title: Proteomic properties reveal phyloecological clusters of Archaea.
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.
authors.affiliation: Mediterranean Institute for Life Sciences, Split, Croatia.
authors.forename: Nela
authors.initials: N
authors.lastname: Nikolic
authors.forename: Zlatko
authors.initials: Z
authors.lastname: Smole
authors.forename: Anita
authors.initials: A
authors.lastname: Krisko
mesh_terms: D001105:Archaea / Q000378:metabolism / Q000502:physiology*; D019843:Archaeal Proteins / Q000378:metabolism*; D016000:Cluster Analysis; D004463:Ecology; D019766:Genes, Archaeal; D006860:Hydrogen Bonding; D005810:Multigene Family; D010802:Phylogeny; D040081:Protein Array Analysis; D011485:Protein Binding; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D013696:Temperature
chemical_list: D019843:Archaeal Proteins; D020543:Proteome; D012336:RNA, Ribosomal, 16S