Deinococcus

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Deinococcus
Deinococcus radiodurans.jpg
A tetrad of D. radiodurans
Scientific classification e
Domain: Bacteria
Phylum: Deinococcus-Thermus
Class: Deinococci
Order: Deinococcales
Family: Deinococcaceae
Brooks and Murray, 1981
Genus: Deinococcus
Rainey et al. 1997
Synonyms
  • Deinobacter Oyaizu et al. 1987

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 Deinococcus-Thermus 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 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]

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]

Species[]

As of August 2011, there were 47 species of Deinococcus described according to the National Center for Biotechnology Information (NCBI):

Phylogeny[]

See also: Bacterial taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [41] and NCBI[42] and the phylogeny is based on 16S rRNA-based LTP release 132 by 'The All-Species Living Tree' Project.[43]

 
 
 

Rainey and da Costa 2005

 
 
 

Rainey et al. 2007

 
 
 

Rainey and da Costa 2005

 
 

Rainey and da Costa 2005

 
 
 
 
 
 
 

Asker et al. 2008

 
 
 

Weon et al. 2007

 
 

Asker et al. 2008

 
 
 
 
 

Rainey and da Costa 2005

 
 
 
 

Rainey and da Costa 2005

 
 
 

Callegan et al. 2008

 
 
 

Callegan et al. 2008

 
 
 

Asker et al. 2009

 
 

Callegan et al. 2008

 
 
 
 
 
 
 

Callegan et al. 2008

 
 
 
 

(ex Lewis 1973) Books and Murray 1981

 
 
 

Shashidhar and Bandekar 2009

 
 

Brooks and Murray 1981

 
 
 
 
 
 

Peng et al. 2009

 
 
 

Dong et al. 2015

 
 
 

Kim et al. 2015

 
 
 

Kämpfer et al. 2008

 
 
 

Thorat et al. 2015

 
 

D. ficus Lai et al. 2006 emend. Kämpfer 2009

 
 
 
 
 
 
 
 
 

Vaishampayan, Venkateswaran & Schwendner 2014

 
 
 

Chen et al. 2012

 
 
 

Ahmed et al. 2014

 
 

Yuan et al. 2009

 
 
 
 
 
 
 

D. indicus Suresh et al. 2004

 
 
 

D. radiodurans (ex Raj et al. 1960) Brooks and Murray 1981 (type sp.)

 
 

Wang et al. 2010

 
 
 
 
 
 

Cha et al. 2015

 
 
 

D. deserti de Groot et al. 2005

 
 
 

Rainey and da Costa 2005

 
 

Rainey and da Costa 2005

 
 
 
 
 
 
 

Im et al. 2008

 
 
 

Im et al. 2008

 
 

Asker et al. 2011

 
 
 
 
 
 

Srinivasan et al. 2012

 
 
 

Joo et al. 2016

 
 

(Oyaizu et al. 1987) Rainey et al. 1997

 
 
 
 
 
 

Feng et al. 2015

 
 

Zhang et al. 2007

 
 
 
 
 

Rainey and da Costa 2005

 
 
 
 

D. murrayi Ferreira et al. 1997

 
 
 

Kim et al. 2015

 
 
 

D. geothermalis Ferreira et al. 1997

 
 
 

D. apachensis Rainey and da Costa 2005

 
 
 

D. aerius Yang et al. 2009

 
 

Yang et al. 2010

 
 
 
 
 
 
 
 
 
 

Yoo et al. 2010

 
 
 

Srinivasan et al. 2012

 
 
 

Yoo et al. 2010

 
 
 

Lee et al. 2015

 
 
 

Brooks and Murray 1981

 
 
 

D. marmoris Hirsch et al. 2006

 
 
 

D. saxicola Hirsch et al. 2006

 
 

D. frigens Hirsch et al. 2006

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Notes[]

  1. ^ Jump up to: a b Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN).

