title: Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
abstract: BACKGROUND
  Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate as parts of complexes to regulate biological processes, we systematically analyzed protein-protein interactions in Pyrococcus using the mammalian two-hybrid system to determine the function of the hypothetical proteins.
  
  
  RESULTS
  We examined 960 soluble proteins from Pyrococcus and selected 107 interactions based on luciferase reporter activity, which was then evaluated using a computational approach to assess the reliability of the interactions. We also analyzed the expression of the assay samples by western blot, and a few interactions by in vitro pull-down assays. We identified 11 hetero-interactions that we considered to be located at the same operon, as observed in Helicobacter pylori. We annotated and classified proteins in the selected interactions according to their orthologous proteins. Many enzyme proteins showed self-interactions, similar to those seen in other organisms.
  
  
  CONCLUSIONS
  We found 13 unannotated proteins that interacted with annotated proteins; this information is useful for predicting the functions of the hypothetical Pyrococcus proteins from the annotations of their interacting partners. Among the heterogeneous interactions, proteins were more likely to interact with proteins within the same ortholog class than with proteins of different classes. The analysis described here can provide global insights into the biological features of the protein-protein interactions in P. horikoshii.
authors.affiliation: CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. kusui@gsc.riken.jp
authors.forename: Kengo
authors.initials: K
authors.lastname: Usui
authors.forename: Shintaro
authors.initials: S
authors.lastname: Katayama
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Kanamori-Katayama
authors.forename: Chihiro
authors.initials: C
authors.lastname: Ogawa
authors.forename: Chikatoshi
authors.initials: C
authors.lastname: Kai
authors.forename: Makiko
authors.initials: M
authors.lastname: Okada
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Takahiro
authors.initials: T
authors.lastname: Arakawa
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Itoh
authors.forename: Koji
authors.initials: K
authors.lastname: Takio
authors.forename: Masashi
authors.initials: M
authors.lastname: Miyano
authors.forename: Satoru
authors.initials: S
authors.lastname: Kidoaki
authors.forename: Takehisa
authors.initials: T
authors.lastname: Matsuda
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Harukazu
authors.initials: H
authors.lastname: Suzuki
mesh_terms: D019766:Genes, Archaeal / Q000235:genetics; D020745:Genome, Archaeal / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D011485:Protein Binding; D025941:Protein Interaction Mapping; D043902:Pyrococcus horikoshii / Q000145:classification / Q000235:genetics / Q000378:metabolism*