Deinococcus radiodurans

Scientific classification
Kingdom: Bacteria Phylum: Deinococcus-Thermus Class: Deinococci Order: Deinococcales Family: Deinococcaceae Genus: Deinococcus Species: radiodurans
Binomial name
Deinococcus radiodurans

Description and significance

Deinococcus radiodurans, meaning "strange berry that withstands radiation", is a non-pathogenic, Gram-positive aerobic bacteria classified as a member of the family Deinococcaceae. Reddish-pink in color due to the presence of carotenoid pigment, the bacterium has a roughly spherical shape, taking the diplococci form (clusters of two cells) in early growth stages and the tetracocci form (clusters of four cells) in later stages of growth. Nicknamed, "superbug" and "Conan the Bacterium" and was named "the world's strongest (by Guinness World Book or Records), D. radiodurans is the most radiation-resistant vegetative cell, resisting radiation in the megarad range. D. radiodurans was discovered and subsequently isolated in 1956 by Arthur W. Anderson during a laboratory experiment at the Oregon Agriculture Experiment Station (Corvalis, Oregon, US). While seeking new methods for preserving package meat, Anderson noticed bacterial growth after ground meat had been sterilized with radiation.

Biologists consider it a polyextremophile, meaning that it can thrive in a very diverse range of extreme habitats, although no one has been able to identify its natural habitat. D. radiodurans has been located everywhere from cow dung to granite in Antartica’s dry valleys. D. radiodurans' ability to endure environmental conditions far more extreme that those presently found on Earth leads Scientists to believe that it evolved and existed during the planet's primitive stages when it was unshielded by a protective ozone layer and when it was exposed to extreme conditions such as Ionic Radiation (IR) and Ultra Violet (UV) rays from the sun.

In addition to high levels of ionizing and ultraviolet radiation, D. radiodurans can also withstand other extreme stresses such as genotoxic chemicals, oxidative damage, electrophilic mutagens, desiccation, and dehydration. In order to gauge how resistant D. radiodurans is to radiation in comparison to other life forms, consider that, while 5 units of gamma radiation is lethal to humans and 2,000 units of gamma radiation is enough to stop all cell activity for E. Coli, D. radiodurans can be exposed to 10,000 units of gamma radiation without dying or mutating. It can continue to survive despit exposure to small amounts of chronic radiation, for example, 6 kilorads/hr as well as large doses of acute radiation exceeding 1500 kilorads/hr. Although biologists do not yet fully understand why or how, D. radiodurans growing in the tetracocci stage are better able to tolerate radiation than the those growing in the diplococci.

Typically, life forms exposed to extreme stresses such as dehydration, IR or UV, or desiccation experience oxidizing DNA damage in which radiation energizes an atom enough to break a chemical bond (such as in a DNA strand) and then act like an atom of oxygen and bind with another atom, ultimately enabling free radicals to cause genetic mutations or DNA breakage. D. radiodurans, however, demonstrates a unique ability to effectively repair broken DNA. Several factors account for its resistance to radiation and other extreme stresses, including additional genomes, redundancy in genetic code, proteins, and DNA-repair pathways. several different biological mechanisms contribute to resistance. Additional genomes: Allows bacterium to recover at least one complete copy of its genome incase others have been damaged by radiation exposure. If one ring in the stack of lifesavers is damaged due to radiation, the additional genomes allow the bacterium to recover another complete copy of its genome. Compared to other bacteria, the microbe's genome is abundant in repetitive sequences such as IS-like transposons and small intergenic repeats. It is known that subsequent to DNA damage, there are changes in the cellular amount of proteins, with enhanced synthesis of four to nine proteins which encode for repair expression. Researchers were surprised to find that D. radiodurans encodes fewer genes for DNA repair than E. coli. Subsequent studies have shown that D. radiodurans key lies in its effectiveness to full potentiate DNA repair (usually within 12-24 hours) as opposed to the sheer abundance in the number of genes encoded for DNA repair.

Genome Structure

D. radiodurans is the only representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. It's circular genome was completely sequenced in 1999 by M.J. Daly and TIGR, The Institute of Genome Research. It has 3,284,156 base pairs, and over 3246 genes. It carries at least four copies of its genome rather than the usual single chromosome copy, and the copies seem to be stacked on top of each other resembling a lifesaver.

