The name Deinococcus radiodurans derives from the Ancient Greek δεινός (deinos) and κόκκος (kokkos) meaning "terrible grain/berry" and the Latinradius 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.[3]
Initially, it was placed in the genus Micrococcus. After evaluation of ribosomalRNA sequences and other evidence, it was placed in its own genus Deinococcus, which is closely related to the genus, Thermus.[4]
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,[5]D. geothermalis, and D. murrayi; the latter two are also thermophilic.[6]
History
D. radiodurans was discovered in 1956 by Arthur Anderson at the Oregon Agricultural Experiment Station in Corvallis, Oregon.[7] 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.[citation needed]
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.[4] 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 the damaged DNA 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.[8]
D. radiodurans is a rather large, spherical bacterium, with a diameter of 1.5 to 3.5 μm.[11] Four cells normally stick together, forming a tetrad. The bacteria are easily cultured and do not appear to cause disease.[4] Under controlled growth conditions, cells of dimer, tetramer, and even multimer morphologies can be obtained.[11] 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.[12]
Deinococcus radiodurans does not form endospores and is nonmotile. It is an obligate aerobicchemoorganoheterotroph, 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.[12]
Its genome consists of two circular chromosomes, one 2.65million 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 approximately 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.[citation needed]
Ionizing-radiation resistance
Deinococcus radiodurans is capable of withstanding an acute dose of 5,000grays (Gy), or 500,000rad, of ionizing radiation with almost no loss of viability, and an acute dose of 15,000Gy with 37% viability.[14][15][16] A dose of 5,000Gy is estimated to introduce several hundred double-strand breaks (DSBs) into the organism's DNA (~0.005DSB/Gy/Mbp (haploid genome)). For comparison, a chest X-ray or Apollo mission involves about 1mGy, 5Gy can kill a human, 200–800Gy will kill E. coli, and more than 4,000Gy will kill the radiation-resistant tardigrade.[citation needed]
Several bacteria of comparable radioresistance are now known, including some species of the genus Chroococcidiopsis (phylum cyanobacteria) and some species of Rubrobacter (phylum Actinomycetota); among the archaea, the species Thermococcus gammatolerans shows comparable radioresistance.[6]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.[17]
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. Theoretically, Deinococcus should have little or even no mutation accumulation.[citation needed]
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 the fragments find complementary partner strands. In the final step, there is crossover by means of RecA-dependent homologous recombination.[19]
Deinococcus 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.[20] When DNA damages (e.g. pyrimidine dimers) 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.[21] In 2007 his team showed that high intracellular levels of manganese(II) in D. radiodurans protect proteins from being oxidized by radiation, and they 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".[22] In 2016, Massimiliano Peana et al. reported a spectroscopic study through NMR, EPR, and ESI-MS techniques on the Mn(II) interaction with two peptides, DP1 (DEHGTAVMLK) and DP2 (THMVLAKGED), 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.[23] In 2018, M. Peana and C. Chasapis reported by a combined approach of bioinformatic strategies based on structural data and annotation, the Mn(II)-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. [24]
A team of Russian and American scientists proposed that the radioresistance of D. radiodurans had a Martian origin. They suggested that evolution of the microorganism could have taken place on the Martian surface until it was delivered to Earth on a meteorite.[25] 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.[26]
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 0.4mGy per year, and the highest known background radiation, near Ramsar, Iran, is only 260mGy per year. With naturally occurring background radiation levels so low, organisms evolving mechanisms specifically to ward off the effects of high radiation are unlikely. In the distant geological past, higher background radiation existed both due to more primordial radionuclides not yet having decayed and due to effects of things like the natural nuclear fission reactors at Oklo, Gabon, which were active some 1.7 billion years ago. However, even if adaptations to such conditions did evolve during that time, genetic drift would almost certainly have eliminated them if they provided no (other) evolutionary benefit.[citation needed]
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 (dryness). To support this hypothesis, she performed an experiment in which she demonstrated that mutant strains of D. radiodurans that 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. It was also shown that desiccation induces double-stranded DNA breaks with patterns similar to extreme ionizing radiation.[27] In addition to DNA repair, D. radiodurans use LEA proteins (Late Embryogenesis Abundant proteins)[28] expression to protect against desiccation.[29]
In this context, also the robust S-layer of D. radiodurans through its main protein complex, the S-layer Deinoxanthin Binding Complex (SDBC), 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 stabilizes the cell wall against possible consequent high temperatures and desiccation.[30][31]
