Proteomic Properties Reveal Phyloecological Clusters of <em>Archaea</em>

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.本研究提出了一种全新的方法，用以描述古菌（Archaea）的各类环境适应性特征。我们通过一套非冗余蛋白质组特征集，对57株古菌进行了聚类分析，并验证所得聚类结果与古菌栖息环境的适应性特征高度匹配。第一类聚类主要包含超嗜热菌与超嗜热嗜酸好氧菌。第二类聚类汇集了嗜盐菌与极端嗜盐古菌，而第三类聚类则包含嗜温古菌（多数为产甲烷古菌）与嗜热嗜酸菌。经分析，这套非冗余蛋白质组特征子集共包含5项特征：带电残基与不带电残基的比例、蛋白质平均长度、β折叠（beta-sheet）归一化频率、延伸结构归一化频率，以及氢键供体数量。本研究建议将该聚类方法命名为系统生态聚类（phyloecological clustering）。该方法可为揭示仅通过系统发育分析所难以发现的古菌物种间关联提供全新视角。