima's genome reported that it totaled 1,860,725 base pairs, containing 1,877 predicted coding regions. Of those, 863 - or 46 percent - are of unknown function. Thermotoga's place on the Tree of Life sets it wide apart from any of the other 20 organisms sequenced to date by laboratories around the world.

That family tree consists of three main branches growing up and spreading from the dawn of life on Earth. Each represents one of the domains into which all life forms are divided: Archaea, Bacteria and Eukaryotes. Archaea are the weird, single-cell, bacteria-like microorganisms that flourish in the life-defying temperatures of deep-sea volcanic vents.

Bacteria, of course, are all those benign and pathogenic prokaryotes, whose single cells contain no nucleus. Eukaryotes, from yeast to Homo sapiens, consist of cells that do boast nuclei.

Where does Thermotoga maritima fit in on that intricately sub-branching tree?

"As you draw a tree of life," explained molecular evolutionist Jonathan Eisen, a TIGR co-author on the Nature paper, "the earlier branching lineages - as in mammals the duck-billed platypus - so in the bacterial world, Thermotoga, was one of these deeply branching organisms. According to ribosomal RNA [rRNA] gene analysis, it separated from the rest of bacteria very early in bacterial evolution.

"rRNA is found in every living organism," Eisen went on, "so you can compare the sequence of its gene in different organisms, trying to create the likely evolutionary history. So one of the deepest-branching and most slowly evolving lineages of bacteria, namely T. maritima, is of evolutionary significance."

But then Eisen revealed one of the organism's genomic surprises: "One of the main parts of our paper," he told BioWorld Today, "is that, first of all, we cannot find a large amount of support for that deep branching of T. maritima. Now there's a big controversy over how accurate and useful that picture is. One reason is that the rRNA tree of life may not even be correct, may be flawed, inaccurate."

"And that's what the second big point of the Nature paper is about," Eisen pointed out. "Based on analysis of the Thermotoga genome, it looks as if there have been enormous numbers of gene transfers between organisms over time. That throws the tree of life into a bit of disarray, because now it seems that those genomes are really highly mosaic. Different parts of them have different histories."

Eisen added, "The most interesting thing was that a large percentage of the Thermotoga genome is very similar to genes in Archaea. So despite the fact that many parts of its genome suggest that Thermotoga is a bacterium, many other parts have this close relationship to archaic Archaea. It looks as if there have been gene exchanges between their two lineages at some time in the past.

Bacterium Has Potential In Renewable Energy

"One reason that TIGR and the U.S. Department of Energy [DOE] - which funded this study - decided to sequence this particular organism," Eisen related, "is that it has some interesting metabolism. In particular, Thermotoga can degrade and process a bunch of plant polymers - xylan, cellulose, for example. And that is of great interest to DOE because these complex carbohydrates, through conversion to fuels such as hydrogen, have major potential as renewable energy and carbon sources."

So far, DOE has funded three of TIGR's eight bacterial genome sequences, plus another that is completed but not yet published. "That one is Deinococcus radiodurans," Eisen allowed, "which - in contrast to extreme heat resistance - is an extremely radiation-resistant organism. It occurs everywhere, but was originally cultured when people started using radiation to sterilize things, and it survived. D. radiodurans is not pathogenic, as far as people know, so that's not really a problem, but it was the only way they found that organism.

"The DOE is very interested," he went on, "because, among other things, D. radiodurans has the potential to be engineered with particular degradation pathways for cleaning up extremely radioactive waste sites."

"Deinococcus is remarkable," biologist Daniel Drell, in DOE's Office of Science, told BioWorld Today, "because it's got a 3-megabase genome that's distributed over a roughly 2.1 mb major chromosome. It's then got two mini-chromosomes of ballpark 400,000 mb or so, and then it's got a tiny little plasmid, ballpark 45,000 base pairs.

"The thing that kicks me in the head about the Deinococcus genome sequence," Drell observed, "is that it isn't immediately apparent how this bug is so radio-resistant. I'm talking amounts of radiation that are literally two to three thousand times the dose that kills a human. In a sense," he concluded, "it's pure Star Trek - going boldly where no one has gone before."