| Deinococcus deserti | |
|---|---|
Scientific classification  | |
| Domain: | Bacteria |
| Phylum: | Deinococcota |
| Class: | Deinococci |
| Order: | Deinococcales |
| Family: | Deinococcaceae |
| Genus: | Deinococcus |
| Species: | D. deserti |
| Binomial name | |
| Deinococcus deserti de Groot et al. 2005 [1] | |
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. [2]
Deinococcus deserti has in common with other Deinococci a highly condensed nucleoid, a high cellular Mn/Fe ratio, and several of the Deinococcus specific radiation tolerance-associated genes, for example, ddrA to ddrD, pprA, and irrE. [3]
The genome of D. deserti VCD115 is composed of four replicons: a main chromosome (2.82 Mb) and three plasmids, P1 (325 kb), P2 (314 kb) and P3 (396 kb). [4]
Two gamma- and UV-radiation-tolerant strains were isolated from a mixture of sand samples collected in the Sahara Desert in Morocco and Tunisia, after exposure of the sand to 15 kGy gamma radiation. The strains did not grow on rich medium such as trypticase soy broth (TSB), but did grow as whitish colonies on tenfold-diluted TSB. The genotypic and phenotypic properties allowed differentiation from recognized Deinococcus species. The strains were therefore identified as representing a novel species, for which the name Deinococcus deserti sp. nov. is proposed. [5]
Chromosomes with numerous radiation or desiccation-induced double-strand breaks can be repaired in a few hours in D. deserti. The extreme radiotolerance of Deinococcaceae was the object of intense investigations using D. radiodurans as model.
In cells subjected to irradiation, DNA recombinase, RecA, was the first protein that was found strongly induced. RecA is essential for radiotolerance and for the fidelity of DNA repair and genome stability in D. radiodurans. The molecular mechanisms underlying DNA repair were also examined by transcriptomics leading to the description of a repertoire of genes responding to acute gamma irradiation, including genes involved in DNA replication, repair and recombination, cell wall metabolism, cellular transport and many with uncharacterized functions.
In previous microarray experiments with D. radiodurans, the five most highly radio-induced genes were the Deinococcus-specific genes ddrA, ddrB, ddrC, ddrD, and pprA. Their homologs in D. deserti were also among the most highly induced, showing that not only their presence but also their strong upregulation in response to radiation damage is conserved. [3]
A common 17-base pair radiation/desiccation response motif (RDRM) has been identified upstream of a set of radiation-induced genes, including various DNA repair genes such as recA, gyrA, uvrB and ssb, strongly suggesting the presence of an RDR regulon that is conserved in Deinococcus species. The irrE gene is essential for radiation resistance and required for the radiation-induced expression of recA and other genes with an RDRM (radiation/desiccation response motif) site in D.radiodurans and D. deserti. DdrO could be the global regulator of the RDR regulon, because it is the only induced and conserved regulator gene preceded by an RDRM site in D. radiodurans, D. geothermalis and D. deserti. IrrE is a site-specific protease that cleaves and inactivates repressor DdrO, resulting in induced expression of genes required for DNA repair and cell survival after exposure to radiation. [6]
RecAC and RecAP are functional proteins that allow repair of massive DNA damage after exposure of D. deserti to high doses of gamma and UV radiation. ImuY and DnaE2 are involved in UV-induced point mutagenesis. [7]
The evolution of organisms that are able to survive acute irradiation doses of 15,000 Gy is difficult to explain given the apparent absence of highly radioactive habitats on Earth over geologic time. Thus, it seems more likely that the natural selection pressure for the evolution of radiation-resistant bacteria was chronic exposure to nonradioactive forms of DNA damage, in particular those promoted by desiccation. [4]
Accurate genome annotation of its 3455 genes was guided at the stage of primary annotation by an extensive proteome analysis. A set of 1348 proteins was uncovered after growth in standard conditions and proteome fractionation by phenyl-Sepharose chromatography.
In this study, 664 N-terminal peptides from 341 proteins were characterized, leading to the validation of 278 and the correction of 63 translation initiation codons in the D. deserti VCD115 genome. Four new open reading frames were also detected in its genome through the detection of peptidic signatures for the corresponding polypeptides. Peptides were identified using the MASCOT search engine against a database consisting of a six-frame translation of the entire D. deserti genome. This database comprised 65,801 hypothetical protein sequences with a large fraction of short ORFs (68% of the ORFs have less than 80 residues).
At this stage, 557 have signatures matched the N termini of 278 different proteins previously annotated.
1119 polypeptides from D. deserti were predicted to contain a signal peptide either by the neural networks or hidden Markov model approaches.
A total of 341 protein N termini were confidently identified in the D. deserti TMPP-labeled proteome. Among these, 63 were not correctly annotated in the first D. deserti genome annotation and should be modified accordingly. There has been a comparison between the gene sequences of the three sequenced Deinococcus genomes. It is proposed that the N termini of 37 and 100 additional proteins from D. geothermalis and D. radiodurans genomes, respectively, should be reannotated. When considering the manually validated TMPP-modified peptides, 664 unique signatures for N termini were identified with 398 tryptic and 266 chymotryptic sequences. These two digestions were thus found to be complementary. The N termini data set corresponds to 10% of the theoretical proteome. A significant number of erroneous annotations have probably still to be corrected. [8]
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 encodes 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.
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.
Halobacterium is a genus in the family Halobacteriaceae.
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.
Artemis is a protein that in humans is encoded by the DCLRE1C gene.
Deinococcus radiodurans is a bacterium, an extremophile and one of the most radiation-resistant organisms known. It can survive cold, dehydration, vacuum, and acid, and therefore is known as a polyextremophile. The Guinness Book Of World Records listed it as the world's toughest known bacterium.
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.
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 ficus strain CC-FR2-10T is a recently discovered gram-positive bacteria which plays a role in the production of nitrogen fertilizer. It was originally isolated from a Ficus plant, hence its name.
BASys is a freely available web server that can be used to perform automated, comprehensive annotation of bacterial genomes. With the advent of next generation DNA sequencing it is now possible to sequence the complete genome of a bacterium within a single day. This has led to an explosion in the number of fully sequenced microbes. In fact, as of 2013, there were more than 2700 fully sequenced bacterial genomes deposited with GenBank. However, a continuing challenge with microbial genomics is finding the resources or tools for annotating the large number of newly sequenced genomes. BASys was developed in 2005 in anticipation of these needs. In fact, BASys was the world’s first publicly accessible microbial genome annotation web server. Because of its widespread popularity, the BASys server was updated in 2011 through the addition of multiple server nodes to handle the large number of queries it was receiving.
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.
Halorhodospira halophila is a species of Halorhodospira distinguished by its ability to grow optimally in an environment of 15–20% salinity. It was formerly called Ectothiorhodospira halophila. It is an anaerobic, rod-shaped Gram-negative bacterium. H. halophila has a flagellum.
Ionizing radiation can cause biological effects which are passed on to offspring through the epigenome. The effects of radiation on cells has been found to be dependent on the dosage of the radiation, the location of the cell in regards to tissue, and whether the cell is a somatic or germ line cell. Generally, ionizing radiation appears to reduce methylation of DNA in cells.
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.