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Study on the mechanism of nucleus symbiosis by homology-hit analysis

Research Project

Project/Area Number 13309002
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field 広領域
Research InstitutionGunma University

Principal Investigator

SHINOZAWA Takao  Gunma University, Department of Biological and Chemical Engineering, Faculty of Engineering, Gunma University, Professor (30025449)

Co-Investigator(Kenkyū-buntansha) KANAYA Shigehiko  奈良先端科学技術大学, Graduate School of Information Science, Nara Institute of Science and Technology, Assistant Professor (90224584)
Project Period (FY) 2001 – 2003
Project Status Completed (Fiscal Year 2003)
Budget Amount *help
¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000)
Fiscal Year 2003: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2002: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
KeywordsNucleus symbiosis hypothesis / Origin of eukaryotic cell / Archaea / Eubacteria / Homology-hit analysis / Bioinfomatics / Catalase / ホモロジーヒット解析
Research Abstract

Study on the mechanism of nucleus symbiosis by homology-hit analysis
Based on phylogenetic tree analysis, it has been considered that the appearance of eukaryotic cells by branching from archae involved those branching from eubacteia. This analysis was mainly carried out using 16S-rRNA genes. However, the above results are confusing when other genes are used for analysis.
Therefore, we have developed a new method, named as the homology-hit analysis, for the analysis of huge numbers of genes. By this method, after the selection of orthologous genes among many organisms, analysis of homologies among orthologous genes at many thresholds is possible. We have applied this new analysis to yeast, as a representative eukaryotic cell, 6 archaea and 9 eubacteria. Homologies of genes for each functional category in yeast were evaluated in comparison With those of archaea or eubacteria. As a result, it was concluded that the origins of genes related to cell nuclei and-cytoplasm, including the cell m … More embrane, are archaea and eubacteria, respectively.
To determine the species involved in symbiosis, phylogenetic tree analysis, evaluating the relationships among organisms by the number of orthologous genes, was carried out for 4 eukaryotes, 13 archaea and 49 eubacteria. For this, new method for the removal of duplicated genes was developed. Finally the origin of eukaryote was clarified as the symbiosis of pyrococcus into γ-proteobacteria.
To consider the background of symbiosis, we have focused on the protection of the cell against oxygen by the molecular chaperones, including catalases. Cloning of the catalase gene from an alkali- and halo-tolerant bacterium and expression of the catalase in E.coli were performed, followed by an improvement in heat stability by gene-technology. A proposal for a systematic computer-oriented nomenclature and constitution of a database for molecular chaperones were also made. In addition, work related to codon usage in eukaryotes, the distribution of repetitive sequences in E.coli, and others were carried out. Less

Report

(4 results)
  • 2003 Annual Research Report   Final Research Report Summary
  • 2002 Annual Research Report
  • 2001 Annual Research Report
  • Research Products

    (42 results)

All 2004 2003 2002 2001 Other

All Journal Article (31 results) Book (1 results) Patent(Industrial Property Rights) (2 results) Publications (8 results)

  • [Journal Article] Alkali-and Halo-tolerant Catalase from Halomonas sp. SK1:Overexpression in Escheridhia coli, Purification, Characteri2ation, and Genetic Modification2004

    • Author(s)
      L.Huyen, Ai Thuy, K.Phucharoen, A.Ideno, T.Maruyama, T.Shinozawa
    • Journal Title

      Biosci.Biotechnol.Biochem. 68・4

      Pages: 814-819

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Molecular Chaperones : Proposal of a Systematic Computer-Oriented Nomenclature and Construction of a Centralized Database2004

    • Author(s)
      H.Sghaier, L.Huyen Ai, T.Horiike, T.Shinozawa
    • Journal Title

      In Silico Biology 4

      Pages: 311-322

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] The OriBin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by PhyloBenetic Tree Based on Gene Content2004

    • Author(s)
      T.Horiike, K.Hamada, D.Miyata, T.Shinozawa
    • Journal Title

      J.Mol.Evol. 59

      Pages: 606-619

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Alkali-and Halo-tolerant Catalase from Halomonas sp. SK1 : Overexpression in Escherichia coli, Purification, Characterization, and Genetic Modification2004

