© 1998 by Kazusa DNA Research Institute
Complete Sequence and Gene Organization of the Genome of a Hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3
1National Institute of Technology and Evaluation 2-49-10 Nishihara, Shibuya, Tokyo 151-0066, Japan
2National Institute of Bioscience and Human-Technology 1-1 Higashi, Tsukuba, Ibaraki 305-0046, Japan
3Center of Marine Biotechnology, Columbus Center, University of Maryland, Biotechnology Institute Baltimore, MD, USA
4Japan Marine Science and Technology Center 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
5University of Tokyo Meguro, Tokyo 153-0041, Japan
6California Institute of Technology Pasadena, CA, USA
* To whom correspondence should be addressed. Tel. +81-3-3481-8951, Fax. +81-3-3481-8424, E-mail: kyutaka{at}kazusa.or.jp
The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http://www.nite.go.jp.
Key words: hyper-thermophilic archaebacterium; Pyrococcus horikoshii OT3; genome sequencing; fosmid; open reading frames; shotgun sequencing
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A. F. Chalker, H. W. Minehart, N. J. Hughes, K. K. Koretke, M. A. Lonetto, K. K. Brinkman, P. V. Warren, A. Lupas, M. J. Stanhope, J. R. Brown, et al. Systematic Identification of Selective Essential Genes in Helicobacter pylori by Genome Prioritization and Allelic Replacement Mutagenesis J. Bacteriol., February 15, 2001; 183(4): 1259 - 1268. [Abstract] [Full Text]
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K. Ishikawa, H. Ishida, I. Matsui, Y. Kawarabayasi, and H. Kikuchi Novel Bifunctional Hyperthermostable Carboxypeptidase/Aminoacylase from Pyrococcus horikoshii OT3 Appl. Envir. Microbiol., February 1, 2001; 67(2): 673 - 679. [Abstract] [Full Text]
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M. Daugherty, V. Vonstein, R. Overbeek, and A. Osterman Archaeal Shikimate Kinase, a New Member of the GHMP-Kinase Family J. Bacteriol., January 1, 2001; 183(1): 292 - 300. [Abstract] [Full Text]
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T. Kawashima, N. Amano, H. Koike, S.-i. Makino, S. Higuchi, Y. Kawashima-Ohya, K. Watanabe, M. Yamazaki, K. Kanehori, T. Kawamoto, et al. Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium PNAS, December 19, 2000; 97(26): 14257 - 14262. [Abstract] [Full Text] [PDF]
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K. Bohlke, F. M. Pisani, C. E. Vorgias, B. Frey, H. Sobek, M. Rossi, and G. Antranikian PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif Nucleic Acids Res., October 15, 2000; 28(20): 3910 - 3917. [Abstract] [Full Text] [PDF]
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W. Fujibuchi, H. Ogata, H. Matsuda, and M. Kanehisa Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping Nucleic Acids Res., October 15, 2000; 28(20): 4029 - 4036. [Abstract] [Full Text] [PDF]
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S. Karlin and J. Mrázek Predicted Highly Expressed Genes of Diverse Prokaryotic Genomes J. Bacteriol., September 15, 2000; 182(18): 5238 - 5250. [Abstract] [Full Text]
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A. T. Bull, A. C. Ward, and M. Goodfellow Search and Discovery Strategies for Biotechnology: the Paradigm Shift Microbiol. Mol. Biol. Rev., September 1, 2000; 64(3): 573 - 606. [Abstract] [Full Text] [PDF]
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M. Takagi, T. Kuzuyama, S. Takahashi, and H. Seto A Gene Cluster for the Mevalonate Pathway from Streptomyces sp. Strain CL190 J. Bacteriol., August 1, 2000; 182(15): 4153 - 4157. [Abstract] [Full Text]
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M. G. Thomas and J. C. Escalante-Semerena Identification of an Alternative Nucleoside Triphosphate: 5'-Deoxyadenosylcobinamide Phosphate Nucleotidyltransferase in Methanobacterium thermoautotrophicum Delta H J. Bacteriol., August 1, 2000; 182(15): 4227 - 4233. [Abstract] [Full Text]
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C. R. Woese Interpreting the universal phylogenetic tree PNAS, July 18, 2000; 97(15): 8392 - 8396. [Abstract] [Full Text] [PDF]
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J. Enoru-Eta, D. Gigot, T.-L. Thia-Toong, N. Glansdorff, and D. Charlier Purification and Characterization of Sa-Lrp, a DNA-Binding Protein from the Extreme Thermoacidophilic Archaeon Sulfolobus acidocaldarius Homologous to the Bacterial Global Transcriptional Regulator Lrp J. Bacteriol., July 1, 2000; 182(13): 3661 - 3672. [Abstract] [Full Text]
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J.-P. Alimi, O. Poirot, F. Lopez, and J.-M. Claverie Reverse Transcriptase-Polymerase Chain Reaction Validation of 25 "Orphan" Genes from Escherichia coli K-12 MG1655 Genome Res., July 1, 2000; 10(7): 959 - 966. [Abstract] [Full Text]
