Deinococcus radiodurans

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Deinococcus radiodurans
A tetrad of D. radiodurans
A tetrad of D. radiodurans
Scientific classification
Kingdom: Bacteria
Phylum: Deinococcus-Thermus
Order: Deinococcales
Genus: Deinococcus
Species: D. radiodurans
Binomial name
Deinococcus radiodurans
Brooks & Murray, 1981

Deinococcus radiodurans is an extremophilic bacterium, one of the most radioresistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world's toughest bacterium in The Guinness Book Of World Records.[citation needed]


[edit] Name and classification

The name Deinococcus radiodurans means "strange berry that withstands radiation". The species was formerly also called Micrococcus radiodurans and Deinobacter radiodurans.[1] As a consequence of its hardiness it has been nicknamed "Conan the Bacterium" (a play on "Conan the Barbarian").[2]

Initially it was placed in the genus Micrococcus. After evaluation of ribosomal RNA sequences and other evidence, it was placed in its own genus Deinococcus, which is closely related to the genus Thermus of heat-resistant bacteria; the group consisting of the two is accordingly known as Deinococcus-Thermus.[3]

Deinococcus is the only genus in the order Deinococcales. D. radiodurans is the type species of this genus, and the best studied member. All known members of the genus are radioresistant: D. proteolyticus, D. radiopugnans, D. radiophilus, D. grandis, D. indicus, D. frigens, D. saxicola, D. marmola, D. geothermalis and D. murrayi; the latter two are also thermophilic.[4]

[edit] History

D. radiodurans was discovered in 1956 by A.W. Anderson at the Oregon Agricultural Experiment Station in Corvallis, Oregon.[5] Experiments were being performed to determine if canned food could be sterilized using high doses of gamma radiation. A tin of meat was exposed to a dose of radiation that was thought to kill all known forms of life, but the meat subsequently spoiled, and D. radiodurans was isolated.

The complete DNA sequence of D. radiodurans was published in 1999 by TIGR. A detailed annotation and analysis of the genome appeared in 2001.[3]

[edit] Description

D. radiodurans is a rather large spherical bacterium, with a diameter of 1.5 to 3.5 µm. Four cells normally stick together, forming a tetrad. The bacteria are easily cultured and do not appear to cause disease.[3] Colonies are smooth, convex, and pink to red in color. The cells stain gram positive, although its cell envelope is unusual and is reminiscent of the cell walls of gram negative bacteria. [6]

D. radiodurans does not form endospores and is nonmotile. It is an obligate aerobic chemoorganoheterotroph, i.e. it uses oxygen to derive energy from organic compounds in its environment. It is often found in habitats rich in organic materials, such as soil, feces, meat, or sewage, but has also been isolated from dried foods, room dust, medical instruments and textiles.[6]

It is extremely resistant to ionizing radiation, ultraviolet light, desiccation, oxidizing and electrophilic agents.

Its genome consists of two circular chromosomes, one 2.65 million base pairs long and the other 412,000 base pairs long, as well as a megaplasmid of 177,000 base pairs and a plasmid of 46,000 base pairs. It has about 3,195 genes. In its stationary phase each bacterial cell contains four copies of this genome; when rapidly multiplying, each bacterium contains 8-10 copies of the genome.

[edit] Radioactivity resistance

While a dose of 10 Gy of ionizing radiation is sufficient to kill a human, and a dose of 60 Gy is sufficient to kill all cells in a culture of E. coli, D. radiodurans is capable of withstanding an instantaneous dose of up to 5,000 Gy with no loss of viability, and an instantaneous dose of up to 15,000 Gy with 37% viability. A dose of 5,000 Gy is estimated to introduce several hundred complete breaks into the organism's DNA.