    • Author(s)
      L.Huyen Ai Thuy, K.Phucharoen, A.Ideno, T.Maruyama, T.shinozawa
    • Journal Title

      Biosci. Biotechnol. Biochem 68(4)

      Pages: 814-819

    • NAID

      10013143677

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Molecular Chaperones : Proposal of a Systematic Computer-Oriented Nomenclature and Construction of a Centralized Database.2004

    • Author(s)
      H.Sghaier, L.Huyen Ai, T.Horiike, T.Shinozawa
    • Journal Title

      Silico Biology 4

      Pages: 311-322

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] The Origin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by Phylogenetic Tree Based on Gene Content2004

    • Author(s)
      T.Horiike, K.Hamada, D.Miyata, T.Shinozawa
    • Journal Title

      J.Mol.Evol. 59

      Pages: 606-619

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Presense af isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of codin8 regions2003

    • Author(s)
      K.Hamada, T.Horiike, H.Ota, K.Mizuno, T.Shinozawa
    • Journal Title

      Genes Genet. Syst. 78

      Pages: 195-198

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Visualization of Gene Classification Based on Expression Profile Using BL-SOM2003

    • Author(s)
      H.Nishio, Md.Altaf-UI-Amin, T.Sato, K.Wada, Y.Wada, K.Minato, K.Kobayashi, N.Ogasawara, S.Kanaya
    • Journal Title

      Workshop on Self-Organizing Maps HIBIKINO 2003? Intelligent Systems and Innovational Computing-Kyusyu Institute of Technology Kitakyusyu Science and Research Park Hibikino, Kitakyusyu, Japan 11-14 September, 2003

      Pages: 101-106

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Informatics for Unveiling Hidden Genome Signatures2003

    • Author(s)
      T.abe, S.Kanaya, M.Kinouchi, Y.Ichiba, T.Kozuki, T.Ikemura
    • Journal Title

      Genome Research 13

      Pages: 693-702

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Comparative Genome Analysis Focused on Periodicity from Prokaryote to Higher Eukaryote Genomes Based on PoWer Spectrum2003

    • Author(s)
      A.Fukushima, T.Ikemura, S.Kanaya
    • Journal Title

      J.Comput.Chem.Jpn. 2・3

      Pages: 95-110

    • NAID

      10012456402

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Presense of isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of coding regions.2003

    • Author(s)
      K.Hamada, T.Horiike, H.Ota, K.Mizuno, T.Shinozawa
    • Journal Title

      Genes Genet.Syst. 78

      Pages: 195-198

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Informatics for Unveiling Hidden Genome Signatures.2003

    • Author(s)
      T.Abe, S.Kanaya, M.Kinouchi, Y.Ichiba, T.Kozuki, T.Ikemura
    • Journal Title

      Genome Research 13

      Pages: 693-702

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Comparative Genome Analysis Focused on Periodicity from Prokaryote to Higher Eukaryote Genomes Based on Power Spectrum2003

    • Author(s)
      A.Fukushima, T.Ikemura, S.Kanaya
    • Journal Title

      J.comput.Chem.Jpn. 2(3)

      Pages: 95-110

    • NAID

      10012456402

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Visualization of Gene Classification Based on Expression Profile Using BL-SOM.2003

    • Author(s)
      H.Nishio, Md.Altaf-UI-Amin, T.Sato, K.Wada, Y.Wada, K.Minato, K.Kobayashi, N.Ogasawara, S.Kanaya
    • Journal Title

      Workshop on Self-Organizing Maps HIBIKINO 2003 -Intelligent Systems and Innovational Computing- Kyusyu Institute of Technology Kitakyusyu Science and Research Park Hibikino, Kitakyusyu, Japan 11-14

      Pages: 101-106

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Origin of Eukaryotic Cell Nuclei by Symbiosis of Archaea in Bacteria supported by the neWly clarified origin of functional genes2002

