Deinococcus

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Deinococcus (from Ancient Greek δεινός (deinós), meaning "dreadful", and κόκκος (kókkos), meaning "grain"[1]) is in the formerly 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 also include a second membrane and are therefore 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 gives 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]

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

Script error: No such module "Labelled list hatnote". 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, there were 47 species of Deinococcus described.

Phylogeny

Root node corresponds to Deinococcaceae.

Branch abbreviation key:

  • Db. = Deinobacterium
  • D., Dc. = Deinococcus
  • (A) = GTDB genus Deinococcus_A
  • (B) = GTDB genus Deinococcus_B
  • (C) = GTDB genus Deinococcus_C, also known as "Deinococcus species-group 2"
  • (*) = GTDB genus Deinococcus, or Deinococcus s.s.
16S rRNA based LTP_10_2024[13][14][15] 120 marker proteins based GTDB 10-RS226[16][17][18]

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Species incertae sedis:

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  • "D. aquivivus" Kaempferet al. 2008
  • "D. gammatolerans" Srinivasan, Kang & Kim 2017
  • "D. guangxiensis" Sun et al. 2009
  • "D. koreense" Kim, Kang & Srinivasan 2017 non Baek et al. 2018
  • "D. populi" Li, Kudo & Tonouchi 2018
  • "D. sahariens" Bouraoui et al. 2012
  • "D. soli" Zhang et al. 2011 non Cha et al. 2016
  • D. xibeiensis Wang et al. 2010[19]

See also

References

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  1. ^ Deinococcus in LPSN; Page Module:Citation/CS1/styles.css has no content.Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (1 November 2020). "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5607–5612. doi:10.1099/ijsem.0.004332.
  2. ^ Brooks BW, Murray RGE (1981) Nomenclature for" Micrococcus radiodurans" and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. International Journal of Systematic and Evolutionary Microbiology 31: 353.
  3. ^ Ekman JV, Raulio M, Busse HJ, Fewer DP, Salkinoja-Salonen M (2010) Deinobacterium chartae gen. nov., sp. nov., an extremely radiation resistant biofilm-forming bacterium isolated from a Finnish paper mill. International Journal of Systematic and Evolutionary Microbiology.
  4. ^ Albuquerque L, Sims C, Nobre MF, Pino NM, Battista JR, et al. (2005) Truepera radiovictrix gen. nov., sp. nov., a new radiation-resistant species and the proposal of Trueperaceae fam. nov. FEMS Microbiology Letters 247: 161-169.
  5. ^ Page Module:Citation/CS1/styles.css has no content.Strickland, Ashley (26 August 2020). "Bacteria from Earth can survive in space and could endure the trip to Mars, according to new study". CNN News. Retrieved 26 August 2020.
  6. ^ Page Module:Citation/CS1/styles.css has no content.Kawaguchi, Yuko; et al. (26 August 2020). "DNA Damage and Survival Time Course of Deinococcal Cell Pellets During 3 Years of Exposure to Outer Space". Frontiers in Microbiology. 11: 2050. doi:10.3389/fmicb.2020.02050. PMC 7479814. PMID 32983036.
  7. ^ a b Page Module:Citation/CS1/styles.css has no content.Ho, Jonathan; Adeolu, Mobolaji; Khadka, Bijendra; Gupta, Radhey S. (October 2016). "Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus–Thermus" and distinguish its main constituent groups". Systematic and Applied Microbiology. 39 (7): 453–463. doi:10.1016/j.syapm.2016.07.003. ISSN 0723-2020. PMID 27506333.
  8. ^ a b c Page Module:Citation/CS1/styles.css has no content.Hassan, F. M. Nazmul; Gupta, Radhey S. (2018-03-08). "Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage". Genes. 9 (3): 149. doi:10.3390/genes9030149. ISSN 2073-4425. PMC 5867870. PMID 29518000.
  9. ^ Page Module:Citation/CS1/styles.css has no content.Inaba, Kenji; Ito, Koreaki (April 2008). "Structure and mechanisms of the DsbB–DsbA disulfide bond generation machine". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1783 (4): 520–529. doi:10.1016/j.bbamcr.2007.11.006. ISSN 0167-4889. PMID 18082634.
  10. ^ a b Page Module:Citation/CS1/styles.css has no content.Groot, Arjan de; Dulermo, Rémi; Ortet, Philippe; Blanchard, Laurence; Guérin, Philippe; Fernandez, Bernard; Vacherie, Benoit; Dossat, Carole; Jolivet, Edmond; Siguier, Patricia; Chandler, Michael; Barakat, Mohamed; Dedieu, Alain; Barbe, Valérie; Heulin, Thierry (2009-03-27). "Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti". PLOS Genetics. 5 (3) e1000434. doi:10.1371/journal.pgen.1000434. ISSN 1553-7404. PMC 2669436. PMID 19370165.
  11. ^ Page Module:Citation/CS1/styles.css has no content.J.P. Euzéby. "Deinococcus". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-07-20.
  12. ^ Page Module:Citation/CS1/styles.css has no content.Sayers; et al. "DeinococcusThermus". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-07-20.
  13. ^ Page Module:Citation/CS1/styles.css has no content."The LTP". Retrieved 10 December 2024.
  14. ^ Page Module:Citation/CS1/styles.css has no content."LTP_all tree in newick format". Retrieved 10 December 2024.
  15. ^ Page Module:Citation/CS1/styles.css has no content."LTP_10_2024 Release Notes" (PDF). Retrieved 10 December 2024.
  16. ^ Page Module:Citation/CS1/styles.css has no content."GTDB release 10-RS226". Genome Taxonomy Database. Retrieved 1 May 2025.
  17. ^ Page Module:Citation/CS1/styles.css has no content."bac120_r226.sp_label". Genome Taxonomy Database. Retrieved 1 May 2025.
  18. ^ Page Module:Citation/CS1/styles.css has no content."Taxon History". Genome Taxonomy Database. Retrieved 1 May 2025.
  19. ^ Cite error: The named reference wang was invoked but never defined (see the help page).

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