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The World’s Toughest Bacterium
Deinococcus radiodurans may be a tool for cleaning up toxic waste and more
  
By
Sarah E. DeWeerdt



Featured article.

Deinococcus radiodurans is listed in the Guinness Book of World Records as "the world's toughest bacterium." And for good reason: The microbe can survive drought conditions, lack of nutrients, and, most important, a thousand times more radiation than a person can. The bacterium, whose name means 'strange berry that withstands radiation,' is the most radiation-resistant organism known.


D. radiodurans viewed by light microscopy.

The red, spherical bacterium was discovered nearly fifty years ago in a can of ground meat that spoiled despite having been sterilized by radiation. Today, scientists are searching for ways to exploit the bacterium's remarkable talents. They believe D. radiodurans will prove useful in cleaning up toxic waste and testing hypotheses about life in extreme environments, among other things.


‘The mere existence of D. radiodurans suggests that almost anything is possible.’

An efficient system for repairing DNA is what makes the microbe so tough. High doses of radiation shatter the D. radiodurans genome, but the organism stitches the fragments back together, sometimes in just a few hours. The repaired genome appears to be as good as new.

"The organism can put its genome back together with absolute fidelity," says Claire M. Fraser, of The Institute for Genome Research (TIGR) in Rockville, Maryland. She was the leader of the TIGR team that sequenced D. radiodurans in 1999.

"I was pretty much blown away by it," says John Battista, a microbiologist at Louisiana State University in Baton Rouge, recalling his introduction to the bacterium in 1988.

The bacterium seems to live everywhere and nowhere. It has been found in environments as diverse as elephant dung and granite in Antarctic dry valleys (the environment on Earth thought to most closely resemble Mars), but no one really knows what the microbe's natural habitat is.

No place on Earth exposes life to more than a fraction of the levels of radiation D. radiodurans can withstand. Certainly none of the environments in which D. radiodurans has been found offers a clue as to why the microbe has evolved such astonishing radiation resistance.

The trait may be related to the organism's response to dehydration, which is not uncommon in nature. Dehydration and radiation, it turns out, cause very similar types of DNA damage.

Scientists have speculated that the physical arrangement of D. radiodurans' genome could help the organism accomplish its feats of DNA repair. The microbe carries between four and ten copies of its genome, rather than the usual single copy, and the copies appear to be stacked on top of each other.


D. radiodurans viewed by electron microscopy.

The additional genomes may allow the bacterium to recover at least one complete copy of its genome after exposure to radiation. The proteins and pathways involved in suturing a fractured genome back together are now the focus of a number of studies. Initially, the genome sequence shed frustratingly little light on this question.

"We went in looking for a whole range of wonderful and interesting DNA repair systems and enzymes," says Michael J. Daly, of the Uniformed Services University of the Health Sciences in Bethesda, Maryland, and a collaborator on the sequencing project. "And they just weren't there."

The team found a rather conventional suite of DNA repair genes. Deinococcus radiodurans has fewer DNA repair genes than the radiation-sensitive bacterium E. coli, which is commonly used in laboratory research. At first glance D. radiodurans doesn't appear to possess any DNA repair genes that some other bacterium doesn't also have.

"There was nothing based on the sequence itself that would give you any clue as to why it was so radiation resistant," says Battista. His team at Louisiana State University and colleagues at TIGR are now using microarrays to identify genes in D. radiodurans that are turned on when the bacterium is exposed to radiation.

Several recent studies of the bacterium's DNA repair pathway have focused on one protein that is now known to be essential for radiation resistance—the RecA protein. As part of a larger effort to discover the molecular basis of the extreme radiation resistance, a team led by Daly and Michael M. Cox, of the University of Wisconsin-Madison, characterized and purified the RecA protein in D. radiodurans. Their findings appeared in March in the Journal of Bacteriology.

Last month, Cox and Jong-Il Kim, also of Wisconsin, compared the functions of the RecA protein in D. radiodurans and E. coli. They found that the process for reconstructing DNA involves different pathways in each of the two species. "When subjected to high levels of radiation, the Deinococcus genome is reduced to fragments," they write in Proceedings of the National Academy of Sciences. "RecA proteins may play role in finding overlapping fragments and splicing them together."

The D. radiodurans sequencing project was funded by the US Department of Energy (DOE), which is interested in using the microbe in environmental cleanup. DOE is responsible for more than 3,000 radioactive waste sites around the country, some of which are also contaminated with heavy metals, such as mercury, and toxic chemicals, such as solvents.

The microbial species commonly used in environmental cleanup—a process known as bioremediation—do not survive radiation. To create a 'superbug' that can clean up the environment and endure radiation, Daly and colleagues have inserted genes from other bacteria into D. radiodurans.


TEM micrograph of a thin section of Deinococcus radiodurans strain R1.

The researchers created a strain of D. radiodurans that can break down toluene, an organic chemical found in radioactive waste sites. Another engineered strain converts mercury, also found at these sites, into a much less toxic form. These genetically engineered strains cannot themselves get rid of radiation, but they may speed the cleanup and save money.

"The idea is ultimately to introduce these bacteria into contaminated environments," says Daly. He adds that the goal is probably a long way off, given the widely shared concerns about releasing genetically engineered organisms into the world.

Meanwhile, Daly and other scientists are also pursuing applications of D. radiodurans in a more exotic environment—outer space. The organism could be used in simulations to help scientists predict where to search for life on Mars or elsewhere, or help them understand how to avoid potential 'cross-contamination' between earthly and alien life forms.

Other potential uses of D. radiodurans in space—such as using the microbe for sewage treatment on long space flights or in environmental engineering to make the Martian surface more suitable for human colonization—remain in the realm of speculation. But who knows? The mere existence of D. radiodurans suggests that almost anything may be possible.

Some general properties and a chromosomal display of the organism can be found at the Deinococcus radiodurans R1genome page of TIGR.

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Kim, J.I. & Cox, M.M. The RecA proteins of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways. Proc Natl Acad Sci USA 99, 7917-7921 (June 11, 2002).
 
Kim, J.I. et al. RecA Protein from the extremely radioresistant bacterium Deinococcus radiodurans: expression, purification, and characterization. J Bacteriol 184, 1649-1660 (March 2002).
 
Makarova, K.S. et al. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microb Mol Biol Rev 65, 44-79 (March 2001).
 
Brim, H. et al. Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments. Nat Biotechnol 18, 85-95 (January 2000).
 
White, O. et al. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286, 1571-1577 (November 19, 1999).
 

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