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==Description and significance==
==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 peptidoglycanIn order to acquire energy, ''D. radiodurans'' extracts it from the environment by use of metabolic pathwaysIt does not take up nitrogen from the ammonia present in soil, but rather consumes sulfur containing amino acids.
''Deinococcus radiodurans'' is a red-pigmented, non-motile, spherical bacterium that is 1-2 µm in size.  It is a resilient bacterium, in that it is resistant to radiation, UV light, hydrogen peroxide, and many other DNA damaging agents. ''D. radiodurans'' was discovered in 1956 in Oregon in a can of processed meat exposed to gamma radiation.  It has an appearance of four cells bound by a cell wall, each carrying multiple copies of its genome (4-10 copies per organism).  ''D. radiodurans'' is a mesophile and is commonly found in soil near radioactive waste sites.  When exposed to radiation, or dehydration, their multiple genomes give them a better chance of recovering a single genome sequence, which is necessary in recovering their entire genomeTheir RecA proteins play a large role in splicing DNA fragments and in the prevention of overlapping in the sequence.  


Because of its physical characteristics and survival mechanisms, it is thought that ''D. radiodurans'' could be used in environmental cleanup. [http://www.eastwoodzhao.com/deinococcus-radiodurans-a-radio-resistant-bacterium-with-a-multitude-of-applications]
''D. radiodurans'' can withstand 1.5 million rads of radiation, making it the most radiation resistant organism in the world.  They are essential for the environmental cleanup of radioactive waste sites, but cannot rid the environment of radiation.  Genes from organisms that carry out bioremediation can be inserted into ''D. radiodurans'' so they may break down toluene and mercury to a less toxic form.   [http://www.eastwoodzhao.com/deinococcus-radiodurans-a-radio-resistant-bacterium-with-a-multitude-of-applications (11)]




[[File:Dish.jpg]]
[[File:Dish.jpg]]
''D. radiodurans'' on a nutrient agar plate. The bacterium is red-pigmented, non-motile, and spherical.[http://science.nasa.gov/science-news/science-at-nasa/1999/ast14dec99_1]
''D. radiodurans'' on a nutrient agar plate. The bacterium is non-motile and spherical.[http://science.nasa.gov/science-news/science-at-nasa/1999/ast14dec99_1 (5)]


==Genome structure==
==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 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. [http://www.ncbi.nlm.nih.gov/pubmed/10567266]
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. [http://www.ncbi.nlm.nih.gov/pubmed/10567266 (10)]


==Cell structure and metabolism==
==Cell structure and metabolism==
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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.  
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. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99018]
''D. radiodurans'' is an obligatory heterotrophic organism, meaning it requires oxygen to obtain energy from organic materials. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99018 (6)]




[[File:Stout123thumb.jpg]]
[[File:Stout123thumb.jpg]]
''D. radiodurans'' viewed under an electron microscope. Note the tetrad structure. [http://www.usuhs.mil/pat/deinococcus/index_20.htm]
''D. radiodurans'' viewed under an electron microscope. Note the tetrad structure. [http://www.usuhs.mil/pat/deinococcus/index_20.htm (3)]


==Ecology==
==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. 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'' is a polyextremophile and can live in a wide range of environments. It can be found in both dry, nutrient-poor environments such as granite in Antarctic Dry Valleys; and nutrient-rich environments such as soil and animal feces.  Though ''D. radiodurans'' has adapted a mechanism to utilize ammonia, they uptake sulfur containing amino acids in the soil as their source of nitrogen.  ''D. radiodurans'' is believed to be able to survive on Mars due to their presence in Antarctic Dry Valleys, which closely resembles the Martian surface.  ''D. radiodurans'' colonizing on Martian soil can expose soil below ground that can decrease radiation in the atmosphere.  This can possibly make the atmosphere more suitable for future human existence; but this theory has yet to be proven.


''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 are 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. [http://www.eastwoodzhao.com/deinococcus-radiodurans-a-radio-resistant-bacterium-with-a-multitude-of-applications/]
''D. radiodurans''' adaptation for radiation resistance is thought to be correlated to their response to dehydration, rather than constant exposure to radiation over timeIt is unclear why this bacterium contains genes that enable it to adapt to these extreme conditions, making its natural origin difficult to determine. [http://www.eastwoodzhao.com/deinococcus-radiodurans-a-radio-resistant-bacterium-with-a-multitude-of-applications (11)]


==Pathology==
==Pathology==
''D. radiodurans'' is currently believed to be non-pathogenic.
''D. radiodurans'' is currently believed to be non-pathogenic. [http://mmbr.asm.org/content/75/1/133.full (9)]


==Current Research==
==Current Research==
Line 54: Line 54:
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.
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." [http://mmbr.asm.org/content/75/1/133.full]
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." [http://mmbr.asm.org/content/75/1/133.full (9)]


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. [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000799]
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. [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000799 (8)]


==Cool Factor==
==Cool Factor==


This 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. [http://www.sciencedaily.com/releases/2000/03/000331090958.htm]
This resilient microbe has earned itself several nicknames, including "Conan the Bacterium" and "Superdrug." It even holds the place of "Toughest Bacterium" in the Guinness Book of World Records. [http://www.sciencedaily.com/releases/2000/03/000331090958.htm (2)]