Cell structure and metabolism

D. radiodurans derives energy from aerobic respiration and overall has a complexly charted metabolic pathway, with most reactions leading to the generation of free radicals during irradiation. Researchers discovered that the microbe is unable to use succinate, fumarate, malate, and alpha-ketoglutarate as the only carbon and energy sources and that D. radiodurans is dependent on exogenous nicotinic acid.

Other cellular structures that function for defense against radiation and other extreme stresses include the red carotenoid pigments that search and destroy free radicals that are responsible for breaking DNA bonds as well as enzymes like superoxide dismutase and catalase that defend against oxygen toxicity, and a distinctive, complex outer membrane made up of three or more protective layers, complex outer membrane lipids, and a thick peptidoglycan layer containing omithine which is an amino acid.

Ecology

D. radiodurans major contribution to the environment is in the field of bioremediation (see Biotechnology Applications). Its effectiveness in bioremediation was one of the main incentives for mapping out its genomic sequence.

Pathology

D. radiodurans is a non-pathogenic, non disease-inducing microbe.

Application to Biotechnology

D. Radiodurans has had beneficial impacts in the field of environmental science and biotechnology. Bioremediation is an application where biological agents such as microbes are used to decontaminate polluted water or soil sites. Typical microbes used for cleaning hazardous sites may have the ability to convert one contaminant, but they may be limited by radioactive waste’s damaging effects. The solution to this developed by inserting genes from other bioremediation bacteria into D. radiodurans. This way, D. radiodurans can be equipped with tools for cleaning up waste sites while resisting radiation.

In the United States, several tons of nuclear waste were generated during the Cold War’s arms race, and the radio active byproducts were dumped in over 3000 sites around the country. 70 million cubed meters of soil and 3 trillion liters of water were contaminated when Uranium, Cesium, Plutonium, Strontium, Technetium, Chromium, Lead, Mercury, TCE, and toulene by leaching. A variant of D. Radiodurans genetically engineered to express decontamination genes of other bioremediating bacteria was introduced to several sites as an in situ decontamination method, a project sponsored by the U.S. Department of Energy. Radiation levels at these sites were toxic for all other bioremediating life forms, however D. radiodurans was observed decontaminating the sites Mercury and Toulene waste. Traditional methods such as dredging and pumping were likely to range above $300 billion, but the economic advantage of using D. radiodurans in bioremediation reduced the cost by millions.

Current Research

Current research includes enhancing D. radiodurans' role in bioremediation by equipping D. radiodurans with genes imported from other bacterium already known to degrade dangerous compounds (M.J. Daly, USUHS).

Researchers from the Craig Venter Institute are initiating projects in genetc engineering to develop a system derived from D. radiodurans quick DNA repair mechanisms to assemble synthetic DNA fragments into chromosomes, with the ultimate goal of producing a synthetic organism they call Mycoplasma laboratorium.

Several researchers are trying to exact the the genes and cellular pathways which underlie D. radiodurans's survival strategies for radiation endurance. It is widely accepted that the microbe's capabilities for withstanding radiation cannot solely be attributed to a singular factor such as DNA repair pathways, but rather to a combination of biological factors.

References

Journal of Molecular Microbiology and Biotechnology p.64-64 Beneficial Bacteria and Bioremediation Milton H. Saier, Jr.

Makarova, K S; L Aravind, Y I Wolf, R L Tatusov, K W Minton, E V Koonin, M J Daly (2001-03). "Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics". Microbiology and molecular biology reviews : MMBR 65 (1): 44-79.

Data stored in multiplying bacteria 11:02 08 January 2003 NewScientist.com news service Natasha McDowell

Annual Review of Microbiology Vol. 51: 203-224 (Volume publication date October 1997)

Against All Odds:The Survival Strategies of Deinococcus radiodurans J. R. Battista Department of Microbiology, 508 Life Sciences Building, Louisiana State University, Baton Rouge, Louisiana 70803;

J. R. Battista, M. M. Cox, Michael J. Daly, I. Narumi, M. Radman, and S. Sommer (2003). "The structure of Deinococcus radiodurans". Science 302: 567-568.