Several bacteria of comparable radioresistance are now known, including some species of the genus Chroococcidiopsis (phylum cyanobacteria) and some species of Rubrobacter (phylum actinobacteria); among the archae, the species Thermococcus gammatolerans shows comparable radioresistance.[4]

[edit] Radioactivity resistance mechanisms

Deinococcus accomplishes its resistance to radiation by having multiple copies of its genome and rapid DNA repair mechanisms. It usually repairs breaks in its chromosomes within 12-24 hours through a 2-step process. First, D. radiodurans reconnects some chromosome fragments through a process called single-strand annealing. In the second step, a protein mends double-strand breaks through homologous recombination. This process does not introduce any more mutations than a normal round of replication would.

A persistent question regarding D. radiodurans is how such a high degree of radioresistance could evolve. Natural background radiation levels are very low -- in most places, on the order of 0.4 mGy per year, and the highest known background radiation, near Guarapari, Brazil is only 175 mGy per year. With naturally-occurring background radiation levels so low, organisms evolving mechanisms specifically to ward off the effects of high radiation are unlikely.

Valerie Mattimore and John R. Battista of Louisiana State University have suggested that the radioresistance of D. radiodurans is simply a side-effect of a mechanism for dealing with prolonged cellular desiccation (dryness). To support this hypothesis, they performed an experiment in which they demonstrated that mutant strains of D. radiodurans which are highly susceptible to damage from ionizing radiation are also highly susceptible to damage from prolonged desiccation, while the wild type strain is resistant to both.[7] In addition to DNA repair, D. radiodurans use LEA (Late Embryogenesis Abundant) protein[8] expression to protect against desiccation.[9]

Scanning electron microscopy analysis has shown that DNA in D. radiodurans is organized into tightly packed toroids, which may facilitate DNA repair.[10]

A team of Croatian and French researchers have bombarded D. radiodurans to study the mechanism of DNA repair. At least two copies of the genome, with random DNA breaks, can form DNA fragments through annealing. Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue extension until they find complementary partner strands. In the final step there is crossover by means of RecA-dependent homologous recombination.[11]

Michael Daly has suggested that the bacterium uses manganese as an antioxidant to protect itself against radiation damage.[12] In 2008 his team showed that high intracellular levels of manganese(II) in D. radiodurans protect proteins from being oxidized by radiation, and proposed the idea that "protein, rather than DNA, is the principal target of the biological action of [ionizing radiation] in sensitive bacteria, and extreme resistance in Mn-accumulating bacteria is based on protein protection".[13]

A team of Russian and American scientists proposed that the radioresistance of D. radiodurans had a Martian origin. Evolution of the microorganism could have taken place on the Martian surface until it was delivered to Earth on a meteorite.[14] However, apart from its resistance to radiation, Deinococcus is genetically and biochemically quite similar to other terrestrial life forms, arguing against an extraterrestrial origin.

[edit] Applications

Using genetic engineering Deinococcus has been used for bioremediation to consume and digest solvents and heavy metals, even in a highly radioactive site. The bacterial mercuric reductase gene has been cloned from Escherichia coli into Deinococcus to detoxify the ionic mercury frequently found in radioactive waste generated from nuclear weapons manufacture.[15] Those researchers developed a strain of Deinococcus that could detoxify both mercury and toluene in mixed radioactive wastes.

The Craig Venter Institute has used a system derived from the rapid DNA repair mechanisms of D. radiodurans to assemble synthetic DNA fragments into chromosomes, with the ultimate goal of producing a synthetic organism they call Mycoplasma laboratorium.[16]

In 2003, U.S. scientists demonstrated that D. radiodurans could be used as a means of information storage that might survive a nuclear catastrophe. They translated the song It's a Small World into a series of DNA segments 150 base pairs long, inserted these into the bacteria, and were able to retrieve them without errors 100 bacterial generations later.[17]

[edit] Cultural references

  • The computer game Anarchy Online features an item called Deinococcus radiodurans which is used to make a "stim" (potion) that reduces damage from radioactive sources.
  • Michael Flynn's short story "The Washer at the Ford" has as its major plot point the development of a radiation "inoculation", consisting of nanomachines with a DNA repair mechanism inspired by Deinococcus radiodurans (referred to by its old name M. Radiodurans).

