Biology:Thermoproteota

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Short description: Phylum of archaea

Thermoproteota
RT8-4.jpg
Archaea Sulfolobus infected with specific virus STSV-1.
Scientific classification e
Domain: Archaea
Kingdom: Proteoarchaeota
Superphylum: TACK group
Phylum: Thermoproteota
Garrity & Holt 2021[1]
Class
Synonyms
  • "Eocyta" Lake et al. 1984
    This also applies to TACK group
  • "Crenarchaeota" Garrity and Holt 2001
  • "Gearchaeota" corrig. Kozubal et al. 2013
  • "Marsarchaeota" Jay et al. 2018
  • "Nezhaarchaeota" Wang et al. 2019
  • "Thermoproteaeota" Oren et al. 2015
  • "Thermoproteota" Whitman et al. 2018
  • "Verstraetearchaeota" Vanwonterghem et al. 2016

The Thermoproteota (also known as Crenarchaea) are prokaryotes that have been classified as a phylum of the Archaea domain.[2][3][4] Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Thermoproteota environmental rRNA indicating the organisms may be the most abundant archaea in the marine environment.[5] Originally, they were separated from the other archaea based on rRNA sequences; other physiological features, such as lack of histones, have supported this division, although some crenarchaea were found to have histones.[6] Until recently all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113°C.[7] These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells.[8]

Thermoproteota were initially classified as a part of Regnum Eocyta in 1984,[9] but this classification has been discarded. The term "eocyte" now applies to either TACK (formerly Crenarchaeota) or to Thermoproteota.

Sulfolobus

One of the best characterized members of the Crenarchaeota is Sulfolobus solfataricus. This organism was originally isolated from geothermally heated sulfuric springs in Italy, and grows at 80 °C and pH of 2–4.[10] Since its initial characterization by Wolfram Zillig, a pioneer in thermophile and archaean research, similar species in the same genus have been found around the world. Unlike the vast majority of cultured thermophiles, Sulfolobus grows aerobically and chemoorganotrophically (gaining its energy from organic sources such as sugars). These factors allow a much easier growth under laboratory conditions than anaerobic organisms and have led to Sulfolobus becoming a model organism for the study of hyperthermophiles and a large group of diverse viruses that replicate within them.

16S rRNA based LTP_06_2022[11][12][13] 53 marker proteins based GTDB 08-RS214[14][15][16]
"TACK"
 

Nitrososphaerota

 
 
Thermoproteota
Thermoproteia
 

Thermoproteales

 
 
 
 

Fervidicoccales

 
 

Desulfurococcales 1

 
 
 
 

Desulfurococcales

 
 

Sulfolobales

 
 
 
 
 
 
 
"TACK"
 

"Korarchaeia"

 
 
"BAT"
 

"Bathyarchaeia" (MCG)

 
 
 

Nitrososphaeria_A ("Aigarchaeota")

 
 

Nitrososphaeria

 
 
 
"Sulfobacteria"
 
"Methanomethylicia"
 

"Methanomethylicales"

 
 

"Nezhaarchaeales"

 
("Verstraetearchaeota")
"Thermoproteia"
 

"Gearchaeales"

 
 
 

"Thermofilales"

 
 

Thermoproteales

 
 
 
 
 
"Sulfolobia"
 

"Marsarchaeales"

 
 

Sulfolobales

 
 
 
 
 
Thermoproteota

Recombinational repair of DNA damage

Irradiation of S. solfataricus cells with ultraviolet light strongly induces formation of type IV pili that can then promote cellular aggregation.[17] Ultraviolet light-induced cellular aggregation was shown by Ajon et al.[18] to mediate high frequency inter-cellular chromosome marker exchange. Cultures that were ultraviolet light-induced had recombination rates exceeding those of uninduced cultures by as much as three orders of magnitude. S. solfataricus cells are only able to aggregate with other members of their own species.[18] Frols et al.[17][19] and Ajon et al.[18] considered that the ultraviolet light-inducible DNA transfer process, followed by homologous recombinational repair of damaged DNA, is an important mechanism for promoting chromosome integrity.

This DNA transfer process can be regarded as a primitive form of sexual interaction.

Marine species

Beginning in 1992, data were published that reported sequences of genes belonging to the Thermoproteota in marine environments.[20],[21] Since then, analysis of the abundant lipids from the membranes of Thermoproteota taken from the open ocean have been used to determine the concentration of these “low temperature Crenarchaea” (See TEX-86). Based on these measurements of their signature lipids, Thermoproteota are thought to be very abundant and one of the main contributors to the fixation of carbon .[citation needed] DNA sequences from Thermoproteota have also been found in soil and freshwater environments, suggesting that this phylum is ubiquitous to most environments.[22]

In 2005, evidence of the first cultured “low temperature Crenarchaea” was published. Named Nitrosopumilus maritimus, it is an ammonia-oxidizing organism isolated from a marine aquarium tank and grown at 28 °C.[23]

Possible connections with eukaryotes

The research about two-domain system of classification has paved the possibilities of connections between crenarchaea and eukaryotes.[24]

DNA analysis from 2008 (and later, 2017) has shown that eukaryotes possible evolved from thermoproteota-like organisms. Other candidates for the ancestor of eukaryotes include closely related asgards. This could suggest that eukaryotic organisms possibly evolved from prokaryotes.