Applications
Deinococcus radiodurans as a model system for studying the cell cycle
Deinococcus radiodurans has been 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 reductasegene has been cloned from Escherichia coli into Deinococcus to detoxify the ionicmercury residue frequently found in radioactive waste generated from nuclear weapons manufacture.[32] 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,[33] and the alkaline phosphatase gene from Sphingomonas[34] 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 defense, 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.[35] 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.[36]
A nanotechnological application of D. radiodurans in the synthesis of silver[37] and gold[38] 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.[39] 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.[40]
Clues for future search of extremophile microbial life on Mars
When cultured and exposed to ionizing radiations in liquid media, Deinococcus radiodurans could survive up to 25 kGy.[41] Horne et al. (2022) have studied the effects of desiccation and freezing on the microbial survivability to ionizing radiations considering the feasibility studies to return Martian subsurface soil samples for microbial characterization and for determining the most favorable landing sites of a future robotic exploration mission.[42] They found that the desiccated and frozen cells could resist to a 5.6 higher radiation dose: up to 140 kGy. They calculated that this could correspond to a theoretical survival time of 280 million years at a depth of 33 feet (10 m) below the present Mars surface. However, this time scale is too short to allow microbial survival at a depth accessible to a rover equipped with a drilling system below the Martian surface when compared to the moment when liquid water disappeared from the Martian surface (2 – 2.5 Ga ago). Nevertheless, Horne et al. (2022) consider the hypothesis that meteorite impacts could have dispersed Martian soil and heated locally the subsurface during the geological history of Mars, heating sporadically from time to time the local environment, melting the frozen ice and giving perhaps a chance to a hypothetical distant Martian extremophile resembling its terrestrial cousin Deinococcus radiodurans to grow again for short moment before to rapidly become again frozen and dormant for millions of years. So, for returning subsurface soil samples from Mars for microbial characterization with a potentially "successful" mission like the European Rosalind Franklin rover, it would be necessary to target a relatively young impact crater to increase the chances of discovering dormant extremophile micro-organisms surviving in the dry and frozen Martian subsurface environment relatively protected from the lethal ionizing radiations.[41]
An extremophile is an organism that is able to live in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, pressure, radiation, salinity, or pH level.
Deinococcota is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria.
Desiccation is the state of extreme dryness, or the process of extreme drying. A desiccant is a hygroscopic substance that induces or sustains such a state in its local vicinity in a moderately sealed container. The word desiccation comes from Latin de- 'thoroughly', and siccare 'to dry'.
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in tens of thousands of individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur. This can eventually lead to malignant tumors, or cancer as per the two-hit hypothesis.
Mycobacterium smegmatis is an acid-fast bacterial species in the phylum Actinomycetota and the genus Mycobacterium. It is 3.0 to 5.0 µm long with a bacillus shape and can be stained by Ziehl–Neelsen method and the auramine-rhodamine fluorescent method. It was first reported in November 1884 by Lustgarten, who found a bacillus with the staining appearance of tubercle bacilli in syphilitic chancres. Subsequent to this, Alvarez and Tavel found organisms similar to that described by Lustgarten also in normal genital secretions (smegma). This organism was later named M. smegmatis.
Radioresistance is the level of ionizing radiation that organisms are able to withstand.
Radiosensitivity is the relative susceptibility of cells, tissues, organs or organisms to the harmful effect of ionizing radiation.
The Brevundimonas are a genus of bacteria. They are Gram-negative, non-fermenting, aerobic bacilli. The Brevundimonas species are ubiquitous in the environment but are rarely isolated from clinical samples., although numbers are increasing. Two species of Brevundimonas originally classified under the genus Pseudomonas have been re-classified by Seger et al. as Brevundimonas vesicularis and Brevundimonas diminuta.
Halobacterium salinarum, formerly known as Halobacterium cutirubrum or Halobacterium halobium, is an extremely halophilic marine obligate aerobic archaeon. Despite its name, this is not a bacterium, but a member of the domain Archaea. It is found in salted fish, hides, hypersaline lakes, and salterns. As these salterns reach the minimum salinity limits for extreme halophiles, their waters become purple or reddish color due to the high densities of halophilic Archaea. H. salinarum has also been found in high-salt food such as salt pork, marine fish, and sausages. The ability of H. salinarum to survive at such high salt concentrations has led to its classification as an extremophile.
