title: Prokaryotic phylogenies inferred from protein structural domains.
abstract: The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic relationships are indeed the methods that are most consistent with theoretical evolutionary models. This work represents, to our knowledge, the first such theoretically motivated phylogeny, as well as the first application of structural information to phylogeny on this scale. Our results have strong implications for the phylogenetic relationships among prokaryotic organisms and for the understanding of protein evolution as a whole.
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Deeds
authors.forename: Hooman
authors.initials: H
authors.lastname: Hennessey
authors.forename: Eugene I
authors.initials: EI
authors.lastname: Shakhnovich
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics; D022761:Gene Transfer, Horizontal; D023281:Genomics; D008957:Models, Genetic; D010802:Phylogeny; D011387:Prokaryotic Cells; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D020543:Proteome
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D005656:Fungal Proteins; D011506:Proteins; D020543:Proteome
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