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Deinococcus radiodurans R1

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Organism Background Edit

The bacterium Deinococcus radiodurans R1 was discovered in 1956 by Arthur Anderson at the Oregon Agriculture Experiment Station. The accidental discovery of this polyextremophile occurred while trying to sterilize canned ham. After exposing the canned ham to extreme radiation it still spoiled. Anderson cultured the spoiled ham and found the only remaining bacteria to be D.radiodurans R1. (2)
220px-Deinococcus radiodurans

D.radiodurans tetrad at 220x magnification. (1)

The bacteria gets its name from deino- (strange) -coccus (grain or berry).

D.radiodurans is the Guiness Book of World Records toughest bacteria and is classified as a polyextremophile due to its high resistance to environments that cause DNA damage, including:

  • Ionizing radiation (200x more resistant than E.coli), D.radiodurans shows normal growth while being exposed to chronic high levels of radiation (6 kilorads/h) and can withstand 1,500 kilorad blasts of radiation. (2,3)
  • Ultraviolet radiation (20x more resistant than E.coli).

Not only is the bacteria highly resistant to radiation but has been found worldwide in areas rich in organic nutrients (soil, feces, processed meats) as well as in nutrient-poor environments such as a weathered granite in an Antarctic valley, dust, irradiated medical instruments, the air and in very dry environments. This extreme resistance to a plethora of less than ideal living environments is contributed to its many DNA damage repair mechanisms along with its unusually thick (150nm), 6 outer membrane layers (1,2,3). The bacteria can be killed as it cannot survive above 39 degrees Celsius and is sensitive to antibiotics that inhibit RNA synthesis, protein synthesis and cell wall synthesis (4).

D.radiodurans R1 is a non-pathogenic, non-motile, non-sporulating bacterial that stains gram (+) despite having a cell wall similar to gram (-) bacteria. Despite the green hue of the image above, D.radiodurans has a reddish pink color and usually occur in tetrads. It is thought that this bacteria shares a common ancestor with the Thermus genus and has acquired many of its other genome attributes via horizontal gene transfer. D.radiodurans is especially susceptible to horizontal gene transfer due to it being the most highly transformable species known (as of 1999). (2, 3)

Genome Attributes (2,3)Edit

The genome of D.radiodurans consists of 4 circular molecules that, in total, are made of 3.2 Mbps:

  • Chromosome I, chromosome II, megaplasmid and a plasmid. See chart below for details.
    D.radiodurans genome chart

    General features of the D.radiodurans genome. (2)

  • The entire genome carries 3,195 genes.
  • Has a high GC content, 66.6%
  • Contains 38 DNA repair genes. No other species to date contains as many DNA glycosylases (single base pair repair), MutY-Nths and UvrAs (recognize DNA damage).
  • The bacterium is a polyploid which contains 4 copies of the genome in its not replicating state and 10 genome equivalents during replication. This contributes to its efficient homologous recombination based repair mechanism for double strand breaks but does not entirely explain the bacterias high resistance to ionizing and UV radiation.
  • Many genes found on Chromosome II and the megaplasmid code for providing a source of noncarbohydrate, nitrogenous precursors for protein production and play a roll in absorbing such compounds from cells that did not survive. Intracellular proteolysis is induced following radiation exposure. It is thought that this method reduces metabolic demand, contributes to antioxidant complexes of amino acids and may expedite cell recovery.
  • The genome of D.radiodurans code for 90 ABC transports for amino acids and 54 ABC transporters for sugars. These genes are upregulated during exposure to unfavorable conditions which suggests the bacteria absorbs more nutrients from its surroundings in situations with low nutrient content.

Managing Oxidative Stress (3,4)Edit

  • Elaborate glucose metabolism converts glucose into ribose-5-phos-phate, glyceraldehyde-3-phosphate, and NADPH, which are all precursors for dNTPs. NADPH is also an important cofactor for glutathione and thioredoxin reductases, which regenerate reduced glutathione and thioredoxin. Glutathione and thioredoxin are antioxidants, which reduce hydrogen peroxide and oxidized cysteines. This glucose metabolism provides substrates for DNA repair and for protection against reactive oxygen species (ROS). When glucose is depleted there is a decrease in radiation resistance. The bacteria usually incorporates about 8% of carbon from glucose into its DNA and incorporates up to 18% of carbon from glucose when under oxidative stress.
  • Another method for reducing ROS is by having fewer respiratory chain enzymes and less iron-sulfer clusters. D. radiodurans also limits the release of NADH and FADH2 by using the glyoxylate bypass of the TCA cycle. The limited release of NADH and FADH2 greatly reduces the number of superoxide radicals and hydrogen peroxide.

There are many methods of DNA repair and oxidative stress resistance exhibited by D. radiodurans, so many that this article could go on for 30+ pages. Highlighted above are just several mechanisms responsible for this bacterias high resistance to radiation.

References:

  1. Wikipedia. Deinococcus Radiodurans R1. Last modified 11/3/2012.
  2. White, Owen, Et Al. Genome Sequence of the Radioresistatnt Bacterium Deinococcus Radiodurans R1. Science. Vol 286, pgs 1571-1577. 19 Nov 1999.
  3. Makarova, K.S., Et Al. Genome of the Extremely Radiation-Resistant Bacterium Deinococcus Radiodurans Views from the Perspective of Comparative Genomics. Microbiology and Molecular Biology Reviews. Vol 65, No.1, p.44-79. Mar 2001.
  4. Slade, D, Et Al. Oxidative Stress Resistance in D.Radiodurans. Microbiology and Molecular Biology Reviews. Vol 75 No.1, p133-191. Mar 2011.

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