Y RNAs are small non-coding RNAs. They are components of the Ro60 ribonucleoprotein particle which is a target of autoimmune antibodies in patients with systemic lupus erythematosus. They are also reported to be necessary for DNA replication through interactions with chromatin and initiation proteins. However, mouse embryonic stem cells lacking Y RNAs are viable and have normal cell cycles.
Evelyn M. Witkin was an American bacterial geneticist at Cold Spring Harbor Laboratory (1944–1955), SUNY Downstate Medical Center (1955–1971), and Rutgers University (1971–1991). Witkin was considered innovative and inspirational as a scientist, teacher and mentor.
Deinococcus is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum Deinococcota highly resistant to environmental hazards. These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to Gram-negative bacteria. Deinococcus survive when their DNA is exposed to high doses of gamma and UV radiation. Whereas other bacteria change their structure in the presence of radiation, such as by forming endospores, Deinococcus tolerate it without changing their cellular form and do not retreat into a hardened structure. They are also characterized by the presence of the carotenoid pigment deinoxanthin that give them their pink color. They are usually isolated according to these two criteria. In August 2020, scientists reported that bacteria from Earth, particularly Deinococcus bacteria, were found to survive for three years in outer space, based on studies conducted on the International Space Station. These findings support the notion of panspermia, the hypothesis that life exists throughout the Universe, distributed in various ways, including space dust, meteoroids, asteroids, comets, planetoids or contaminated spacecraft.
Thermococcus gammatolerans is an archaea extremophile and the most radiation-resistant organism known to exist.
Chroococcidiopsis is a photosynthetic, coccoidal bacterium, and the only genus in the order Chroococcidiopsidales and in the family Chroococcidiopsidaceae. A diversity of species and cultures exist within the genus, with a diversity of phenotypes. Some extremophile members of Chroococcidiopsis are known for their ability to survive harsh environmental conditions, including both high and low temperatures, ionizing radiation, and high salinity.
Deinococcus geothermalis is a non-pathogenic, sphere-shaped, Gram-positive, heterotrophic bacterium, where geothermalis means 'hot earth' or 'hot springs'. This bacterium was first obtained from the hot springs of Agnano, Naples, Italy and São Pedro do Sul, Portugal. It resides primarily in hot springs and in deep ocean environments.
Deinococcus frigens is a species of low temperature and drought-tolerating, UV-resistant bacteria from Antarctica. It is Gram-positive, non-motile and coccoid-shaped. Its type strain is AA-692. Individual Deinococcus frigens range in size from 0.9-2.0 μm and colonies appear orange or pink in color. Liquid-grown cells viewed using phase-contrast light microscopy and transmission electron microscopy on agar-coated slides show that isolated D. frigens appear to produce buds. Comparison of the genomes of Deiococcus radiodurans and D. frigens have predicted that no flagellar assembly exists in D. frigens.
Deinococcus marmoris is a Gram-positive bacterium isolated from Antarctica. As a species of the genus Deinococcus, the bacterium is UV-tolerant and able to withstand low temperatures.
Deinococcus deserti is a Gram-negative, rod-shaped bacterium that belongs to the Deinococcaceae, a group of extremely radiotolerant bacteria. D. deserti and other Deinococcaceae exhibit an extraordinary ability to withstand ionizing radiation.
Truepera is one genus of bacteria in the family Trueperaceae from the phylum Deinococcota. The following points accounts for its characteristics:
Deinococcus aerius is an anaerobic bacterium that can be found in the atmosphere above the island of Japan. Living in such conditions makes these bacteria highly resistant to desiccation, UV-C, and gamma radiation. Although previously unidentified as strain TR0125, this bacterium was determined to be Deinococcus aerius by 16S rRNA sequencing.
↑ 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.
↑ Clark, D.P, Dunlap, P.V., Madigan, M.T., Martinko, J.M. Brock Biology of Microorganisms. San Francisco: Pearson; 2009. 481 p [ISBNmissing]
↑ Murray RGE. 1992. "The family Deino- coccaceae". In The Prokaryotes, ed. A Ballows, HG Truper, M Dworkin, W Harder, KH Schleifer 4:3732–3744. New York: Springer-Verlag[ISBNmissing]
↑ 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. PMID11846468.
↑ Farci D, Slavov C, Piano D (2018). "Coexisting properties of thermostability and ultraviolet radiation resistance in the main S-layer complex of Deinococcus radiodurans". Photochem Photobiol Sci. 17 (1): 81–88. Bibcode:2018PcPbS..17...81F. doi:10.1039/c7pp00240h. PMID29218340. S2CID4343655.
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