Korarchaeum cryptofilum: Difference between revisions
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==Discovery== | ==Discovery== | ||
The phylum <i>Korarchaeota</i> was only recently discovered in 1996 by a team studying Archaea in hot springs located in Yellowstone National Park. By sequencing the ribosomal RNA of many uncultivated archaeans found in a hot spring, two outlying sequences were found. The two outlying sequences were used as evidence for the proposal of a new phylum "Korarchaeota".<ref name="Barns" /> The organisms of the <i>Korarchaeota</i> phylum are found mainly in extremophile environments such as hot springs(such as <i>Candidatus</i> Korarchaeum cryptofilum) while others live in hot biomes like deep ocean floors and icelandic volcanic vents.<ref name="Reigstad /> | The phylum <i>Korarchaeota</i> was only recently discovered in 1996 by a team studying Archaea in hot springs located in Yellowstone National Park. By sequencing the ribosomal RNA of many uncultivated archaeans found in a hot spring, two outlying sequences were found. The two outlying sequences were used as evidence for the proposal of a new phylum "Korarchaeota".<ref name="Barns" /> The organisms of the <i>Korarchaeota</i> phylum are found mainly in extremophile environments such as hot springs(such as <i>Candidatus</i> Korarchaeum cryptofilum) while others live in hot biomes like deep ocean floors and icelandic volcanic vents.<ref name="Reigstad /> <i>Candidatus</i> Korarchaeum cryptofilum was most likely originally discovered when the phylum was discovered in 1996 and refered to as pJP27, however this is not confirmed. The archaeon was named in a published study in 2008, where a korarcaeota genome was sequenced using whole-genome shotgun sequencing.<ref name="Elkins" /> | ||
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<br> <i>Candidatus</i> Korarchaeum cryptofilum is an ultrathin filamentous<ref name="Barns">[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC43212/ Barns, S M et al. “Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment.” Proceedings of the National Academy of Sciences of the United States of America vol. 91,5 (1994): 1609-13. doi:10.1073/pnas.91.5.1609] </ref> heterotroph, mostly living through anaerobic metabolism of peptide fermentation and protein broken down into H<sub>2</sub>. The organism uses enzymes such as peptidase, transaminases, and ATPase. <ref name="Nealson /> | <br> <i>Candidatus</i> Korarchaeum cryptofilum is an ultrathin filamentous<ref name="Barns">[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC43212/ Barns, S M et al. “Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment.” Proceedings of the National Academy of Sciences of the United States of America vol. 91,5 (1994): 1609-13. doi:10.1073/pnas.91.5.1609] </ref> heterotroph, mostly living through anaerobic metabolism of peptide fermentation and protein broken down into H<sub>2</sub>. The organism uses enzymes such as peptidase, transaminases, and ATPase. <ref name="Nealson /> | ||
The genome of <i>Ca.</i> | The genome of <i>Ca.</i> Korarcheaum cryptofilum is a circular chromosome 1,590,757 base pairs long with an average G+C content of 49%. AUG is the start codon for 72.4% of the genome for understood protein-coding genes, with UUG and GUG at 17.6% and 10% respectively. Being a reference species for Archaean evolution, much of its genome is compared with organisms of other archean phyla. The arCOG of Crenarchaeota and Euryarchaeota when compared with the sequenced genome of <i>Ca.</i> Korarcheaum cryptofilum, showed that the organism shares similar replication, recombination, repair, and cell division genes with <i>crenarchaeota</i> while it shares most of its transcription and translation genes with <i>euryarcahaeota</i>. | ||
<ref name=Miller-Coleman>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3344838/> Miller-Coleman, Robin L et al. “Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.” PloS one vol. 7,5 (2012): e35964. doi:10.1371/journal.pone.0035964]</ref> The unusual similarity to Crenarchaeota and Euryarchaeota in the archaeons genome suggest its genome has "retained features that represent an ancestral archaeal form, existing before the occurence of the evolutionary bifurcation into Crenarchaeota and Euryarchaeota"<ref name="Herrick>Baltscheffsky, H. & Persson, B. J Mol Evol (2014) 78: 140</ref>. | <ref name=Miller-Coleman>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3344838/> Miller-Coleman, Robin L et al. “Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.” PloS one vol. 7,5 (2012): e35964. doi:10.1371/journal.pone.0035964]</ref> The unusual similarity to Crenarchaeota and Euryarchaeota in the archaeons genome suggest its genome has "retained features that represent an ancestral archaeal form, existing before the occurence of the evolutionary bifurcation into Crenarchaeota and Euryarchaeota"<ref name="Herrick>Baltscheffsky, H. & Persson, B. J Mol Evol (2014) 78: 140</ref>. | ||
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==Microbiome== | ==Microbiome== | ||
