Deinococcus–Thermus

Deinococcus–Thermus is a phylum of bacteria that are highly resistant to environmental hazards, also known as extremophiles.[1] 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.[2][3][4] Cavalier-Smith calls this clade Hadobacteria[5] (from Hades, the Greek underworld).

Deinococcus–Thermus
Scientific classification
Domain:	Bacteria
(unranked):	Terrabacteria
Phylum:	Deinococcus–Thermus
Class:	Deinococci
Orders & Families
Deinococcales Deinococcaceae Trueperaceae Thermales Thermaceae
Synonyms
Deinococcaeota Oren et al. 2015

Taxonomy

The phylum Deinococcus-Thermus consists of a single class (Deinococci) and two orders:

• The Deinococcales include two families (Deinococcaceae and Trueperaceae), with three genera, Deinococcus, Deinobacterium and Truepera.[6][7][8] Truepera radiovictrix is the earliest diverging member of the order.[6] Within the order, Deinococcus forms a distinct monophyletic cluster with respect to Deinobacterium and Truepera species.[9] The genus includes several species that are resistant to radiation; they have become famous for their ability to eat nuclear waste and other toxic materials, survive in the vacuum of space and survive extremes of heat and cold.[10]
• The Thermales include several genera resistant to heat (Marinithermus, Meiothermus, Oceanithermus, Thermus, Vulcanithermus, Rhabdothermus) placed within a single family, Thermaceae.[7][8][11] Phylogenetic analyses demonstrate that within the Thermales, Meiothermus and Thermus species form a monophyletic cluster, with respect to Marinithermus, Oceanithermus, Vulcanithermus and Rhabdothermus that branch as outgroups within the order.[9] This suggests that Meiothermus and Thermus species are more closely related to one another relative to other genera within the order. Thermus aquaticus was important in the development of the polymerase chain reaction where repeated cycles of heating DNA to near boiling make it advantageous to use a thermo-stable DNA polymerase enzyme.[12]

Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent.[9][13]

Molecular signatures

Molecular signatures in the form of conserved signature indels (CSIs) and proteins (CSPs) have been found that are uniquely shared by all members belonging to the Deinococcus-Thermus phylum.[1][9] These CSIs and CSPs are distinguishing characteristics that delineate the unique phylum from all other bacterial organisms, and their exclusive distribution is parallel with the observed differences in physiology. CSIs and CSPs have also been found that support order and family-level taxonomic rankings within the phylum. Some of the CSIs found to support order level distinctions are thought to play a role in the respective extremophilic characteristics.[9] The CSIs found in DNA-directed RNA polymerase subunit beta and DNA topoisomerase I in Thermales species may be involved in thermophilicity,[14] while those found in Excinuclease ABC, DNA gyrase, and DNA repair protein RadA in Deinococcales species may be associated with radioresistance.[15] Two CSPs that were found uniquely for all members belonging to the Deinococcus genus are well characterized and are thought to play a role in their characteristic radioresistant phenotype.[9] These CSPs include the DNA damage repair protein PprA the single-stranded DNA-binding protein DdrB.

Additionally, some genera within this group, including Deinococcus, Thermus and Meiothermus, also have molecular signatures that demarcate them as individual genera, inclusive of their respective species, providing a means to distinguish them from the rest of the group and all other bacteria.[9] CSIs have also been found specific for Truepera radiovictrix .

Phylogeny

See also: Bacterial taxonomy

The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project.[16]

Thermaceae     Rhabdothermus arcticus Steinsbu et al. 2011     Vulcanithermus mediatlanticus Miroshnichenko et al. 2003       Oceanithermus   O. desulfurans Mori et al. 2004     O. profundus Miroshnichenko et al. 2003 (type sp.)         Marinithermus hydrothermalis Sako et al. 2003       Meiothermus     Thermus           Deinococcales   Truepera radiovictrix Albuquerque et al. 2005   Deinococcaceae   Deinobacterium chartae Ekman et al. 2011     Deinococcus

Note:
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[17] and National Center for Biotechnology Information (NCBI)[18]

• Phylum Deinococcus-Thermus [Deinococcaeota Oren et al. 2015]
  • Class Deinococci Garrity & Holt 2002 ["Hadobacteria" Cavalier-Smith 1992 emend. Cavalier-Smith 1998; Hadobacteria Cavalier-Smith 2002; "Xenobacteria"]
    • Order Deinococcales Rainey et al. 1997
      • Family Deinococcaceae Brooks and Murray 1981 emend. Rainey et al. 1997
        • Genus Deinococcus Brooks and Murray 1981 emend. Rainey et al. 1997
        • Genus Deinobacterium Ekman et al. 2011
      • Family Trueperaceae Rainey et al. 2005
        • Genus Truepera da Costa, Rainey and Albuquerque 2005
    • Order Thermales Rainey and Da Costa 2002
      • Family Thermaceae Da Costa and Rainey 2002
        • Genus Thermus Brock and Freeze 1969 emend. Nobre et al. 1996
        • Genus Meiothermus Nobre et al. 1996 emend. Albuquerque et al. 2009
        • Genus Marinithermus Sako et al. 2003
        • Genus Oceanithermus Miroshnichenko et al. 2003 emend. Mori et al. 2004
        • Genus Rhabdothermus Steinsbu et al. 2011
        • Genus Vulcanithermus Miroshnichenko et al. 2003

