Deinococcus radiodurans


Deinococcus radiodurans is an extremophilic bacterium, one of the most radiation-resistant 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.

Name and classification

The name Deinococcus radiodurans derives from the Ancient Greek δεινός and κόκκος meaning "terrible grain/berry" and the Latin radius and durare, meaning "radiation surviving". The species was formerly called Micrococcus radiodurans. As a consequence of its hardiness, it has been nicknamed “Conan the Bacterium” in reference to Conan the Barbarian.
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. The term "Deinococcus-Thermus group" is sometimes used to refer to members of Deinococcus and Thermus.
Deinococcus is one genus of three 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. marmoris, D. deserti, D. geothermalis and D. murrayi; the latter two are also thermophilic.

History

D. radiodurans was discovered in 1956 by Arthur Anderson at the Oregon Agricultural Experiment Station in Corvallis, Oregon. Experiments were being performed to determine whether 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 The Institute for Genomic Research. A detailed annotation and analysis of the genome appeared in 2001. The sequenced strain was ATCC BAA-816.
Deinococcus radiodurans has a unique quality in which it can repair both single- and double-stranded DNA. When damage is apparent to the cell, it brings it into a compartmental ring-like structure, where the DNA is repaired and then is able to fuse the nucleoids from the outside of the compartment with the damaged DNA.

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. Under controlled growth conditions, cells of dimer, tetramer, and even multimer morphologies can be obtained. 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.
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 sewage, meat, feces, or, soil but has also been isolated from medical instruments, room dust, textiles, and dried foods.
It is extremely resistant to ionizing radiation, ultraviolet light, desiccation, and 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.

Ionizing-radiation resistance

D. radiodurans is capable of withstanding an acute dose of 5,000 grays, or 500,000 rad, of ionizing radiation with almost no loss of viability, and an acute dose of 15,000 Gy with 37% viability. A dose of 5,000 Gy is estimated to introduce several hundred double-strand breaks into the organism's DNA. For comparison, a chest X-ray or Apollo mission involves about 1 mGy, 5 Gy can kill a human, 200-800 Gy will kill E. coli, and over 4,000 Gy will kill the radiation-resistant tardigrade.
Several bacteria of comparable radioresistance are now known, including some species of the genus Chroococcidiopsis and some species of Rubrobacter ; among the archaea, the species Thermococcus gammatolerans shows comparable radioresistance. Deinococcus radiodurans also has a unique ability to repair damaged DNA. It isolates the damaged segments in a controlled area and repairs it. These bacteria can also repair many small fragments from an entire chromosome.

Mechanisms of ionizing-radiation resistance

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 by a 2-step process. First, D. radiodurans reconnects some chromosome fragments by a process called single-stranded annealing. In the second step, multiple proteins mend double-strand breaks through homologous recombination. This process does not introduce any more mutations than a normal round of replication would.
Scanning electron microscopy analysis has shown that DNA in D. radiodurans is organized into tightly packed toroids, which may facilitate DNA repair.
A team of Croatian and French researchers led by Miroslav Radman 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.
D. radiodurans is capable of genetic transformation, a process by which DNA derived from one cell can be taken up by another cell and integrated into the recipient genome by homologous recombination. When DNA damages are introduced into donor DNA by UV irradiation, the recipient cells efficiently repair the damages in the transforming DNA as they do in cellular DNA when the cells themselves are irradiated.
Michael Daly has suggested the bacterium uses manganese complexes as antioxidants to protect itself against radiation damage. In 2007 his team showed that high intracellular levels of manganese 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 in sensitive bacteria, and extreme resistance in Mn-accumulating bacteria is based on protein protection".
In 2016, Massimiliano Peana et al. reported a spectroscopic study through NMR, EPR and ESI-MS techniques on the Mn interaction with two peptides, DP1 and DP2, whose amino acid composition was selected to include the majority of the most prevalent amino acids present in a Deinococcus radiodurans bacterium cell-free extract that contains components capable of conferring extreme resistance to ionizing radiation.
Recently M. Peana and C. Chasapis reported, by a combined approach of bioinformatic strategies based on structural data and annotation, the Mn-binding proteins encoded by the genome of DR and proposed a model for Manganese interaction with DR proteome network involved in ROS response and defense.
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. However, apart from its resistance to radiation, Deinococcus is genetically and biochemically very similar to other terrestrial life forms, arguing against an extraterrestrial origin not common to them.
In 2009, nitric oxide was reported to play an important role in the bacteria's recovery from radiation exposure: the gas is required for division and proliferation after DNA damage has been repaired. A gene was described that increases nitric oxide production after UV radiation, and in the absence of this gene, the bacteria were still able to repair DNA damage, but would not grow.

