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The Info List - Deinococcus-Thermus


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DEINOCOCCUS–THERMUS is a phylum of bacteria 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. Cavalier-Smith calls this clade HADOBACTERIA (from Hades
Hades
, the Greek underworld).

CONTENTS

* 1 Taxonomy * 2 Molecular Signatures * 3 Phylogeny * 4 Taxonomy * 5 Sequenced genomes * 6 References

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 _. _ Truepera radiovictrix _ is the earliest diverging member of the order. Within the order, _ Deinococcus _ forms a distinct monophyletic cluster with respect to _ Deinobacterium _ and _ Truepera species _. 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. * The _ Thermales _ include several genera resistant to heat (_Marinithermus _, _ Meiothermus _, _Oceanithermus _, _ Thermus _, _Vulcanithermus _, _Rhabdothermus _) placed within a single family, _Thermaceae _. 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. 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.

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

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. 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. The CSIs found in DNA-directed RNA polymerase subunit beta and DNA topoisomerase I in _ Thermales _ species may be involved in thermophilicity , while those found in Excinuclease ABC, DNA gyrase , and DNA repair protein RadA in _ Deinococcales _ species may be associated with radioresistance . 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. 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. CSIs have also been found specific for _ Truepera radiovictrix _ .

PHYLOGENY

See also: Bacterial taxonomy
Bacterial taxonomy

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

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) and National Center for Biotechnology Information (NCBI)

* Phylum
Phylum
_DEINOCOCCUS_-_THERMUS_

* Class DEINOCOCCI Garrity 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.

* _ 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
Bacteria
and Archaea project (GEBA), which aims at sequencing organisms based on phylogenetic novelty and not on pathogenicity or notoriety. Currently, the genome of _Thermus aquaticus_ Y51MC23 is in the final stages of assembly by the DOE Joint Genome Institute

REFERENCES

* ^ _A_ _B_ 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. * ^ 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. PMC 3133647  _. PMID 21717204 . doi :10.1007/s10482-011-9616-8 . * ^ Campbell C, Sutcliffe IC, Gupta RS (2014). "Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria". Arch Microbiol_. 196 (4): 307–310. PMID 24535491 . doi :10.1007/s00203-014-0964-4 . * ^ Sutcliffe IC (2010). "A phylum level perspective on bacterial cell envelope architecture". _Trends Microbiol_. 18 (10): 464–470. PMID 20637628 . doi :10.1016/j.tim.2010.06.005 . * ^ Cavalier-Smith T (2006). "Rooting the tree of life by transition analyses". _Biol. Direct_. 1: 19. PMC 1586193  _. PMID 16834776 . doi :10.1186/1745-6150-1-19 . * ^ A_ _B_ 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. PMID 15927420 . doi :10.1016/j.femsle.2005.05.002 . * ^ _A_ _B_ Garrity GM, Holt JG. (2001) Phylum
Phylum
BIV. "Deinococcus–Thermus". In: Bergey’s manual of systematic bacteriology, pp. 395-420. Eds D. R. Boone, R. W. Castenholz. Springer-: New York. * ^ _A_ _B_ Garrity GM, Bell JA, Lilburn TG. (2005) Phylum
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. * ^ _A_ _B_ _C_ _D_ _E_ _F_ _G_ 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. PMID 27506333 . doi :10.1016/j.syapm.2016.07.003 . * ^ Battista JR, Earl AM, Park MJ (1999). "Why is Deinococcus radiodurans so resistant to ionizing radiation?". _Trends Microbiol_. 7 (9): 362–5. PMID 10470044 . doi :10.1016/S0966-842X(99)01566-8 . * ^ http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus * ^ 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. PMID 2530914 . doi :10.1016/0003-2697(89)90103-6 . * ^ 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. PMC 1274311  _. PMID 16242020 . doi :10.1186/1471-2148-5-57 . * ^ 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. PMID 10499798 . doi :10.1016/S0092-8674(00)81515-9 . * ^ 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. PMC 1448114  _. PMID 15454524 . doi :10.1534/genetics.104.029249 . * ^ \'The All-Species Living Tree\' Project ."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database . Retrieved 2016-03-20. * ^ J.P. Euzéby. ""Deinococcus-Thermus"". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20. * ^ Sayers; et al. ""Deinococcus-Thermus"". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20. * ^ http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html * ^ 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
Bacteria
and Archaea" . Nature_. 462 (7276): 1056–1060. Bibcode :2009Natur.462.1056W. PMC 3073058  . PMID 20033048 . doi :10.1038/nature08656 . * ^ http://www.ncbi.nlm.nih.gov/genomeprj/55053

