Thermoproteota
| Thermoproteota | |
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| Archaea Sulfolobus infected with specific virus STSV-1. | |
Scientific classification 
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| Domain: | Archaea |
| Clade: | Proteoarchaeota |
| Kingdom: | Thermoproteati |
| Phylum: | Thermoproteota Garrity & Holt 2021[1] |
| Classes | |
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| Synonyms | |
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The Thermoproteota are prokaryotes that have been classified as a phylum of the domain Archaea.[3][4][5] 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.[6] 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.[7] Until 2005 all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C.[8] These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells.[9] Recent evidence shows that some members of the Thermoproteota are methanogens.
Thermoproteota were initially classified as a part of regnum Eocyta in 1984,[10] but this classification has been discarded. The term "eocyte" now applies to either TACK (formerly Crenarchaeota) or to Thermoproteota.
Sulfolobus
[edit]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.[11] 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.
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Verstraetearchaeota
[edit]Verstraetearchaeota is a candidate phylum in Thermoproteota.[2] Other valid names for this phylum are Nitrososphaerota and Thermoproteota. This candidate phylum has not been cultured.[18] This domain is capable of Methanogenesis.[19]
Recombinational repair of DNA damage
[edit]Irradiation of S. solfataricus cells with ultraviolet light strongly induces formation of type IV pili that can then promote cellular aggregation.[20] Ultraviolet light-induced cellular aggregation was shown by Ajon et al.[21] 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.[21] Frols et al.[20][22] and Ajon et al.[21] 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
[edit]Beginning in 1992, data were published that reported sequences of genes belonging to the Thermoproteota in marine environments.[23],[24] 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.[25]
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.[26]
Possible connections with eukaryotes
[edit]The research about two-domain system of classification has paved the possibilities of connections between crenarchaea and eukaryotes.[27]
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.[10] 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
[edit]References
[edit]- ^ Oren A, Garrity GM (Oct 2021). "Valid publication of the names of forty-two phyla of prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
- ^ a b Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, et al. (2016-10-03). "Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota". Nature Microbiology. 1 (12): 16170. doi:10.1038/nmicrobiol.2016.170. ISSN 2058-5276. PMID 27694807.
- ^ See the NCBI webpage on Crenarchaeota
- ^ C.Michael Hogan. 2010. Archaea. eds. E.Monosson & C.Cleveland, Encyclopedia of Earth. National Council for Science and the Environment, Washington DC.
- ^ Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
- ^ M M, ed. (2005). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 978-0-13-144329-7.
- ^ Cubonova L, Sandman K, Hallam SJ, Delong EF, Reeve JN (Aug 2005). "Histones in Crenarchaea". Journal of Bacteriology. 187 (15): 5482–5485. doi:10.1128/JB.187.15.5482-5485.2005. PMC 1196040. PMID 16030242.
- ^ Blochl E, Rachel R, Burggraf S, Hafenbradl D, Jannasch HW, Stetter KO (Feb 1997). "Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 °C". Extremophiles : Life Under Extreme Conditions. 1 (1): 14–21. doi:10.1007/s007920050010. PMID 9680332. S2CID 29789667.
- ^ Garrity GM, Boone DR, eds. (2001). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria (2nd ed.). Springer. ISBN 978-0-387-98771-2.
- ^ a b Lake JA, Henderson E, Oakes M, Clark MW (June 1984). "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. Bibcode:1984PNAS...81.3786L. doi:10.1073/pnas.81.12.3786. PMC 345305. PMID 6587394.
- ^ Zillig W, Stetter KO, Wunderl S, Schulz W, Priess H, Scholz I (1980). "The Sulfolobus-"Caldariellard" group: Taxonomy on the basis of the structure of DNA-dependent RNA polymerases". Arch. Microbiol. 125 (3): 259–269. Bibcode:1980ArMic.125..259Z. doi:10.1007/BF00446886. S2CID 5805400.
- ^ "The LTP". Retrieved 10 May 2023.
- ^ "LTP_all tree in newick format". Retrieved 10 May 2023.