These results are similar to the eocyte hypothesis of 1984, proposed by James A. Lake.[9] The classification according to Lake, states that both crenarchaea and asgards belong to Kingdom Eocyta. Though this has been discarded by scientists, the main concept remains. The term "Eocyta" now either refers to the TACK group or to Phylum Thermoproteota itself.

However, the topic is highly debated and research is still going on.

See also

References

  1. ↑ "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol 71 (10): 5056. 2021. doi:10.1099/ijsem.0.005056. PMID 34694987. https://www.microbiologyresearch.org/pubmed/content/journal/ijsem/10.1099/ijsem.0.005056. 
  2. ↑ See the NCBI webpage on Crenarchaeota
  3. ↑ C.Michael Hogan. 2010. Archaea. eds. E.Monosson & C.Cleveland, Encyclopedia of Earth. National Council for Science and the Environment, Washington DC.
  4. ↑ Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. http://ftp.ncbi.nih.gov/pub/taxonomy/. 
  5. ↑ Madigan M, ed (2005). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 978-0-13-144329-7. 
  6. ↑ "Histones in Crenarchaea". Journal of Bacteriology 187 (15): 5482–5485. 2005. doi:10.1128/JB.187.15.5482-5485.2005. PMID 16030242. 
  7. ↑ "Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 °C". Extremophiles 1 (1): 14–21. 1997. doi:10.1007/s007920050010. PMID 9680332. 
  8. ↑ Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria (2nd ed.). Springer. 2001. ISBN 978-0-387-98771-2. https://archive.org/details/bergeysmanualofs00boon. 
  9. ↑ 9.0 9.1 "Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes". Proceedings of the National Academy of Sciences of the United States of America 81 (12): 3786–3790. June 1984. doi:10.1073/pnas.81.12.3786. PMID 6587394. Bibcode: 1984PNAS...81.3786L. 
  10. ↑ "The Sulfolobus-"Caldariellard" group: Taxonomy on the basis of the structure of DNA-dependent RNA polymerases". Arch. Microbiol. 125 (3): 259–269. 1980. doi:10.1007/BF00446886. 
  11. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  12. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_06_2022.ntree. 
  13. ↑ "LTP_06_2022 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_06_2022_release_notes.pdf. 
  14. ↑ "GTDB release 08-RS214". https://gtdb.ecogenomic.org/about#4%7C. 
  15. ↑ "ar53_r214.sp_label". https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/ar53_r214.sp_labels.tree. 
  16. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  17. ↑ 17.0 17.1 Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV. UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol. 2008 Nov;70(4):938-52. doi: 10.1111/j.1365-2958.2008.06459.x. PMID: 18990182
  18. ↑ 18.0 18.1 18.2 Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, Schleper C. UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Mol Microbiol. 2011 Nov;82(4):807-17. doi: 10.1111/j.1365-2958.2011.07861.x. Epub 2011 Oct 18. PMID: 21999488
  19. ↑ Fröls S, White MF, Schleper C. Reactions to UV damage in the model archaeon Sulfolobus solfataricus. Biochem Soc Trans. 2009 Feb;37(Pt 1):36-41. doi: 10.1042/BST0370036. PMID: 19143598
  20. ↑ "Novel major archaebacterial group from marine plankton". Nature 356 (6365): 148–9. 1992. doi:10.1038/356148a0. PMID 1545865. Bibcode: 1992Natur.356..148F. 
  21. ↑ DeLong EF (1992). "Archaea in coastal marine environments". Proc Natl Acad Sci USA 89 (12): 5685–9. doi:10.1073/pnas.89.12.5685. PMID 1608980. Bibcode: 1992PNAS...89.5685D. 
  22. ↑ "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proc Natl Acad Sci USA 93 (17): 9188–93. 1996. doi:10.1073/pnas.93.17.9188. PMID 8799176. Bibcode: 1996PNAS...93.9188B. 
  23. ↑ "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature 437 (7058): 543–6. 2005. doi:10.1038/nature03911. PMID 16177789. Bibcode: 2005Natur.437..543K. 
  24. ↑ Yutin, Natalya; Makarova, Kira S.; Mekhedov, Sergey L.; Wolf, Yuri I.; Koonin, Eugene V. (2008). "The deep archaeal roots of eukaryotes". Molecular Biology and Evolution 25 (8): 1619–1630. doi:10.1093/molbev/msn108. PMID 18463089. 

Further reading

Scientific journals

Scientific handbooks

Scientific databases


External links

Wikidata ☰ Q499078 entry



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