title: The origin of polynucleotide phosphorylase domains.
abstract: In this report, we document the presence of polynucleotide phosphorylase (PNPase) in the animal eukaryotes. These proteins contain several domains, including 2 RNase PH domains (PNPase 1 and PNPase 2) which are closely related functionally and in sequence similarity to ribonuclease PH (RPH) protein. Phylogenetic analysis of the gene genealogy of these three domains suggests that PNPase was formed via a duplication event that also produced the RNase PH protein. Given the current distribution of these domains in the tree of life, these duplication events most likely occurred in the common ancestor of the three organismal superkingdoms, Archaea, Eukarya, and Bacteria. In particular, PNPase 2 and RPH are more closely related to each other than either one is to PNPase 1, suggesting a deeper differentiation of PNPase 1 in the common organismal ancestor. In addition, while PNPase 1 and PNPase 2 appear to have the same evolutionary signal as determined by the incongruence length difference (ILD) test, RPH appears to have an incongruent signal with both of the PNPase domains. This result suggests that RPH experienced different evolutionary divergence patterns than the PNPase domains, consistent with the linked nature of the two PNPase domains.
authors.affiliation: Division of Invertebrates, American Museum of Natural History, New York, NY 10024, USA.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Leszczyniecka
authors.forename: Rob
authors.initials: R
authors.lastname: DeSalle
authors.forename: Dong-Chul
authors.initials: DC
authors.lastname: Kang
authors.forename: Paul B
authors.initials: PB
authors.lastname: Fisher
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001105:Archaea / Q000235:genetics; D005057:Eukaryotic Cells / Q000502:physiology; D019143:Evolution, Molecular; D005095:Exoribonucleases / Q000737:chemistry / Q000502:physiology; D006801:Humans; D051379:Mice; D010802:Phylogeny; D011117:Polyribonucleotide Nucleotidyltransferase / Q000737:chemistry / Q000502:physiology*; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid
chemical_list: D020121:5' Untranslated Regions; C056502:ribonuclease PH; D011117:Polyribonucleotide Nucleotidyltransferase; D005095:Exoribonucleases