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B. H. Lower, K. M. Bischoff, and P. J. Kennelly The Archaeon Sulfolobus solfataricus Contains a Membrane-Associated Protein Kinase Activity That Preferentially Phosphorylates Threonine Residues In Vitro J. Bacteriol., June 15, 2000; 182(12): 3452 - 3459. [Abstract] [Full Text]
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Y.-i. Watanabe and M. W. Gray Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: Cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria Nucleic Acids Res., June 15, 2000; 28(12): 2342 - 2352. [Abstract] [Full Text] [PDF]
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D. Kihara and M. Kanehisa Tandem Clusters of Membrane Proteins in Complete Genome Sequences Genome Res., June 1, 2000; 10(6): 731 - 743. [Abstract] [Full Text]
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Y. Inagaki and W. Ford Doolittle Evolution of the Eukaryotic Translation Termination System: Origins of Release Factors Mol. Biol. Evol., June 1, 2000; 17(6): 882 - 889. [Abstract] [Full Text] [PDF]
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J. D. A. van Embden, T. van Gorkom, K. Kremer, R. Jansen, B. A. M. van der Zeijst, and L. M. Schouls Genetic Variation and Evolutionary Origin of the Direct Repeat Locus of Mycobacterium tuberculosis Complex Bacteria J. Bacteriol., May 1, 2000; 182(9): 2393 - 2401. [Abstract] [Full Text]
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D. E. Ward, S. W. M. Kengen, J. van der Oost, and W. M. de Vos Purification and Characterization of the Alanine Aminotransferase from the Hyperthermophilic Archaeon Pyrococcus furiosus and Its Role in Alanine Production J. Bacteriol., May 1, 2000; 182(9): 2559 - 2566. [Abstract] [Full Text]
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E. Martusewitsch, C. W. Sensen, and C. Schleper High Spontaneous Mutation Rate in the Hyperthermophilic Archaeon Sulfolobus solfataricus Is Mediated by Transposable Elements J. Bacteriol., May 1, 2000; 182(9): 2574 - 2581. [Abstract] [Full Text]
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W. Hausner, U. Lange, and M. Musfeldt Transcription Factor S, a Cleavage Induction Factor of the Archaeal RNA Polymerase J. Biol. Chem., April 21, 2000; 275(17): 12393 - 12399. [Abstract] [Full Text] [PDF]
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A. Schramm, B. Siebers, B. Tjaden, H. Brinkmann, and R. Hensel Pyruvate Kinase of the Hyperthermophilic Crenarchaeote Thermoproteus tenax: Physiological Role and Phylogenetic Aspects J. Bacteriol., April 1, 2000; 182(7): 2001 - 2009. [Abstract] [Full Text]
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S. H. Bhuiyan, K. Gowda, H. Hotokezaka, and C. Zwieb Assembly of archaeal signal recognition particle from recombinant components Nucleic Acids Res., March 15, 2000; 28(6): 1365 - 1373. [Abstract] [Full Text] [PDF]
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Z. Kelman and J. Hurwitz A Unique Organization of the Protein Subunits of the DNA Polymerase Clamp Loader in the Archaeon Methanobacterium thermoautotrophicum Delta H J. Biol. Chem., March 15, 2000; 275(10): 7327 - 7336. [Abstract] [Full Text] [PDF]
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B. K. Tye From the Cover: Insights into DNA replication from the third domain of life PNAS, March 14, 2000; 97(6): 2399 - 2401. [Full Text] [PDF]
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R. Bernander, A. Poplawski, and D. W. Grogan Altered patterns of cellular growth, morphology, replication and division in conditional-lethal mutants of the thermophilic archaeon Sulfolobus acidocaldarius Microbiology, March 1, 2000; 146(3): 749 - 757. [Abstract] [Full Text]
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J. M. Dunwell, S. Khuri, and P. J. Gane Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily Microbiol. Mol. Biol. Rev., March 1, 2000; 64(1): 153 - 179. [Abstract] [Full Text] [PDF]
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I. Matsui, E. Matsui, Y. Sakai, H. Kikuchi, Y. Kawarabayasi, H. Ura, S.-i. Kawaguchi, S. Kuramitsu, and K. Harata The Molecular Structure of Hyperthermostable Aromatic Aminotransferase with Novel Substrate Specificity from Pyrococcus horikoshii J. Biol. Chem., February 18, 2000; 275(7): 4871 - 4879. [Abstract] [Full Text] [PDF]
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M. Kähler and G. Antranikian Cloning and Characterization of a Family B DNA Polymerase from the Hyperthermophilic Crenarchaeon Pyrobaculum islandicum J. Bacteriol., February 1, 2000; 182(3): 655 - 663. [Abstract] [Full Text]
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