Proteomic properties reveal phyloecological clusters of Archaea
Proteomic properties reveal phyloecological clusters of Archaea
In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.
Archaea/metabolism, Archaeal Proteins/metabolism, Cluster Analysis, Ecology, Genes, Archaeal, Hydrogen Bonding, Multigene Family, Phylogeny, Protein Array Analysis, Protein Binding, Proteome, Proteomics/methods, RNA, Ribosomal, 16S/metabolism, Temperature
e48231
Nikolic, Nela
88a8f576-d9e2-4eb6-9219-39b7065963d3
Smole, Zlatko
d217141b-e908-4806-a2ea-4495c89b9b37
Krisko, Anita
0b80c4e2-8b04-4055-87a4-2f3f42ab79df
2012
Nikolic, Nela
88a8f576-d9e2-4eb6-9219-39b7065963d3
Smole, Zlatko
d217141b-e908-4806-a2ea-4495c89b9b37
Krisko, Anita
0b80c4e2-8b04-4055-87a4-2f3f42ab79df
Nikolic, Nela, Smole, Zlatko and Krisko, Anita
(2012)
Proteomic properties reveal phyloecological clusters of Archaea.
PLoS ONE, 7 (10), .
(doi:10.1371/journal.pone.0048231).
Abstract
In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.
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Published date: 2012
Keywords:
Archaea/metabolism, Archaeal Proteins/metabolism, Cluster Analysis, Ecology, Genes, Archaeal, Hydrogen Bonding, Multigene Family, Phylogeny, Protein Array Analysis, Protein Binding, Proteome, Proteomics/methods, RNA, Ribosomal, 16S/metabolism, Temperature
Identifiers
Local EPrints ID: 488029
URI: http://eprints.soton.ac.uk/id/eprint/488029
ISSN: 1932-6203
PURE UUID: 14d688fb-c3f2-4cbe-b7f9-6e2d3fa2a8e7
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Date deposited: 12 Mar 2024 18:21
Last modified: 18 Mar 2024 04:18
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Author:
Nela Nikolic
Author:
Zlatko Smole
Author:
Anita Krisko
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