By David N. Leff

Dinosaurs, the largest land animals ever to roam the earth, owe their name to two telling Greek words: dino for deinos, meaning fearful, terrible, monstrous; and saur, meaning lizard.

Deinococcus - a bacterium zillions of times smaller than that terrible lizard - combines deinos with kokkos - a spherical seed or berry. Deinococcus bacteria surfaced back in 1956 when food scientists at the Oregon Agricultural Experiment Station in Corvallis detected the round, pink terrible-berry bacteria in a can of spoiled ground beef and pork.

They had been testing these meat cans for sterilization by gamma irradiation, which had indeed killed off all the other microbes. When their assays revealed that this anonymous bacterium was six to eight times more resistant to radiation than a reference Staphylococcus bacterium, they and other microbiologists named it Deinococcus radiodurans - "terrible berry bacterium that endures radiation."

The pink, berry-shaped bug has since proved capable of surviving ionizing radiation 1,000 times higher than levels lethal to humans. Not that the heroic bacterium simply shrugged off such unprecedented, DNA-pulverizing, doses of radiation. Instead, amazingly, it could - in just 24 hours - reassemble the hundreds of scattered DNA shards into their original conformation.

This was a bug to be reckoned with. So reckoned the U.S. Department of Energy (DOE). Three years ago, its Office of Biological and Environmental Research gave $2.1 million to The Institute for Genomic Research (TIGR) in Rockville, Md., to sequence the complete genome of Deinococcus radiodurans.

Today's issue of Science, dated Nov. 19, 1999, reports completion of that feat, in an article titled: "Genome sequence of the radioresistant bacterium Deinococcus radiodurans R 1."

The medium-size microbe, 2 to 3 microns in diameter, consists of 3,284,156 base pairs, composed of two chromosomes plus two smaller plasmids. Chromosome I is 2,648,638 bp long; chromosome II, 412,348. The auxiliary "megaplasmid" has 177,466 bp; the smaller plasmid, 45,704.

Hunting Down Genes Under Deep Cover

Genomicist/molecular biologist Owen White is TIGR's project leader for sequencing D. radiodurans, and lead author of the Science paper. "The number of genes in the genome," he told BioWorld Today, is 3,193, of which the total genes identified to have an assigned function number of 1,482." That is, just over 46 percent of unknown function remain.

"What's interesting about Deinococcus," White observed, "is its ability to repair DNA. A number of DNA-repair genes have been characterized in other organisms, and at first glance, by sequence homology similarities, D. radiodurans seems to have a garden variety of those genes. But, for example," he went on," in Escherichia coli there might be one pathway for excising a damaged base and removing it from the cell, and there might be a different such pathway in Bacillus subtilis. Whereas D. radiodurans has got them both."

In oral presentations, White draws the analogy that "you can think of Deinococcus as being like a Cadillac, an automobile that doesn't necessarily have any new features that aren't seen in at least one other car, but a Cadillac is considered a luxury car because it has all the features."

The TIGR genomicist expects that "knowledge of the sequence is going to increase dramatically the number of Deinococcus researchers in the field. Until now," he pointed out," because it was shown long ago not to be a human pathogen - didn't pose any kind of health risk - it has remained a research backwater. The number of people that have been doing Deinococcus research," White continued, "would fit in a minivan. And that compares to the really quite considerable number involved in DNA repair."

TIGR considers the sequencing of D. radiodurans as a work still in progress. "We are continuing to do research on the bacterium," White said. "We will take all the genes associated with the organism and spot the DNA of each of them onto microarray chips. We will be performing experiments looking at the expression of these genes under certain environmental conditions, such as exposure to irradiation, using microarray technology.

"Another thing about Deinococcus that's kind of interesting," White pointed out, "is that if you think of just 1 gram of organically rich soil, there's probably 10 to the 9^th - a billion - different bacteria in that gram. Let's say that there's only one or two Deinococcus cells among them. You don't just discover Deinococcus, which doesn't compete very well with other organisms, unless you kill everything else. If you select for it by irradiating that soil, you'll then plate it out and see it. It's found in a lot of different places on the planet.

"As for what Deinococcus feeds on," White recounted, "as a likely soil-borne bacterium, it's probably eating the different organics that you see there. The fact that the microbe is isolated on meats suggests that it's good at metabolizing proteins. And from what we found in analyzing the genome, there are other components that suggest the bacterium is probably good at growing on its dead cousins.

"People in the biotech community," White concluded, "are going to be interested in Deinococcus from the point of view of it being an exquisite organism to be used for industrial processes, and may outcompete E. coli for that activity."

Tackling Nuclear Weapons Waste Sites

DOE has a number of toxic waste sites in its former nuclear weapons complex that are contaminated with mixtures of highly radioactive materials and poisonous chemicals. D. radiodurans can be engineered to degrade the organic solvent, toluene, and "fix" mercury, thus simplifying the bioremediation challenge.

At DOE's Office of Biological And Environmental Research, biologist Daniel Drell observed, "What strikes me about Deinococcus is that, despite having the complete genomic sequence, the now-familiar significant percentage of predicted genes don't appear to have any relationships to genes that we know anything about. In this microbe," he told BioWorld Today, "we've got the usual number of hypothetical proteins, about which we can say literally nothing, because they just don't look like anything we've experienced."

Drell went on: "Another remarkable feature of D. radiodurans is that, with the full sequence in hand, given what we have discovered in the past about DNA repair systems in other organisms, it's just not obvious why the bacterium can withstand the radiation doses that it can. We don't know how it works. The sequence," he concluded, "constitutes essentially a parts list, but it's not an owner's manual."