    • Author(s)
      T.Horiike, K.Hamada, T.Shinozawa
    • Journal Title

      Genes Genet. Syst. 77

      Pages: 369-376

    • NAID

      10010380961

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Purification, characterization and gene sequencing of a catalase from an alkali- and halo- tolerant bacterium, Halomonas sp. SK1.2002

    • Author(s)
      K.Phucharoen, K.Hoshino, Y.Takenaka, T.Shinozawa
    • Journal Title

      Biosci. Biotechnol. Biochem. 66・5

      Pages: 955-962

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Changes in body temperature pattern in vertebrates do not influence the codon usages of α-globin genes2002

    • Author(s)
      K.Hamada, T.Horiike, S.Kanaya, H.Nakamura, H.Ota, T.Yatogo, K.Okada, H.Nakamura, K.Okada, H.Nakamura, T.Shinozawa
    • Journal Title

      Genes Genet. Syst. 77

      Pages: 197-207

    • NAID

      130000060816

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Distribution of Repetitive Sequences on the Leading and Lagging Strands of the Escherichia coli Genome : Comparative Study of Lons Direct Repeat (LDR) Sequences2002

    • Author(s)
      M.Kawano, S.Kanaya, T.Oshima, Y.Matsuda, T.Ara, H.Mori
    • Journal Title

      DNA Research 9

      Pages: 1-10

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Transcriptome analysis of all two-component regulatory system mutants of Escherichia cali K-122002

    • Author(s)
      T.Oshima, H.Aiba, Y.Masuda, S.Kanaya, M.Sugiura, B.L.Wanner, H.Mori, T.Mizuno
    • Journal Title

      Molecular Microbiology 46・1

      Pages: 281-291

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Origin of Eukaryotic Cell Nuclei by Symbiosis of Archaea in Bacteria supported by the newly clarified origin of functional genes.2002

    • Author(s)
      T.Horiike, K.Hamada, T.Shinozawa
    • Journal Title

      Genes Genet. Syst. 77

      Pages: 369-376

    • NAID

      10010380961

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Purification, Characterization, and Gene Sequencing of a Catalase from an Alkali- and Halo-tolerant Bacterium, Halomonas sp. SK1, Biosci.2002

    • Author(s)
      K.Phucharone, K.Hoshino, Y.Takenaka, T.Shinozawa
    • Journal Title

      Biotechnol. Biochem. 66(5)

      Pages: 955-962

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Distribution of Repetitive Sequences on the Leading and Lagging Strands of the Escherichia coli Genome : Comparative Study of Long Direct Repeat(LDR)Sequences.2002

    • Author(s)
      M.Kawano, S.Kanaya, T.Oshima, Y.Matsuda, T.Ara, H.Mori
    • Journal Title

      DNA Research 9

      Pages: 1-10

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.2002

    • Author(s)
      T.Oshima, H.Aiba, Y.Masuda, S.Kanaya, M.Sugiura, B.L.Wanner, H.Mori, T.Mizuno
    • Journal Title

      Molecular Microbiology 46(1)

      Pages: 281-291

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis2001

    • Author(s)
      T.Horiike, K.Hamada, S.Kanaya, T.Shinozawa
    • Journal Title

      Nature Cell Biology 3・2

      Pages: 210-214

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Does endosymbiosis explain the origin of the nucleus? (reply)2001

    • Author(s)
      T.ShinozaWa, T.Horiike, K.Hamada
    • Journal Title

      Nature Cell Biology 3

      Pages: 173-174

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Molecular cloning and DNA sequencinB of the manganese catalase gene from Thermoleophilum album NM.2001

    • Author(s)
      K.Phucharoen, Y.Takenaka, T.Shinozawa
    • Journal Title

      DNA Sequence Issue5-6

      Pages: 413-417

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Codon Usage and tRNA Genes in Eukaryotes : Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis2001

    • Author(s)
      S.Kanaya, Y.Yamada, M.Kinouchi, Y.Kudo, T.Ikemura
    • Journal Title

