User:StoutA: Difference between revisions

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''D. radiodurans'' viewed under an electron microscope. [http://www.usuhs.mil/pat/deinococcus/index_20.htm]
''D. radiodurans'' viewed under an electron microscope. [http://www.usuhs.mil/pat/deinococcus/index_20.htm]
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==Genome structure==
==Genome structure==

Revision as of 20:46, 25 February 2012

This student page has not been curated.

A Microbial Biorealm page on the genus StoutA

Classification

Higher order taxa

Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaaceae [1]

Species

NCBI: Taxonomy

Deinococcus radiodurans

Description and significance

Deinococcus radiodurans is a red-pigmented, non-motile, spherical bacterium 1.5-3.5 µm in diameter. It usually occurs as four cells sticking to one another. This is why the bacterium carries between four and 10 copies of its genome stacked on top of each other, rather than just one. By carrying so many genomes, the bacteria is able to repair itself after exposure to radiation, making it the most radiation-resistant organism on earth. D. radiodurans is also Gram positive, meaning it has a thick layer of peptidoglycan. In order to acquire energy, D. radiodurans extracts it from the environment by use of metabolic pathways. It does not take up nitrogen from the ammonia present in soil, but rather consumes sulfur containing amino acids.

Because of its physical characteristics and survival mechanisms, it is thought that D. radiodurans could be used in environmental cleanup. [2]


Stout123thumb.jpg D. radiodurans viewed under an electron microscope. [3]


Genome structure

The genome of the R1 strain of D. radiodurans was sequenced in 1999 using whole-genome shotgun sequencing. It is 3,284,156 base pairs long in total and has four major components: chromosome I (2,648,638 base pairs), chromosome II (412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs).

The chromosomes and the megaplasmid contain several genes that allow the bacterium to survive under extreme conditions, including starvation and stress. The bacterium’s genome also reveals a large array of DNA repair mechanisms, including base excision repair, nucleotide excision repair, and mismatch excision repair, all of which exhibit a high amount of redundancy. It is thought that the redundancy of these repair mechanisms explains the bacterium’s ability to resist a variety of mutagens. [4]

Cell structure and metabolism

D. radiodurans is a gram positive, red-pigmented bacterium, usually growing to approximately 1-2μm. Each cell of D. radiodurans exhibits 2 perpendicular furrows that lead to a tetrad structure, and each quarter of the tetrad houses a complete genome. The bacterium is characterized by 6 distinct layers - (from inner to outer) the plasma membrane, the peptidoglycan-containing cell wall (the peptidoglycan layer is 14-20nm thick), the compartmentalized layer, the outer membrane, the electrolucent zone, and the S-layer. Septum formation involves only the cytoplasmic and peptidoglycan layer.

D. radiodurans is an obligatory heterotrophic organism, meaning it requires oxygen to obtain energy from organic materials. [5]

Ecology

D. radiodurans is easy to culture because, apart from being resistant to radiation, it can also live in extreme conditions -- conditions so extreme that its natural habitat is still unknown. D. radiodurans can withstand dry conditions and a lack of nutrients in the environment, making it "The World’s Toughest Bacterium," according to the Guinness Book of World Records. Though this organism can survive in extreme conditions, it has also been found in nutrient-rich environments, such as soil, animal feces, and processed meats, as well as dry environments like Antarctic Dry Valleys, which is supposed to be extremely similar to Mars' environment.

D. radiodurans was originally discovered in a can of ground meat that spoiled after sterilized with radiation. Scientists believe that its ability to repair itself after doses of radiation is similar to its response to dehydration. Though the genes this bacterium possesses is essential to environmental cleanup due to its ability to withstand extreme conditions, genes from other organisms that carry out bioremediation can be injected into D. radiodurans to create a "superbug." It has also been said that D. radiodurans might make life more suitable for humans on Mars, but this has yet to be proven.

Pathology

D. radiodurans is currently believed to be non-pathogenic.

Current Research

Given that reactive oxygen species (ROS) accumulation is a leading cause of cancer and other diseases correlated with aging, D. radiodurans has been extensively studied for its incredible ability to combat oxidative stress. D. radiodurans is 30 to 1000 times more resilient to ionizing radiation than humans. [6]

ROS cause both DNA breaks and protein damage in bacterial genomes. Upon investigation, D. radiodurans was discovered to incur the same number of DNA breaks as other bacterial species, but it incurred less protein damage when subjected to ionizing radiation. This discovery suggests that the amount of protein damage, not DNA damage, determines a bacterial species’ ability to combat oxidative stress.

Particularly important in protecting proteins from damage in the bacterium are divalent manganese complexes that act as ROS "scavengers." Upon exposure to radiation, the bacterium loses up to 30% of its wet weight originating from the cell wall. This loss of water is thought to be responsible for concentrating the cytosol with molecules needed to form these "scavengers."

Other research on the DNA repair mechanisms of D. radiodurans has shown that radiation stress induces the transposition of ISDra2, a single insertion sequence. Exposure to γ-irradiation induces the excision of the lone copy of ISDra2, and the resealing of the recently emptied site. These events are associated with the start of the process of genome assembly of the chromosomes broken by radiation. This discovery lends itself useful as it demonstrates a potential way to trigger DNA repair. [7]

Cool Factor

The resilient microbe has earned itself nicknames including, “Conan the Bacterium” and “Superdrug”, and even holds the place of “World’s Toughest Bacterium” in the Guinness Book of World Records. [8]

Additionally, scientists have recently considered using the microbe for sewage treatments on long-duration flights to outer space. [9]

References

Arnold, M. "Deinococcus radiodurans - World's Toughest Bacteria." http://bioweb.uwlax.edu. April 2008.

Makarova, K.; Aravind, L.; Wolf, Y., et al. "Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics." Microbiology and Molecular Biology Reviews 65 (2001): 44–79.

NCBI Taxonomy Browser. ncbi.nlm.nih.gov.

Pasternak, C.; Ton-Hoang, B.; Coste, G.; Bailone, A., et al. "Irradiation-Induced Deinococcus radiodurans Genome Fragmentation Triggers Transposition of a Single Resident Insertion Sequence." PLoS Genet 6 (2010): 1.

Slade, D.; Radman, M. "Oxidative Stress Resistance in Deinococcus radiodurans." Microbiology and Molecular Biology Reviews 75 (2011): 133-191.

White, O.; Eisen, J.A.; Heidelberg, J.F.; Hickey, E.K., et al. "Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1." Science 286 (1999): 1571-7.

Zhao, E.; Bisnar, A.; Hinchey, G. Deinococcus radiodurans: a radio-resistant bacterium with a multitude of applications. University of British Columbia. March 2009.


Edited by students of Iris Keren