[edit] See also

[edit] References

  1. ^ {}
  2. ^ Huyghe, Patrick (July/August 1998). "Conan the Bacterium" (PDF). The Sciences (New York Academy of Sciences): 16–19. 
  3. ^ a b c 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. doi:10.1128/MMBR.65.1.44-79.2001. PMID 11238985. 
  4. ^ a b Cox, Michael M; John R Battista (2005-11). "Deinococcus radiodurans — the consummate survivor" (PDF). Nature reviews. Microbiology 3 (11): 882–92. doi:10.1038/nrmicro1264. PMID 16261171. 
  5. ^ Anderson, A W; H C Nordan, R F Cain, G Parrish, D Duggan (1956). "Studies on a radio-resistant micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation". Food Technol. 10 (1): 575–577. 
  6. ^ a b Battista, J R (1997). "Against all odds: the survival strategies of Deinococcus radiodurans" (PDF). Annual review of microbiology 51: 203–24. doi:10.1146/annurev.micro.51.1.203. PMID 9343349. 
  7. ^ Mattimore V, Battista JR (01 Feb 1996). "Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation". Journal of Bacteriology 178 (3): 633–637. PMID 8550493. 
  8. ^ Goyal K, Walton LJ, Tunnacliffe A (2005). "LEA proteins prevent protein aggregation due to water stress". Biochemical Journal 388 (Pt 1): 151–157. doi:10.1042/BJ20041931. PMID 15631617. 
  9. ^ Battista JR, Park MJ, McLemore AE (2001). "Inactivation of two homologues of proteins presumed to be involved in the desiccation tolerance of plants sensitizes Deinococcus radiodurans R1 to desiccation". Cryobiology 43 (2): 133–139. doi:10.1006/cryo.2001.2357. PMID 11846468. 
  10. ^ Levin-Zaidman S, Englander J, Shimoni E, Sharma AK, Minton KW, Minsky A (2003). "Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance?". Science 299 (5604): 254–256. doi:10.1126/science.1077865. PMID 12522252. 
  11. ^ Zahradka K, Slade D, Bailone A, Sommer S, Averbeck D, Petranovic M, Lindner AB, Radman M (2006). "Reassembly of shattered chromosomes in Deinococcus radiodurans" (PDF). Nature 443 (7111): 569–573. doi:10.1038/nature05160. PMID 17006450. 
  12. ^ Pearson, Helen (30 September 2004). "Secret of radiation-proof bugs proposed" (PDF). Retrieved on 2006-06-19. 
  13. ^ Daly, Michael J.; Elena K. Gaidamakova, Vera Y. Matrosova, Alexander Vasilenko, Min Zhai, Richard D. Leapman, Barry Lai, Bruce Ravel, Shu-Mei W. Li, Kenneth M. Kemner, James K. Fredrickson (2007-04-01). "Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance". PLoS Biology 5 (4): e92 EP -. doi:10.1371/journal.pbio.0050092. 
  14. ^ Pavlov AK, Kalinin VL, Konstantinov AN, Shelegedin VN, Pavlov AA (2006). "Was Earth ever infected by martian biota? Clues from radioresistant bacteria" (PDF). Astrobiology 6 (6): 911–918. doi:10.1089/ast.2006.6.911. PMID 17155889. 
  15. ^ Brim H, McFarlan SC, Fredrickson JK, Minton KW, Zhai M, Wackett LP, Daly MJ (2000). "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments" (PDF). Nature Biotechnology 18 (1): 85–90. doi:10.1038/71986. PMID 10625398. 
  16. ^ Craig Venter's TED talk (February 2005) mentions D. radiodurans as the ultimate genome assembly machine
  17. ^ Data stored in multiplying bacteria, New Scientist, 8 January 2003

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