References[]

  1. ^ Deinococcus entry in LPSN; Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". International Journal of Systematic and Evolutionary Microbiology. 47 (2): 590–2. doi:10.1099/00207713-47-2-590. PMID 9103655.
  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. ^ 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. ^ 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. ^ Jump up to: a b 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.
  8. ^ Jump up to: a b c 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.
  9. ^ 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.
  10. ^ Jump up to: a b c d e f g h i j k l m n Parte, A.C. "Deinococcus". LPSN.
  11. ^ Yang Y, Itoh T, Yokobori S, Itahashi S, Shimada H, Satoh K, Ohba H, Narumi I, Yamagishi A. Deinococcus aerius sp. nov., isolated from the high atmosphere. Int J Syst Evol Microbiol. 2009 Aug;59(Pt 8):1862-6.
  12. ^ Jump up to: a b Yoo SH, Weon HY, Kim SJ, Kim YS, Kim BY, Kwon SW. Deinococcus aerolatus sp. nov. and Deinococcus aerophilus sp. nov., isolated from air samples. Int J Syst Evol Microbiol. 2010 May;60(Pt 5):1191-5.
  13. ^ Yang Y, Itoh T, Yokobori S, Shimada H, Itahashi S, Satoh K, Ohba H, Narumi I, Yamagishi A. Deinococcus aetherius sp. nov., isolated from the stratosphere. Int J Syst Evol Microbiol. 2010 Apr;60(Pt 4):776-9
  14. ^ Jump up to: a b c d Callegan RP, Nobre MF, McTernan PM, Battista JR, Navarro-González R, McKay CP, da Costa MS, Rainey FA. Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments. Int J Syst Evol Microbiol. 2008 May;58(Pt 5):1252-8.
  15. ^ Jump up to: a b c d e f g h i Rainey FA, Ray K, Ferreira M, Gatz BZ, Nobre MF, Bagaley D, Rash BA, Park MJ, Earl AM, Shank NC, Small AM, Henk MC, Battista JR, Kämpfer P, da Costa MS. Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample. Appl Environ Microbiol. 2005 Sep;71(9):5225-35. Erratum in: Appl Environ Microbiol. 2005 Nov;71(11):7630.
  16. ^ Jump up to: a b Im WT, Jung HM, Ten LN, Kim MK, Bora N, Goodfellow M, Lim S, Jung J, Lee ST. Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol. 2008 Oct;58(Pt 10):2348-53.
  17. ^ Kämpfer P, Lodders N, Huber B, Falsen E, Busse HJ. Deinococcus aquatilis sp. nov., isolated from water. Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2803-6.
  18. ^ Asker D, Awad TS, Beppu T, Ueda K. Deinococcus aquiradiocola sp. nov., isolated from a radioactive site in Japan. Int J Syst Evol Microbiol. 2009 Jan;59(Pt 1):144-9.
  19. ^ Weon HY, Kim BY, Schumann P, Son JA, Jang J, Go SJ, Kwon SW. Deinococcus cellulosilyticus sp. nov., isolated from air. Int J Syst Evol Microbiol. 2007 Aug;57(Pt 8):1685-8.
  20. ^ Srinivasan S, Kim MK, Lim S, Joe M, Lee M. Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. Int J Syst Evol Microbiol. 2011 Jul 15
  21. ^ Asker D, Awad TS, McLandsborough L, Beppu T, Ueda K. Deinococcus depolymerans sp. nov., a gamma- and UV-radiation-resistant bacterium, isolated from a naturally radioactive site. Int J Syst Evol Microbiol. 2011 Jun;61(Pt 6):1448-53
  22. ^ 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.
  23. ^ Lai WA, Kämpfer P, Arun AB, Shen FT, Huber B, Rekha PD, Young CC. Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L. Int J Syst Evol Microbiol. 2006 Apr;56(Pt 4):787-91
  24. ^ Jump up to: a b c Hirsch P, Gallikowski CA, Siebert J, Peissl K, Kroppenstedt R, Schumann P, Stackebrandt E, Anderson R. Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica. Syst Appl Microbiol. 2004 Nov;27(6):636-45.