Evolution of ionizing-radiation resistance

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 Ramsar, Iran is only 260 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 of Louisiana State University has suggested the radioresistance of D. radiodurans is simply a side effect of a mechanism for dealing with prolonged cellular desiccation. To support this hypothesis, she performed an experiment in which she 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. In addition to DNA repair, D. radiodurans use LEA proteins expression to protect against desiccation.
In this context, also the robust S-layer of D. radiodurans through its main protein complex, the S-layer Deinoxanthin Binding Complex, strongly contributes to its extreme radioresistance. In fact, this S-layer acts as a shield against electromagnetic stress as in the case of ionizing radiation exposure, but also stabilize the cell wall against possible consequent high temperatures and desiccation

Applications

Deinococcus radiodurans has shown to have a great potential to be used in different fields of investigation. Not only has D.radiodurans been genetically modified for bioremediation applications, but also it has been discovered that it could perform a major role in biomedical research and in nanotechnology.
Bioremediation refers to any process that uses microorganisms, fungi, plants or the enzymes derived from them to return an environment altered by contaminants to its natural condition. Large areas of soils, sediments and groundwater are contaminated with radionuclides, heavy metals and toxic solvents. There are microorganisms that are able to decontaminate soils with heavy metals by immobilizing them, but in the case of nuclear waste, ionizing radiation limits the amount of microorganisms that can be useful. In this sense, D. radiodurans, due to its characteristics, can be used for the treatment of nuclear energy waste. Deinococcus radiodurans has been genetically engineered to consume and digest solvents and heavy metals in these radioactive environments. The mercuric reductase gene has been cloned from Escherichia coli into Deinococcus to detoxify the ionic mercury residue frequently found in radioactive waste generated from nuclear weapons manufacture. Those researchers developed a strain of Deinococcus that could detoxify both mercury and toluene in mixed radioactive wastes. Moreover, a gene encoding a non-specific acid phosphatase from Salmonella enterica serovar Typhi and the alkaline phosphatase gene from Sphingomonas have been introduced in strains of D.radiodurans for the bioprecipitation of uranium in acid and alkaline solutions, respectively.
In the biomedical field, Deinococcus radiodurans could be used as a model to study the processes that lead to aging and cancer. The main causes of these physiological changes are related to the damage in DNA, RNA and proteins resulting from oxidative stress, the weakening of antioxidant defence and the inability of repair mechanisms to deal with the damage originated by reactive oxygen species, also known as ROS. To this extent, D.radiodurans mechanisms of protection against oxidative damage and of DNA reparation could be the starting points in research aimed to develop medical procedures to prevent aging and cancer. Some lines of investigation are focused on the application of D. radiodurans antioxidant systems in human cells to prevent ROS damaging and the study of the development of resistance to radiation in tumoral cells.
A nanotechnological application of D.radiodurans in the synthesis of silver and gold nanoparticles has also been described. Whereas chemical and physical methods to produce these nanoparticles are expensive and generate a huge amount of pollutants, biosynthetic processes represent an ecofriendly and cheaper alternative. The importance of these nanoparticles relies on their medical applications as they have been demonstrated to exhibit activity against pathogenic bacteria, antifouling effects and cytotoxicity to tumoral cells.
Moreover, there are other uncommon applications of Deinococcus radiodurans. 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. In 2003, U.S. scientists demonstrated 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.