Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System
In this study, the metabolic and physiological potential evaluator system based on Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules was employed to establish a functional classification of archaeal species and to determine the comprehensive functions (functionome) of the previously...
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| creator | Takami, Hideto Arai, Wataru Takemoto, Kazuhiro Uchiyama, Ikuo Taniguchi, Takeaki |
| description | In this study, the metabolic and physiological potential evaluator system based on Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules was employed to establish a functional classification of archaeal species and to determine the comprehensive functions (functionome) of the previously uncultivated thermophile "Candidatus Caldiarchaeum subterraneum" (Ca. C. subterraneum). A phylogenetic analysis based on the concatenated sequences of proteins common among 142 archaea and 2 bacteria, and among 137 archaea and 13 unicellular eukaryotes suggested that Ca. C. subterraneum is closely related to thaumarchaeotic species. Consistent with the results of the phylogenetic analysis, clustering and principal component analyses based on the completion ratio patterns for all KEGG modules in 79 archaeal species suggested that the overall metabolic and physiological potential of Ca. C. subterraneum is similar to that of thaumarchaeotic species. However, Ca. C. subterraneum possessed almost no genes in the modules required for nitrification and the hydroxypropionate-hydroxybutyrate cycle for carbon fixation, unlike thaumarchaeotic species. However, it possessed all genes in the modules required for central carbohydrate metabolism, such as glycolysis, pyruvate oxidation, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, as well as multiple sets of sugar and branched chain amino acid ABC transporters. These metabolic and physiological features appear to support the predominantly aerobic character of Ca. C. subterraneum, which lives in a subsurface thermophilic microbial mat community with a heterotrophic lifestyle. |
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C. subterraneum). A phylogenetic analysis based on the concatenated sequences of proteins common among 142 archaea and 2 bacteria, and among 137 archaea and 13 unicellular eukaryotes suggested that Ca. C. subterraneum is closely related to thaumarchaeotic species. Consistent with the results of the phylogenetic analysis, clustering and principal component analyses based on the completion ratio patterns for all KEGG modules in 79 archaeal species suggested that the overall metabolic and physiological potential of Ca. C. subterraneum is similar to that of thaumarchaeotic species. However, Ca. C. subterraneum possessed almost no genes in the modules required for nitrification and the hydroxypropionate-hydroxybutyrate cycle for carbon fixation, unlike thaumarchaeotic species. However, it possessed all genes in the modules required for central carbohydrate metabolism, such as glycolysis, pyruvate oxidation, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, as well as multiple sets of sugar and branched chain amino acid ABC transporters. These metabolic and physiological features appear to support the predominantly aerobic character of Ca. C. subterraneum, which lives in a subsurface thermophilic microbial mat community with a heterotrophic lifestyle.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0132994</identifier><identifier>PMID: 26196861</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acids ; Amino acids ; Ammonia - chemistry ; Analysis ; Archaea ; Archaea - classification ; Archaea - genetics ; Archaea - physiology ; Bacteria ; Bacteria - genetics ; Bacteria - metabolism ; Branched chain amino acids ; Candidate species ; Candidatus Caldiarchaeum subterraneum ; Carbohydrate metabolism ; Carbohydrates ; Carbohydrates - chemistry ; Carbon Cycle ; Carbon fixation ; Chain branching ; Cladistic analysis ; Classification ; Classification systems ; Cluster Analysis ; Clustering ; Computational Biology - methods ; Databases, Genetic ; Earth science ; Encyclopedias ; Enzymes ; Eukaryotes ; Genes ; Genomes ; Genomics ; Glucose metabolism ; Glycolysis ; Glyoxylate cycle ; Metabolism ; Methods ; Microorganisms ; Modules ; Nitrification ; Nitrogen ; Oxidation ; Phenotype ; Phylogenetics ; Phylogeny ; Physiological aspects ; Physiology ; Principal Component Analysis ; Principal components analysis ; Proteins ; Pyruvic acid ; Species ; Species classification ; Species Specificity ; Sugar ; Thermophilic bacteria ; Thermophilic microorganisms ; Tricarboxylic acid cycle</subject><ispartof>PloS one, 2015-07, Vol.10 (7), p.e0132994-e0132994</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Takami et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Takami et al 2015 Takami et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-405bd76a8fdeb5ffd61bc4ca5bca4034353709b389db389b9ea6b079cbcc0bef3</citedby><cites>FETCH-LOGICAL-c758t-405bd76a8fdeb5ffd61bc4ca5bca4034353709b389db389b9ea6b079cbcc0bef3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510362/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510362/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2101,2927,23865,27923,27924,53790,53792,79471,79472</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26196861$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Berg, Ivan</contributor><creatorcontrib>Takami, Hideto</creatorcontrib><creatorcontrib>Arai, Wataru</creatorcontrib><creatorcontrib>Takemoto, Kazuhiro</creatorcontrib><creatorcontrib>Uchiyama, Ikuo</creatorcontrib><creatorcontrib>Taniguchi, Takeaki</creatorcontrib><title>Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>In this study, the metabolic and physiological potential evaluator system based on Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules was employed to establish a functional classification of archaeal species and to determine the comprehensive functions (functionome) of the previously uncultivated thermophile "Candidatus Caldiarchaeum subterraneum" (Ca. C. subterraneum). A phylogenetic analysis based on the concatenated sequences of proteins common among 142 archaea and 2 bacteria, and among 137 archaea and 13 unicellular eukaryotes suggested that Ca. C. subterraneum is closely related to thaumarchaeotic species. Consistent with the results of the phylogenetic analysis, clustering and principal component analyses based on the completion ratio patterns for all KEGG modules in 79 archaeal species suggested that the overall metabolic and physiological potential of Ca. C. subterraneum is similar to that of thaumarchaeotic species. However, Ca. C. subterraneum possessed almost no genes in the modules required for nitrification and the hydroxypropionate-hydroxybutyrate cycle for carbon fixation, unlike thaumarchaeotic species. However, it possessed all genes in the modules required for central carbohydrate metabolism, such as glycolysis, pyruvate oxidation, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, as well as multiple sets of sugar and branched chain amino acid ABC transporters. These metabolic and physiological features appear to support the predominantly aerobic character of Ca. C. subterraneum, which lives in a subsurface thermophilic microbial mat community with a heterotrophic lifestyle.</description><subject>Acids</subject><subject>Amino acids</subject><subject>Ammonia - chemistry</subject><subject>Analysis</subject><subject>Archaea</subject><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Archaea - physiology</subject><subject>Bacteria</subject><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Branched chain amino acids</subject><subject>Candidate species</subject><subject>Candidatus Caldiarchaeum subterraneum</subject><subject>Carbohydrate metabolism</subject><subject>Carbohydrates</subject><subject>Carbohydrates - chemistry</subject><subject>Carbon Cycle</subject><subject>Carbon fixation</subject><subject>Chain branching</subject><subject>Cladistic analysis</subject><subject>Classification</subject><subject>Classification systems</subject><subject>Cluster Analysis</subject><subject>Clustering</subject><subject>Computational Biology - methods</subject><subject>Databases, Genetic</subject><subject>Earth science</subject><subject>Encyclopedias</subject><subject>Enzymes</subject><subject>Eukaryotes</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Glucose metabolism</subject><subject>Glycolysis</subject><subject>Glyoxylate cycle</subject><subject>Metabolism</subject><subject>Methods</subject><subject>Microorganisms</subject><subject>Modules</subject><subject>Nitrification</subject><subject>Nitrogen</subject><subject>Oxidation</subject><subject>Phenotype</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Physiology</subject><subject>Principal Component Analysis</subject><subject>Principal components analysis</subject><subject>Proteins</subject><subject>Pyruvic acid</subject><subject>Species</subject><subject>Species classification</subject><subject>Species Specificity</subject><subject>Sugar</subject><subject>Thermophilic bacteria</subject><subject>Thermophilic microorganisms</subject><subject>Tricarboxylic acid 