Additionally, scientists have recently considered using the microbe for sewage treatments on long-duration flights to outer space. [http://www.genomenewsnetwork.org/articles/07_02/deinococcus.shtml]
Additionally, scientists have recently considered using the microbe for sewage treatments on long-duration flights to outer space. It is thought that the microbe's resiliency would make it good for biological clean-up, even in the extreme conditions of outer space. [http://www.genomenewsnetwork.org/articles/07_02/deinococcus.shtml (4)]


==References==
==References==
1. [http://bioweb.uwlax.edu/bio203/s2008/arnold_meag/Phylogeny.htm Arnold, M. "''Deinococcus radiodurans'' - World's Toughest Bacteria." http://bioweb.uwlax.edu. April 2008.]
1. [http://bioweb.uwlax.edu/bio203/s2008/arnold_meag/Phylogeny.htm Arnold, M. "''Deinococcus radiodurans'' - World's Toughest Bacteria." http://bioweb.uwlax.edu. April 2008.]


2. [http://www.sciencedaily.com/releases/2000/03/000331090958.htm Bozeman. "''Reports on 'Weird Life' Almost Better Than Fiction''". Science Daily. March 2000.]
2. [http://www.sciencedaily.com/releases/2000/03/000331090958.htm Bozeman. "''Reports on 'Weird Life' Almost Better Than Fiction.''" Science Daily. March 2000.]


3. [http://www.usuhs.mil/pat/deinococcus/index_20.htm Daly, M. "''Deinococcus radiodurans'' - a radiation-resistant bacterium." http://www.usuhs.mil/pat/deinococcus/index_20.htm. November 2011.]
3. [http://www.usuhs.mil/pat/deinococcus/index_20.htm Daly, M. "''Deinococcus radiodurans'' - a radiation-resistant bacterium." http://www.usuhs.mil/pat/deinococcus/index_20.htm. November 2011.]

Latest revision as of 13:58, 28 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 that is 1-2 µm in size. It is a resilient bacterium, in that it is resistant to radiation, UV light, hydrogen peroxide, and many other DNA damaging agents. D. radiodurans was discovered in 1956 in Oregon in a can of processed meat exposed to gamma radiation. It has an appearance of four cells bound by a cell wall, each carrying multiple copies of its genome (4-10 copies per organism). D. radiodurans is a mesophile and is commonly found in soil near radioactive waste sites. When exposed to radiation, or dehydration, their multiple genomes give them a better chance of recovering a single genome sequence, which is necessary in recovering their entire genome. Their RecA proteins play a large role in splicing DNA fragments and in the prevention of overlapping in the sequence.

D. radiodurans can withstand 1.5 million rads of radiation, making it the most radiation resistant organism in the world. They are essential for the environmental cleanup of radioactive waste sites, but cannot rid the environment of radiation. Genes from organisms that carry out bioremediation can be inserted into D. radiodurans so they may break down toluene and mercury to a less toxic form. (11)


Dish.jpg D. radiodurans on a nutrient agar plate. The bacterium is non-motile and spherical.(5)

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. (10)

Cell structure and metabolism

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. (6)


Stout123thumb.jpg D. radiodurans viewed under an electron microscope. Note the tetrad structure. (3)

Ecology

D. radiodurans is a polyextremophile and can live in a wide range of environments. It can be found in both dry, nutrient-poor environments such as granite in Antarctic Dry Valleys; and nutrient-rich environments such as soil and animal feces. Though D. radiodurans has adapted a mechanism to utilize ammonia, they uptake sulfur containing amino acids in the soil as their source of nitrogen. D. radiodurans is believed to be able to survive on Mars due to their presence in Antarctic Dry Valleys, which closely resembles the Martian surface. D. radiodurans colonizing on Martian soil can expose soil below ground that can decrease radiation in the atmosphere. This can possibly make the atmosphere more suitable for future human existence; but this theory has yet to be proven.

D. radiodurans' adaptation for radiation resistance is thought to be correlated to their response to dehydration, rather than constant exposure to radiation over time. It is unclear why this bacterium contains genes that enable it to adapt to these extreme conditions, making its natural origin difficult to determine. (11)

Pathology

D. radiodurans is currently believed to be non-pathogenic. (9)

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.

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." (9)

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. (8)

Cool Factor

This resilient microbe has earned itself several nicknames, including "Conan the Bacterium" and "Superdrug." It even holds the place of "Toughest Bacterium" in the Guinness Book of World Records. (2)

Additionally, scientists have recently considered using the microbe for sewage treatments on long-duration flights to outer space. It is thought that the microbe's resiliency would make it good for biological clean-up, even in the extreme conditions of outer space. (4)

References

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

2. Bozeman. "Reports on 'Weird Life' Almost Better Than Fiction." Science Daily. March 2000.

3. Daly, M. "Deinococcus radiodurans - a radiation-resistant bacterium." http://www.usuhs.mil/pat/deinococcus/index_20.htm. November 2011.

4. DeWeerdt, S.E. "Deinococcus radiodurans may be a tool for cleaning up toxic waste and more." Genome News Network. July 2002.

5. Dooling, D. "Meet Conan the Bacterium." NASA Science: Science News. http://science.nasa.gov/science-news/science-at-nasa/1999/ast14dec99_1. December 1999.

6. 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.

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

8. 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.

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

10. 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.

11. 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