Deinococcus

Deinococcus (from the Greek: δεινός, deinos, "dreadful, strange" and κόκκος, kókkos, "granule"^[1]) is in the monotypic family Deinococcaceae, and one genus^[2] of three in the order Deinococcales^[3][4] 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.^[5][6]

Deinococcus
A tetrad of D. radiodurans
Scientific classification
Domain:	Bacteria
Phylum:	Deinococcota
Class:	Deinococci
Order:	Deinococcales
Family:	Deinococcaceae Brooks and Murray 1981
Genus:	Deinococcus Rainey et al. 1997
Type species
Deinococcus radiodurans Raj et al. 1960 ex Brooks and Murray 1981
Species
See text.
Synonyms
Deinobacter Oyaizu et al. 1987

Molecular signatures

Members of Deinococcus can be distinguished from all other bacteria through molecular signatures known as conserved signature indels (CSIs) and proteins (CSPs). An earlier study on Deinococcus identified nine CSIs and 58 CSPs which were exclusively shared by members of this genus.^[7] Some of the identified CSPs such as the DNA damage repair protein PprA and the single-stranded DNA-binding protein DdrB are thought to have functional roles in the DNA repair mechanism and radioresistance phenotype of Deinococcus.^[7]

In a more recent work focused on DNA repair proteins an additional 22 CSIs were identified as specific to this genus, including a 30 amino acid insert in the UvrA1 protein that is suggested to play in a role in the resistance ability of Deinococcus species against radiation and oxidation damage.^[8]

The uvrA1 gene in Deinococcus was found to form a novel genetic linkage with the genes of the proteins dCSP-1 (a transmembrane protein found only in Deinococcus species), DsbA and DsbB. The latter two proteins play a central role in the formation of disulfide bonds in proteins via oxidation-reduction of cysteine rich motifs (CXXC).^[9] The above cluster of genes forms a novel operon unique to Deinococcus species and the encoded proteins are predicted to function together to combat against DNA damage caused by reactive oxidative species from radiation.^[8]

The 30 aa CSI present in UvrA1 and another 5-7 aa CSI present in DsbA are located on surface loops of the proteins. The surface exposed loops/patches formed by these CSIs are thought to mediate protein-protein interactions with the transmembrane protein dCSP-1, thus facilitating a sequence of electron transfers that ultimately ameliorates oxidative damage.^[8]

Comparative genomics

 

Orthologous gene comparison between three sequenced Deinococcus strains. The numbers correspond to the number of shared orthologs between two or all three species.^[10]

Although all species of the genus Deinococcus are related by definition, they exhibit substantial differences across their genomes. Most species appear to have about 3,000 genes, but only a fraction of them are shared in other species. For example, a 3-species comparison among D. radiodurans, D. deserti, and D. geothermalis shows that about two thirds of each genome is shared by all three species, but close to a third is specific and only found in one of the species (see figure). Once more genomes are included in such comparisons, the core genome will almost certainly be much smaller.^[10]

Taxonomy

See also: Bacterial taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) ^[11] and National Center for Biotechnology Information (NCBI).^[12] As of August 2011^[update], there were 47 species of Deinococcus described

Phylogeny

16S rRNA based LTP_08_2023^[13]^[14]^[15]

120 marker proteins based GTDB 08-RS214^[16]^[17]^[18]