The Microbiome of <i>Candidatus</i> Korarchaeum cryptofilum is extreme compared to humans. The archaeon is found in obsidian pools at the Yellowstone National Park in Wyoming, United States. The overall phylum population of the<i>Korachaeota</i> is generally minute in its microbiome (with <i> Candidatus</i> Korarchaeum cryptofilum even less of that) living in the biome. However in some cases they constitute 7% of all Archaea. The obsidian pools are very hot and high in saline concentration with only unicellular organisms living in it.<ref name="Reigstad">[http://web.b.ebscohost.com.libproxy.kenyon.edu/ehost/detail/detail?vid=0&sid=644f27fc-0fae-4646-8be1-1e8ac0adc257%40pdc-v-sessmgr05&bdata=JnNpdGU9ZWhvc3QtbGl2ZQ%3d%3d#AN=48092345&db=eih Reigstad, Laila Johanne, et al. “Diversity and Abundance of Korarchaeota in Terrestrial Hot Springs of Iceland and Kamchatka.” ISME Journal: Multidisciplinary Journal of Microbial Ecology, vol. 4, no. 3, Mar. 2010, pp. 346–356. EBSCOhost, doi:10.1038/ismej.2009.126.]</ref> | The Microbiome of <i>Candidatus</i> Korarchaeum cryptofilum is extreme compared to humans. The archaeon is found in obsidian pools at the Yellowstone National Park in Wyoming, United States. The overall phylum population of the<i>Korachaeota</i> is generally minute in its microbiome (with <i> Candidatus</i> Korarchaeum cryptofilum even less of that) living in the biome. However in some cases they constitute 7% of all Archaea. The obsidian pools are very hot and high in saline concentration with only unicellular organisms living in it.<ref name="Reigstad">[http://web.b.ebscohost.com.libproxy.kenyon.edu/ehost/detail/detail?vid=0&sid=644f27fc-0fae-4646-8be1-1e8ac0adc257%40pdc-v-sessmgr05&bdata=JnNpdGU9ZWhvc3QtbGl2ZQ%3d%3d#AN=48092345&db=eih Reigstad, Laila Johanne, et al. “Diversity and Abundance of Korarchaeota in Terrestrial Hot Springs of Iceland and Kamchatka.” ISME Journal: Multidisciplinary Journal of Microbial Ecology, vol. 4, no. 3, Mar. 2010, pp. 346–356. EBSCOhost, doi:10.1038/ismej.2009.126.]</ref> Obsidian pools | ||
[[Image:Obsidian Pool.jpg|thumb|444px|right| Obsidian pool at Yellowstone National Park, similar to the habitat of <i>Candidatus</i> Korarchaeum cryptofilum https://ucmp.berkeley.edu/archaea/archaea.html]] | [[Image:Obsidian Pool.jpg|thumb|444px|right| Obsidian pool at Yellowstone National Park, similar to the habitat of <i>Candidatus</i> Korarchaeum cryptofilum https://ucmp.berkeley.edu/archaea/archaea.html]] | ||
Revision as of 16:57, 5 December 2019
Introduction
Candidatus Korarchaeum cryptofilum is a species of the proposed phylum Korarchaeota, or Xenarchaeota of the Archaea. The phylum is notoriously difficult to study given the environment in which it lives.[1] The Archean phylum is found mainly in hydrothermal environments such as hot springs, shallow water, and deep ocean. The organism's genome has mainly been studied to open understanding of Archaean evolution due to its distant detachment on the Archaea phyla. The name of Candidatus Korarchaeum cryptofilum comes from the greek words "koros" meaning "young man", "kryptos" meaning "hidden" in greek, and "filum" which is latin for "a thread". [2]
Discovery
The phylum Korarchaeota was only recently discovered in 1996 by a team studying Archaea in hot springs located in Yellowstone National Park. By sequencing the ribosomal RNA of many uncultivated archaeans found in a hot spring, two outlying sequences were found. The two outlying sequences were used as evidence for the proposal of a new phylum "Korarchaeota".[3] The organisms of the Korarchaeota phylum are found mainly in extremophile environments such as hot springs(such as Candidatus Korarchaeum cryptofilum) while others live in hot biomes like deep ocean floors and icelandic volcanic vents.[4] Candidatus Korarchaeum cryptofilum was most likely originally discovered when the phylum was discovered in 1996 and refered to as pJP27, however this is not confirmed. The archaeon was named in a published study in 2008, where a korarcaeota genome was sequenced using whole-genome shotgun sequencing.[2]
Genetics and Structure
Candidatus Korarchaeum cryptofilum is an ultrathin filamentous[3] heterotroph, mostly living through anaerobic metabolism of peptide fermentation and protein broken down into H2. The organism uses enzymes such as peptidase, transaminases, and ATPase. [1]
The genome of Ca. Korarcheaum cryptofilum is a circular chromosome 1,590,757 base pairs long with an average G+C content of 49%. AUG is the start codon for 72.4% of the genome for understood protein-coding genes, with UUG and GUG at 17.6% and 10% respectively. Being a reference species for Archaean evolution, much of its genome is compared with organisms of other archean phyla. The arCOG of Crenarchaeota and Euryarchaeota when compared with the sequenced genome of Ca. Korarcheaum cryptofilum, showed that the organism shares similar replication, recombination, repair, and cell division genes with crenarchaeota while it shares most of its transcription and translation genes with euryarcahaeota.