* v * t * e

Extremophiles

TYPES

* Acidophile * Alkaliphile * Capnophile * Cryozoa * Endolith * Halophile * Hypolith * Lipophile * Lithoautotroph * Lithophile * Methanogen * Metallotolerant * Oligotroph * Osmophile * Piezophile * Polyextremophile * Psammophile * Psychrophile * Radioresistant * Thermophile / Hyperthermophile * Thermoacidophile * Xerophile

Notable extremophiles

BACTERIA

* _ Chloroflexus aurantiacus _ * _ Deinococcus radiodurans _ * Deinococcus–Thermus * Snottite * _ Thermus aquaticus _ * _ Thermus thermophilus _ * _ Spirochaeta americana _ * GFAJ-1

ARCHAEA

* _ Pyrococcus furiosus _ * Strain 121 * _ Pyrolobus fumarii _

EUKARYOTA

* _ Cyanidioschyzon merolae _ * _ Galdieria sulphuraria _ * _ Paralvinella sulfincola _ * _ Halicephalobus mephisto _ * Pompeii worm * _Tardigrada _

RELATED ARTICLES

* Abiogenic petroleum origin * Acidithiobacillales * Acidobacteria * Acidophiles in acid mine drainage
Acidophiles in acid mine drainage
* Archaeoglobaceae * Berkeley Pit * Blood Falls
Blood Falls
* Crenarchaeota * Grylloblattidae * Halobacteria * _ Halobacterium _ * _ Helaeomyia petrolei
Helaeomyia petrolei
_ * Hydrothermal vent * _ Methanopyrus _ * Movile Cave * Radiotrophic fungus * Rio Tinto * _Taq_ polymerase * Thermostability * Thermotogae

* v * t * e

Prokaryotes : Bacteria
Bacteria
classification (phyla and orders )

*

Domain Archaea Bacteria
Bacteria
Eukaryota (Supergroup Plant Hacrobia Heterokont Alveolata Rhizaria Excavata Amoebozoa Opisthokonta Animal Fungi )

G- / OM

Terra-/ Glidobacteria (BV1 )

EOBACTERIA

* Deinococcus- Thermus

* Deinococcales * Thermales

* Chloroflexi

* Anaerolineales * Caldilineales * Chloroflexales * Herpetosiphonales * Dehalococcoidales * Ktedonobacterales * Thermogemmatisporales * Thermomicrobiales * Sphaerobacterales

OTHER GLIDOBACTERIA

* Thermodesulfobacteria

* _thermophiles _

* Aquificae * Thermotogae

* Cyanobacteria

Proteobacteria (BV2 )

ALPHA

* Caulobacterales * Kiloniellales * Kordiimonadales * Magnetococcales * Parvularculales * Rhizobiales * Rhodobacterales * Rhodospirillales * Rickettsiales * Sneathiellales * Sphingomonadales

BETA

* Burkholderiales
Burkholderiales
* Hydrogenophilales * Methylophilales * Neisseriales * Nitrosomonadales * Procabacteriales * Rhodocyclales

GAMMA

* Acidithiobacillales * Aeromonadales * Alteromonadales * Cardiobacteriales * Chromatiales * Enterobacteriales * Legionellales * Methylococcales * Oceanospirillales * Orbales * Pasteurellales * Pseudomonadales * Salinisphaerales * Thiotrichales * Vibrionales * Xanthomonadales

DELTA

* Bdellovibrionales * Desulfarculales * Desulfobacterales * Desulfovibrionales * Desulfurellales * Desulfuromonadales * Myxococcales * Syntrophobacterales * Syntrophorhabdales

EPSILON

* Campylobacterales * Nautiliales

ZETA

* Mariprofundales

BV4

SPIROCHAETES

* Spirochaetes

Sphingobacteria ( FCB group )

* Fibrobacteres
Fibrobacteres

* Chlorobi

* Chlorobiales * Ignavibacteriales

* Bacteroidetes

* Bacteroidales * Cytophagales * Flavobacteriales * Sphingobacteriales

Planctobacteria / ( PVC group )

* Chlamydiae

* Lentisphaerae

* Lentisphaerales * Oligosphaerales * Victivallales

* Planctomycetes

* Phycisphaerales * Planctomycetales

* Verrucomicrobia

* Puniceicoccales * Opitutales * Chthoniobacterales * Verrucomicrobiales

* " Poribacteria "

OTHER GN

* Acidobacteria

* Acidobacteriales * Acanthopleuribacterales * Holophagales * Solibacterales

* Armatimonadetes

* Armatimonadales * Chthonomonadales * Fimbriimonadales

* Caldiserica * Chrysiogenetes * Deferribacteres * Dictyoglomi * Elusimicrobia * Fusobacteria * Gemmatimonadetes * Nitrospirae * Synergistetes

G+ / no OM

Firmicutes
Firmicutes
(BV3 )

BACILLI

* Bacillales * Lactobacillales

CLOSTRIDIA

* Clostridiales * Halanaerobiales *