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Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Kengo Usui123, Shintaro Katayama23, Mutsumi Kanamori-Katayama23, Chihiro Ogawa23, Chikatoshi Kai23, Makiko Okada23, Jun Kawai23, Takahiro Arakawa23, Piero Carninci23, Masayoshi Itoh23, Koji Takio4, Masashi Miyano5, Satoru Kidoaki6, Takehisa Matsuda6, Yoshihide Hayashizaki23 and Harukazu Suzuki23*

Author Affiliations

1 CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

2 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

3 Genome Science Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan

4 Highthroughput Factory, RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan

5 Structural Biophysics Laboratory, RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan

6 Division of Biomedical Engineering, Graduate School of Medicine, Kyushu University, Fukuoka 815-8582, Japan

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Genome Biology 2005, 6:R98  doi:10.1186/gb-2005-6-12-r98

Published: 18 November 2005



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.


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.


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.