- ^ "LTP_06_2022 Release Notes" (PDF). Retrieved 10 May 2023.
- ^ "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.
- ^ "ar53_r220.sp_label". Genome Taxonomy Database. Retrieved 10 May 2024.
- ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.
- ^ "Phylum: Verstraetearchaeota". lpsn.dsmz.de. Retrieved 2024-12-05.
- ^ Wu K, Zhou L, Tahon G, Liu L, Li J, Zhang J, et al. (August 2024). "Isolation of a methyl-reducing methanogen outside the Euryarchaeota". Nature. 632 (8027): 1124–1130. Bibcode:2024Natur.632.1124W. doi:10.1038/s41586-024-07728-y. ISSN 1476-4687. PMID 39048829.
- ^ a b Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, et al. (November 2008). "UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation". Molecular Microbiology. 70 (4): 938–952. doi:10.1111/j.1365-2958.2008.06459.x. PMID 18990182.
- ^ a b c Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, et al. (November 2011). "UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili". Molecular Microbiology. 82 (4): 807–817. doi:10.1111/j.1365-2958.2011.07861.x. PMID 21999488.
- ^ Fröls S, White MF, Schleper C (February 2009). "Reactions to UV damage in the model archaeon Sulfolobus solfataricus". Biochemical Society Transactions. 37 (Pt 1): 36–41. doi:10.1042/BST0370036. PMID 19143598.
- ^ Fuhrman JA, McCallum K, Davis AA (Mar 1992). "Novel major archaebacterial group from marine plankton". Nature. 356 (6365): 148–149. Bibcode:1992Natur.356..148F. doi:10.1038/356148a0. PMID 1545865. S2CID 4342208.
- ^ DeLong EF (Jun 1992). "Archaea in coastal marine environments". Proceedings of the National Academy of Sciences of the United States of America. 89 (12): 5685–5689. Bibcode:1992PNAS...89.5685D. doi:10.1073/pnas.89.12.5685. PMC 49357. PMID 1608980.
- ^ Barns SM, Delwiche CF, Palmer JD, Pace NR (Aug 1996). "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proceedings of the National Academy of Sciences of the United States of America. 93 (17): 9188–9193. Bibcode:1996PNAS...93.9188B. doi:10.1073/pnas.93.17.9188. PMC 38617. PMID 8799176.
- ^ Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (Sep 2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature. 437 (7058): 543–546. Bibcode:2005Natur.437..543K. doi:10.1038/nature03911. PMID 16177789. S2CID 4340386.
- ^ Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV (2008). "The deep archaeal roots of eukaryotes". Molecular Biology and Evolution. 25 (8): 1619–1630. doi:10.1093/molbev/msn108. PMC 2464739. PMID 18463089.
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- Whitman WB, Keswani J (Mar 2001). "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 51 (Pt 2): 667–678. doi:10.1099/00207713-51-2-667. PMID 11321113.
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- Kawamura Y, Li N, Zhao L, Li TM, Li ZY, Shu S, et al. (Jul 2000). "A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube". International Journal of Systematic and Evolutionary Microbiology. 50 (4): 1463–1469. doi:10.1099/00207713-50-4-1463. PMID 10939651.
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- Martin W, Hansmann S (Jul 2000). "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis". International Journal of Systematic and Evolutionary Microbiology. 50 (4): 1655–1663. doi:10.1099/00207713-50-4-1655. PMID 10939673.
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Scientific handbooks
[edit]- Garrity GM, Holt JG (2001). "Phylum AI. Crenarchaeota phy. nov.". In DR Boone, RW Castenholz (eds.). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria (2nd ed.). New York: Springer Verlag. pp. 169. ISBN 978-0-387-98771-2.
External links
[edit]
- "Crenarchaeota". Virtual Microbiology (bact.wisc.edu). University of Wisconsin.
- "Comparative analysis of crenarchaeal genomes". Integrated Microbial Genomes System. United States Department of Energy. Archived from the original on 2010-09-01.