[5] The unusual similarity to Crenarchaeota and Euryarchaeota in the archaeons genome suggest its genome has "retained features that represent an ancestral archaeal form, existing before the occurence of the evolutionary bifurcation into Crenarchaeota and Euryarchaeota"[6].
Chromosome replication is provoked by two orc1/cdc6 homologous and one minichromosome maintenance protein complex. There are multiple DNA-dependent DNA polymerases. For transcription, Ca. K. cryptofilum has typical archaeal DNA-dependent RNA polymerase subunits.
The Archaeon has three rRNA genes (16S, 23S, and 5S rRNA). The organism has shown to produce 33 23S r-proteins and 27 16S r-proteins on its rRNA operon. The species is also found to have 45 tRNA genes on its genome with one initiator and 45 elongator tRNAs.[5][2]
The size of Candidatus Korarchaeum cryptofilum is 0.16-0.18μm in diameter with a varying length. [2].
Microbiome
The Microbiome of Candidatus Korarchaeum cryptofilum is extreme compared to humans. The archaeon is found in obsidian pools at the Yellowstone National Park in Wyoming, United States. The overall phylum population of theKorachaeota is generally minute in its microbiome (with Candidatus Korarchaeum cryptofilum even less of that) living in the biome. However in some cases they constitute 7% of all Archaea. The obsidian pools are very hot and high in saline concentration with only unicellular organisms living in it.[4] Obsidian pools
Conclusion
Candidatus Korarchaeum cryptofilum is a relative unknown Archaeon microorganism of the minor phylum Korarchaeota. Little research has been performed on it but key insights on Archaean evolution has been discovered, causing Candidatus Korarchaeum cryptofilum to be used as a reference species. The microorganism has never bene successfully cultivated which is the reason for the Archaeon to be considered a "Candidatus" species. What is known about the species has come through 16S ribosomal RNA.[1]
References
- ↑ 1.0 1.1 1.2 Nealson, Ken. “A Korarchaeote yields to genome sequencing.” Proceedings of the National Academy of Sciences of the United States of America vol. 105,26 (2008): 8805-6. doi:10.1073/pnas.0804670105
- ↑ 2.0 2.1 2.2 2.3 Elkins, James G et al. “A korarchaeal genome reveals insights into the evolution of the Archaea.” Proceedings of the National Academy of Sciences of the United States of America vol. 105,23 (2008): 8102-7. doi:10.1073/pnas.0801980105
- ↑ 3.0 3.1 Barns, S M et al. “Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment.” Proceedings of the National Academy of Sciences of the United States of America vol. 91,5 (1994): 1609-13. doi:10.1073/pnas.91.5.1609
- ↑ 4.0 4.1 Reigstad, Laila Johanne, et al. “Diversity and Abundance of Korarchaeota in Terrestrial Hot Springs of Iceland and Kamchatka.” ISME Journal: Multidisciplinary Journal of Microbial Ecology, vol. 4, no. 3, Mar. 2010, pp. 346–356. EBSCOhost, doi:10.1038/ismej.2009.126.
- ↑ 5.0 5.1 > Miller-Coleman, Robin L et al. “Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.” PloS one vol. 7,5 (2012): e35964. doi:10.1371/journal.pone.0035964
- ↑ Baltscheffsky, H. & Persson, B. J Mol Evol (2014) 78: 140
Edited by [Charlie Stutz], student of Joan Slonczewski for BIOL 116 Information in Living Systems, 2019,