  25. ^ Jump up to: a b Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, da Costa MS. Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol. 1997 Oct;47(4):939-47.
  26. ^ Yuan M, Zhang W, Dai S, Wu J, Wang Y, Tao T, Chen M, Lin M. Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium. Int J Syst Evol Microbiol. 2009 Jun;59(Pt 6):1513-7
  27. ^ Oyaizu H, Stackebrandt E, Schleifer KH, Ludwig W, Pohla H, Ito H, Hirata A, Oyaizu Y, Komagata K. A radiation-resistant rod-shaped bacterium, Deinobacter grandis gen. nov., sp. nov., with peptidoglycan containing ornithine. Int. J. Syst. Bacteriol., 1987, 37, 62-67.
  28. ^ Rainey FA, Nobre MF, Schumann P, Stackebrandt E, Da Costa MS. Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison. Int. J. Syst. Bacteriol., 1997, 47, 510-514
  29. ^ Suresh K, Reddy GS, Sengupta S, Shivaji S. Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India. Int J Syst Evol Microbiol. 2004 Mar;54(Pt 2):457-61.
  30. ^ Jump up to: a b Asker D, Awad TS, Beppu T, Ueda K. Deinococcus misasensis and Deinococcus roseus, novel members of the genus Deinococcus, isolated from a radioactive site in Japan. Syst Appl Microbiol. 2008 Mar;31(1):43-9.
  31. ^ Rainey FA, Ferreira M, Nobre MF, Ray K, Bagaley D, Earl AM, Battista JR, Gómez-Silva B, McKay CP, da Costa MS. Deinococcus peraridilitoris sp. nov., isolated from a coastal desert. Int J Syst Evol Microbiol. 2007 Jul;57(Pt 7):1408-12.
  32. ^ Shashidhar R, Bandekar JR. Deinococcus piscis sp. nov., a radiation-resistant bacterium isolated from a marine fish. Int J Syst Evol Microbiol. 2009 Nov;59(Pt 11):2714-7
  33. ^ Kobatake, M., Tanabe, S., Hasegawa, S. Nouveau micrococcus radioresistant a pigment rouge, isole de feces de Lama glama, et son utilisation comme indicateur microbiologique de la radiosterilisation. C.R. Seances Soc. Biol. Fil. (1973)167, 1506–1510.
  34. ^ 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.
  35. ^ Lewis NF. Radio-resistant Micrococcus radiophilus sp. nov. isolated from irradiated Bombay duck (Harpodon nehereus). Curr. Sci. (India)1976, v. 42, no. 14, p. 504
  36. ^ Davis, N.S., Silverman, G.J., Mausurosky, E.B. Radiation-resistant, pigmented coccus isolated from haddock tissue. J. Bacteriol. 1963;86, 294–298.
  37. ^ Chen W, Wang B, Hong H, Yang H, Liu SJ. Deinococcus reticulitermitis sp. nov., isolated from a termite gut.Int J Syst Evol Microbiol. 2011 Feb 18
  38. ^ Jump up to: a b Wang W, Mao J, Zhang Z, Tang Q, Xie Y, Zhu J, Zhang L, Liu Z, Shi Y, Goodfellow M. Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol. 2010 Sep;60(Pt 9):2006-10
  39. ^ Peng F, Zhang L, Luo X, Dai J, An H, Tang Y, Fang C. Deinococcus xinjiangensis sp. nov., isolated from desert soil. Int J Syst Evol Microbiol. 2009 Apr;59(Pt 4):709-13.
  40. ^ Zhang YQ, Sun CH, Li WJ, Yu LY, Zhou JQ, Zhang YQ, Xu LH, Jiang CL. Deinococcus yunweiensis sp. nov., a gamma- and UV-radiation-resistant bacterium from China. Int J Syst Evol Microbiol. 2007 Feb;57(Pt 2):370-5.
  41. ^ J.P. Euzéby. "Deinococcus-Thermus". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2018-07-20.
  42. ^ Sayers; et al. "DeinococcusThermus". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2018-07-20.
  43. ^ "16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. Retrieved 2018-07-20.
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