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Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System</title><author>Takami, Hideto ; Arai, Wataru ; Takemoto, Kazuhiro ; Uchiyama, Ikuo ; Taniguchi, Takeaki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-405bd76a8fdeb5ffd61bc4ca5bca4034353709b389db389b9ea6b079cbcc0bef3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Acids</topic><topic>Amino acids</topic><topic>Ammonia - chemistry</topic><topic>Analysis</topic><topic>Archaea</topic><topic>Archaea - classification</topic><topic>Archaea - genetics</topic><topic>Archaea - physiology</topic><topic>Bacteria</topic><topic>Bacteria - genetics</topic><topic>Bacteria - metabolism</topic><topic>Branched chain amino acids</topic><topic>Candidate species</topic><topic>Candidatus Caldiarchaeum subterraneum</topic><topic>Carbohydrate 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One</addtitle><date>2015-07-21</date><risdate>2015</risdate><volume>10</volume><issue>7</issue><spage>e0132994</spage><epage>e0132994</epage><pages>e0132994-e0132994</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>In this study, the metabolic and physiological potential evaluator system based on Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules was employed to establish a functional classification of archaeal species and to determine the comprehensive functions (functionome) of the previously uncultivated thermophile "Candidatus Caldiarchaeum subterraneum" (Ca. C. subterraneum). A phylogenetic analysis based on the concatenated sequences of proteins common among 142 archaea and 2 bacteria, and among 137 archaea and 13 unicellular eukaryotes suggested that Ca. C. subterraneum is closely related to thaumarchaeotic species. Consistent with the results of the phylogenetic analysis, clustering and principal component analyses based on the completion ratio patterns for all KEGG modules in 79 archaeal species suggested that the overall metabolic and physiological potential of Ca. C. subterraneum is similar to that of thaumarchaeotic species. However, Ca. C. subterraneum possessed almost no genes in the modules required for nitrification and the hydroxypropionate-hydroxybutyrate cycle for carbon fixation, unlike thaumarchaeotic species. However, it possessed all genes in the modules required for central carbohydrate metabolism, such as glycolysis, pyruvate oxidation, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, as well as multiple sets of sugar and branched chain amino acid ABC transporters. These metabolic and physiological features appear to support the predominantly aerobic character of Ca. C. subterraneum, which lives in a subsurface thermophilic microbial mat community with a heterotrophic lifestyle.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26196861</pmid><doi>10.1371/journal.pone.0132994</doi><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2015-07, Vol.10 (7), p.e0132994-e0132994 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1697759272 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acids Amino acids Ammonia - chemistry Analysis Archaea Archaea - classification Archaea - genetics Archaea - physiology Bacteria Bacteria - genetics Bacteria - metabolism Branched chain amino acids Candidate species Candidatus Caldiarchaeum subterraneum Carbohydrate metabolism Carbohydrates Carbohydrates - chemistry Carbon Cycle Carbon fixation Chain branching Cladistic analysis Classification Classification systems Cluster Analysis Clustering Computational Biology - methods Databases, Genetic Earth science Encyclopedias Enzymes Eukaryotes Genes Genomes Genomics Glucose metabolism Glycolysis Glyoxylate cycle Metabolism Methods Microorganisms Modules Nitrification Nitrogen Oxidation Phenotype Phylogenetics Phylogeny Physiological aspects Physiology Principal Component Analysis Principal components analysis Proteins Pyruvic acid Species Species classification Species Specificity Sugar Thermophilic bacteria Thermophilic microorganisms Tricarboxylic acid cycle |
| title | Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-08T09%3A03%3A07IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Functional%20Classification%20of%20Uncultured%20%22Candidatus%20Caldiarchaeum%20subterraneum%22%20Using%20the%20Maple%20System&rft.jtitle=PloS%20one&rft.au=Takami,%20Hideto&rft.date=2015-07-21&rft.volume=10&rft.issue=7&rft.spage=e0132994&rft.epage=e0132994&rft.pages=e0132994-e0132994&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0132994&rft_dat=%3Cgale_plos_%3EA422565370%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1697759272&rft_id=info:pmid/26196861&rft_galeid=A422565370&rft_doaj_id=oai_doaj_org_article_83264928ad84473f97b72b14b6c337ed&rfr_iscdi=true |