Deinococcus D. peraridilitoris Rainey et al. 2007^[19] D. cellulosilyticus Weon et al. 2007^[20] D. lacus Park et al. 2018 D. radiophilus (ex Lewis 1973) Books and Murray 1981^[21] D. piscis Shashidhar and Bandekar 2009^[22] D. proteolyticus Brooks and Murray 1981^[23] D. maricopensis Rainey and da Costa 2005^[24] D. misasensis Asker et al. 2008^[25] D. roseus Asker et al. 2008^[25] D. pimensis Rainey and da Costa 2005^[24] D. papagonensis Rainey and da Costa 2005^[24] D. yavapaiensis Rainey and da Costa 2005^[24] D. ruber Kim et al. 2017^[26] D. aquiradiocola Asker et al. 2009^[27] D. radiomollis Callegan et al. 2008^[28] D. altitudinis Callegan et al. 2008^[28] D. claudionis Callegan et al. 2008^[28] D. sonorensis Rainey and da Costa 2005^[24] D. persicinus Jeon et al. 2016^[26] D. irradiatisoli Kim et al. 2018 D. alpinitundrae Callegan et al. 2008^[28] D. detaillensis Zhang et al. 2021 D. psychrotolerans Tian et al. 2019 D. murrayi Ferreira et al. 1997^[29] D. terrestris Wang et al. 2020 D. carri Kim et al. 2015^[26] D. budaensis Makk et al. 2016^[26] D. phoenicis Vaishampayan, Venkateswaran & Schwendner 2014 D. geothermalis Ferreira et al. 1997^[29] D. aluminii Kim et al. 2018 D. metallilatus Kim et al. 2015 "D. aestuarii" Yin et al. 2022 D. aetherius Yang et al. 2010^[30] D. aerius Yang et al. 2009^[31] D. apachensis Rainey and da Costa 2005^[24] D. terrigena Ten et al. 2019 D. enclensis Thorat et al. 2015 D. ficus Lai et al. 2006 emend. Kämpfer 2009^[32] D. radiodurans (ex Raj et al. 1960) Brooks and Murray 1981^[33] D. wulumuqiensis Wang et al. 2010^[34] D. xinjiangensis Peng et al. 2009^[35] D. antarcticus Dong et al. 2015^[26] D. cavernae Zhu et al. 2022 D. fonticola Makk et al. 2019 D. reticulitermitis Chen et al. 2012^[36] D. petrolearius Xi et al. 2019 D. citri Ahmed et al. 2014^[26] D. gobiensis Yuan et al. 2009^[37] D. metalli Feng et al. 2015 D. aquatilis Kämpfer et al. 2008^[38] D. puniceus Lee et al. 2014^[26] D. radioresistens Srinivasan et al. 2016 D. rufus Wang et al. 2018 D. yunweiensis Zhang et al. 2007^[39] D. koreensis Baek et al. 2018 D. hopiensis Rainey and da Costa 2005^[24] D. aerolatus Yoo et al. 2010^[40] D. aerophilus Yoo et al. 2010^[40] D. humi Srinivasan et al. 2012 D. swuensis Lee et al. 2015 D. radiopugnans Brooks and Murray 1981^[41] D. marmoris Hirsch et al. 2006^[42] D. saxicola Hirsch et al. 2006^[42] D. frigens Hirsch et al. 2006^[42] D. taklimakanensis Liu et al. 2017 D. arcticus Wang et al. 2019 "D. aquaedulcis" Yin et al. 2022 D. multiflagellatus Kim et al. 2018 D. arboris Bae et al. 2022 D. betulae Bae et al. 2022 D. hohokamensis Rainey and da Costa 2005^[24] D. navajonensis Rainey and da Costa 2005^[24] D. deserti de Groot et al. 2005^[43] D. malanensis Zhu et al. 2017 D. indicus Suresh et al. 2004^[44] D. caeni Im et al. 2008^[45] D. depolymerans Asker et al. 2011^[46] D. aquaticus Im et al. 2008^[45] D. knuensis Lee et al. 2017 D. seoulensis Lee et al. 2016^[26] D. radiotolerans Cha et al. 2015 D. grandis (Oyaizu et al. 1987) Rainey et al. 1997 ^[47]^[48] D. daejeonensis Srinivasan et al. 2012 ^[49] D. sedimenti Lee et al. 2017^[26] D. hibisci Moya et al. 2018 D. saudiensis Hussain et al. 2016^[26] D. soli Cha et al. 2016 non Zhang et al. 2011^[26] D. kurensis Akita et al. 2021^[26] D. actinosclerus Joo et al. 2016^[26] D. arenae Lee et al. 2016^[26]

Deinococcaceae Deinobacterium chartae Deinococcus Deinococcus misasensis Deinococcus cellulosilyticus Deinococcus roseus species‑group 2 Deinococcus D. peraridilitoris D. pimensis D. yavapaiensis D. maricopensis D. irradiatisoli D. alpinitundrae D. alpinitundrae D. psychrotolerans D. ruber D. aquiradiocola D. altitudinis D. claudionis D. radiophilus D. piscis D. proteolyticus D. hopiensis D. phoenicis D. geothermalis D. metallilatus D. budaensis D. murrayi D. terrestris "D. aestuarii" "D. planocerae" Lin et al. 2017 D. aerius D. apachensis D. aquatilis D. puniceus D. ficus D. deserti D. malanensis D. gobiensis D. fonticola [incl. D. cavernae] D. reticulitermitis D. radiodurans D. wulumuqiensis D. metalli D. koreensis D. aerophilus D. aerolatus D. humi D. radiopugnans D. marmoris D. frigens D. indicus D. seoulensis [incl. D. knuensis] D. arcticus "D. aquaedulcis" D. multiflagellatus D. radiotolerans D. actinosclerus [incl. D. arenae; D. kurensis] D. soli [incl. D. saudiensis] D. grandis [incl. D. daejeonensis; "D. xianganensis" Zheng et al. 2014] D. sedimenti

Species incertae sedis:

• "D. aquivivus" Kaempferet al. 2008
• "D. gammatolerans" Srinivasan, Kang & Kim 2017
• "D. guangxiensis" Sun et al. 2009
• D. hibisci Moya et al. 2018
• "D. koreense" Kim, Kang & Srinivasan 2017
• D. papagonensis Rainey & da Costa 2005
• "D. populi" Li, Kudo & Tonouchi 2018
• "D. sahariens" Bouraoui et al. 2012
• "D. soli" Zhang et al. 2011 non Cha et al. 2016
• "D. taeanensis" Lee et al. 2022
• D. xibeiensis Wang et al. 2010^[34]

See also

• List of bacteria genera
• List of bacterial orders

References

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43. de Groot A, Chapon V, Servant P, Christen R, Saux MF, Sommer S, Heulin T. Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol. 2005 Nov;55(Pt 6):2441-6.
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