Sequenced genomes

Currently there are 10 sequenced genomes of strains in this phylum.[19]

• Deinococcus radiodurans R1
• Thermus thermophilus HB27
• Thermus thermophilus HB8
• Deinococcus geothermalis DSM 11300
• Deinococcus deserti VCD115
• Meiothermus ruber DSM 1279
• Meiothermus silvanus DSM 9946
• Truepera radiovictrix DSM 17093
• Oceanithermus profundus DSM 14977

The two Meiothermus species were sequenced under the auspices of the Genomic Encyclopedia of Bacteria and Archaea project (GEBA), which aims at sequencing organisms based on phylogenetic novelty and not on pathogenicity or notoriety.[20] Currently, the genome of Thermus aquaticus Y51MC23 is in the final stages of assembly by the DOE Joint Genome Institute [21]

References

1. Griffiths E, Gupta RS (September 2007). "Identification of signature proteins that are distinctive of the Deinococcus–Thermus phylum" (PDF). Int. Microbiol. 10 (3): 201–8. PMID 18076002. Archived from the original (PDF) on 2011-06-14.
2. Gupta RS (2011). "Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes". Antonie van Leeuwenhoek. 100 (2): 171–182. doi:10.1007/s10482-011-9616-8. PMC 3133647. PMID 21717204.
3. Campbell C, Sutcliffe IC, Gupta RS (2014). "Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria" (PDF). Arch Microbiol. 196 (4): 307–310. doi:10.1007/s00203-014-0964-4. PMID 24535491.
4. Sutcliffe IC (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends Microbiol. 18 (10): 464–470. doi:10.1016/j.tim.2010.06.005. PMID 20637628.
5. Cavalier-Smith T (2006). "Rooting the tree of life by transition analyses". Biol. Direct. 1: 19. doi:10.1186/1745-6150-1-19. PMC 1586193. PMID 16834776.
6. Albuquerque L, Simões C, Nobre MF, et al. (2005). "Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov". FEMS Microbiol Lett. 247 (2): 161–169. doi:10.1016/j.femsle.2005.05.002. PMID 15927420.
7. Garrity GM, Holt JG. (2001) Phylum BIV. "Deinococcus–Thermus". In: Bergey’s manual of systematic bacteriology, pp. 395-420. Eds D. R. Boone, R. W. Castenholz. Springer-: New York.
8. Garrity GM, Bell JA, Lilburn TG. (2005) Phylum BIV. The revised road map to the Manual. In: Bergey’s manual of systematic bacteriology, pp. 159-220. Eds Brenner DJ, Krieg NR, Staley JT, Garrity GM. Springer-: New York.
9. Ho J, Adeolu M, Khadka B, Gupta RS (2016). "Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus-Thermus" and distinguish its main constituent groups". Syst Appl Microbiol. 39 (7): 453–463. doi:10.1016/j.syapm.2016.07.003. PMID 27506333.
10. Battista JR, Earl AM, Park MJ (1999). "Why is Deinococcus radiodurans so resistant to ionizing radiation?". Trends Microbiol. 7 (9): 362–5. doi:10.1016/S0966-842X(99)01566-8. PMID 10470044.
11. http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus Archived 2013-01-27 at the Wayback Machine
12. Nelson RM, Long GL (1989). "A general method of site-specific mutagenesis using a modification of the Thermus aquaticus". Anal Biochem. 180 (1): 147–151. doi:10.1016/0003-2697(89)90103-6. PMID 2530914.
13. Omelchenko MV, Wolf YI, Gaidamakova EK, et al. (2005). "Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance". BMC Evol. Biol. 5: 57. doi:10.1186/1471-2148-5-57. PMC 1274311. PMID 16242020.
14. Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA (1999). "Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution". Cell. 98 (6): 811–824. doi:10.1016/S0092-8674(00)81515-9. PMID 10499798.
15. Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR (2004). "Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance". Genetics. 168 (1): 21–23. doi:10.1534/genetics.104.029249. PMC 1448114. PMID 15454524.
16. 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.
17. J.P. Euzéby. "Deinococcus-Thermus". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
18. Sayers; et al. "Deinococcus-Thermus". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
19. "Microbial Genomes".
20. Wu, D.; Hugenholtz, P.; Mavromatis, K.; Pukall, R. D.; Dalin, E.; Ivanova, N. N.; Kunin, V.; Goodwin, L.; Wu, M.; Tindall, B. J.; Hooper, S. D.; Pati, A.; Lykidis, A.; Spring, S.; Anderson, I. J.; d'Haeseleer, P.; Zemla, A.; Singer, M.; Lapidus, A.; Nolan, M.; Copeland, A.; Han, C.; Chen, F.; Cheng, J. F.; Lucas, S.; Kerfeld, C.; Lang, E.; Gronow, S.; Chain, P.; Bruce, D. (2009). "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature. 462 (7276): 1056–1060. Bibcode:2009Natur.462.1056W. doi:10.1038/nature08656. PMC 3073058. PMID 20033048.
21. "BioProject - NCBI".