      J.Mol.Evol 53

      Pages: 290-298

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis2001

    • Author(s)
      T.Horiike, K.Hamada, S.Kanaya, T.Shinozawa
    • Journal Title

      Nature Cell Biology 3(2)

      Pages: 210-214

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Does endosymbiosis explain the origin of the nucleus? (reply)2001

    • Author(s)
      T.Shinozawa, T.Horiike, K.Hamada
    • Journal Title

      Nature Cell Biology 3

      Pages: 173-174

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Molecular cloning and DNA sequencing of the manganese catalase gene from Thermoleophilum album NM.2001

    • Author(s)
      K.Phucharoen, Y.Takenaka, T.Shinozawa
    • Journal Title

      DNA sequence 12

      Pages: 413-417

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Codon Usage and tRNA Genes in Eukaryotes : Correlation of Codon Usage Diversity with Translation Efficietf and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis2001

    • Author(s)
      S.Kanaya, Y.Yamada, M.Kinouchi, Y.Kudo, T.Ikemura
    • Journal Title

      J.Mol.Evol. 53

      Pages: 290-298

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Book] 「CELLULAR ORIGIN AND LIFE IN EXTREME HABITATS」 NUCLEUS SYNBIOSIS HYPOTHESIS : Formation of Eukaryotic Cell Nuclei by the Symbiosis of Archaea in Bacteria.2001

    • Author(s)
      T.Shinozawa, T.Horiike, K.Hamada
    • Total Pages
      5
    • Publisher
      Kluwer academic publishers (J.Seckbach(ed))
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Patent(Industrial Property Rights)] 相同性解析システム、相同性解析方法、相同性解析プログラムおよび取引成立システム2001

    • Inventor(s)
      篠沢隆雄, 金谷重彦, 堀池徳祐, 濱田一男
    • Industrial Property Rights Holder
      科学技術振興事業団篠沢隆雄金谷重彦
    • Filing Date
      2001-07-31
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Patent(Industrial Property Rights)] 相同性解析システム、相同性解析方法、相同性解析プログラムおよび取引成立システム2001

    • Inventor(s)
      篠沢隆雄, 金谷重彦, 堀池徳祐, 濱田一男
    • Industrial Property Rights Holder
      科学技術振興事業団篠沢隆雄金谷重彦
    • Filing Date
      2001-11-22
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kazuo Hamada: "Presense of isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of coding regions."Genes Genet.Syst.. 78. 195-198 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Marisa Motomura: "Purification and characterization of an aflatoxin degradation enzyeme."Microbiol.Res.. 158. 237-242 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Le Huyen Ai Thuy: "Alkali-and halo-tolerant catalase from Halomonas sp. SK1 : Overexpression in Escherichia coli, purification, characterization, and genetic modification."Biosci.Biotechnol.Biochem.. 68・4(in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] T.Horiike, K.Hamada, T.Shinozawa: "Origin of Eukaryotic Cell Nuclei by Symbiosis of Archaea in Bacteria supported by the newly clarified origin of functional genes"Genes Genet : Syst. 77. 369-376 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Phucharoen. Krisana: "Molecular cloning and DNA sequencing of the manganese catalase gene from Thermoleophilum album NM."DNA Sequence. Issue5-6. 413-417 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Phucharoen. Krisana: "Purification, characterization and gene sequencing of a catalase froom an alkai and halo-atolerentbacterium, Halomonas sp. SK1"Biosci.Biotechnal.Biochem. (in press). 1

    • Related Report
      2001 Annual Research Report
  • [Publications] Horiike Tokumasa: "Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis"Nature Cell Biol. 3. 210-214 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Shinozawa T, Horiike T, Hamada K.: "「CELLULAR ORIGIN AND LIFE IN EXTREME HABITAIS」 Symbiosis NUCLEUS SYMBIOSIS HYPOTHESIS : Formation of Eukaryotic Cell Nuclei by the Symbiosis of Archaea in Bacteria"Kluwer academic publishers (in press).

    • Related Report
      2001 Annual Research Report

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Published: 2002-04-01   Modified: 2016-04-21  

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