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Researches on ribozymes at molecular and atomic level

Research Project

Project/Area Number 09278103
Research Category

Grant-in-Aid for Scientific Research on Priority Areas (A)

Allocation TypeSingle-year Grants
Research InstitutionKyoto University

Principal Investigator

INOUE Tan  Kyoto University, Graduate School of Biostudies, Professor, 大学院・生命科学研究科, 教授 (40114855)

Co-Investigator(Kenkyū-buntansha) SHIRAISHI Hideaki  Kyoto University, Graduate School of Biostudies, Associate Professor, 大学院・生命科学研究科, 助教授 (90202118)
TANI Tokio  Kyushu University, Graduate School of Science, Associate Professor, 大学院・理学研究科, 助教授 (80197516)
TAIRA Kazunari  The University of Tokyo, Graduate School of Engineering, Professor, 大学院・工学系研究科, 教授 (10261778)
SAKAMOTO Kensaku  The University of Tokyo, Graduate School of Science, Research Associate, 大学院・理学系研究科, 助手 (50240685)
SUZUKI Tsutomu  The University of Tokyo, Graduate School of Frontier Sciences, Lecturer, 大学院・新領域創成科学研究科, 講師 (20292782)
小松 康雄  北海道大学, 薬学部, 助手 (30271670)
新田 至  東京大学, 工学系研究科, 助手 (30272404)
Project Period (FY) 1997 – 2000
Project Status Completed (Fiscal Year 2001)
Budget Amount *help
¥154,000,000 (Direct Cost: ¥154,000,000)
Fiscal Year 2000: ¥37,400,000 (Direct Cost: ¥37,400,000)
Fiscal Year 1999: ¥36,600,000 (Direct Cost: ¥36,600,000)
Fiscal Year 1998: ¥40,000,000 (Direct Cost: ¥40,000,000)
Fiscal Year 1997: ¥40,000,000 (Direct Cost: ¥40,000,000)
KeywordsRNA / ribozyme / catakytic RNA / snRNA / RNP / group I introns / hammerhead ribozyme / splicing / ヘアピン型リボザイム / ンマーヘッド型リボザイム / G167 / GNRA-receptor 4 / マキシザイム / U6snRNA / RNase P / 23SリボソームRNA / 酵素 / 分子設計 / 反応機構 / スプライシング / catalyticRNA
Research Abstract

The molecular design, structure and reaction mechanism of the naturally occurring ribozymes were investigated. The minimal catalytic unit of Group I intron ribozymes was identified. The RNA folding pathways and the intermolecular long-range interactions of the intron were identified. In vitro selection te4chnique was successfully employed for producing artificial ribozymes and RNPs. Hammerhead ribozyme was engineered successfully for in vivo use. New gene discovery system was developed. Ribosomal RNAs of mammalian mitochondria and the corresponding protein components were identified and analyzed. It was elucidated that the binding of stalk proteins to rRNA in the ribosomal GTPase center is involved in formation of the functional structure of two RNA domains. These complexes affected not only elongation factor-binding site in the rRNA but also the functional structure of the decoding site. A gene coding for the Prp12 which interacts with Prp1 (pre-mRNA processing 1) of fission yeast which is a component of U4/U6 snRNP was cloned. As a result, it was elucidated that the interaction of U4/U6 snRNP with U2 snRNP which is necessary for conversion of a commitment complex to a spliceosome at the early stage of splicing depends on not only interaction due to hydrogen bonding between U2 and U6 snRNAs, but also interaction among proteins bound to the snRNAs.

Report

(5 results)
  • 2001 Final Research Report Summary
  • 2000 Annual Research Report
  • 1999 Annual Research Report
  • 1998 Annual Research Report
  • 1997 Annual Research Report
  • Research Products

    (75 results)

All Other

All Publications (75 results)

  • [Publications] Atsumi, S.: "Design and development of a catalytic ribonucleoprotein"EMBO.J.. 20. 5453 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Oe Y.: "Conserved Base-Pairings between C266-A268 and U307-G309 in the P7 of the Tetrahyme na Ribozyme Is Nonessential for the in vitro Self-Splicing Reaction"Biochem Biophys Res Commun. 284. 948 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ikawa, Y.: "A group I ribozyme derived from the Tetrahymena intron performs the self-splicing without the conserved base-triples"Genes to Cells. 6. 411-420 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ohki, Y.: "A deteriorated triple-helical scaffold accelerates formation of the Tetrahymena ribozyme active-structure"FEBS Lett.. 493. 95-100 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] 井川 善也: "究極のグループIイントロン"蛋白質 核酸 酵素. 46. 644-651 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ohki,Y.,Ikawa,Y.,Shiraishi,H. and Inoue,T.: ""A deteriorated triple-helical scaffold accelerates formation of the Tetrahymena ribozyme active-structure""FEBS Lett.. 493. 95-100 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ikawa,Y.,Yoshioka,W.,Shiraishi,H.and Inoue,T.: ""A group I ribozyme derived from the Tetrahymena intron performs the self-splicing without the conserved base-triples""Genes to Cells. 6. 411-420 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Oe Y, Ikawa Y, Shiraishi H, Inoue T.: ""Conserved Base-Pairings between C266-A268 and U307-G309in the P7 of the Tetrahymena Ribozyme Is Nonessential for the in vitro Self-Splicing Reaction""Biochem Biophys Res Commun. 284(4). 948-54 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ikawa,Y.,Nohmi,K.,Atsumi,S.,Shiraishi,H.and Inoue,T.: ""A comparative study on two GNRA-tetraloop receptors : 11-nt and IC3 motifs""J.Biochem. 130. 251-255 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Atsumi,S., Ikawa,Y., Shiraishi,H.and Inoue,T.: ""Design and development of a catalytic ribonucleoprotein""EMBO.J.. 20(19). 5453-5460 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ikawa,Y: "Minimal catalytic domain of a group I self-splicing intron"Nature Struct Biol.. 11. 1032-1035 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ikawa,Y: "A group I ribozyme derived from the Tetrahymena intron performs the self-splicing without the conserved base-triples"Genes to Cells. (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] K.Sakamoto: "Molecular computation by DNA hairpin formation."Science. 288. 1223-1226 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Suzuki,T: "Structural compensation for deficit of rRNA with proteins in mammalian mitochondrial ribosome ; systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria"J.Biol.Chem. (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Warashina,M: "Novel RNA-protein hybrid ribozymes efficiently cleave any mRNA independently of the structure of the target RNA."Proc.Natl.Acad.Sci.USA. (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Habara,Y: "Mutation in the prp12+ gene encoding a homologue of SAP130/SF3b130 causes differential inhibition of pre-mRNA splicing and arrest of cell-cycle progression in Schizosaccharomyces pombe."RNA. (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Tan Inoue: "Trans-activation of the Tetrahymena group I intron ribozyme via a non-native RNA-RNA interaction"Nucleic Acids Research. 27・7. 1650-1655 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Tan Inoue: "A conserved motif in group IC3 introns is a new class of GNRA receptor"Nucleic Acids Research. 27・8. 1859-1865 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Tan Inoue: "Characterization of P8 and J8/7 elements in the conserved core of the Tetrahymena group IO intron ribozyme"Biochemical and Biophysical Research Communications. 267. 85-90 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] Tan Inoue: "Requiremwnts for alternative forms of the activator domain, P5abc< in the Tetrahymena ribozyme"FEBS Letters. 462. 273-278 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] Komatsu, Y.: "Effects of a high-affinity antibody fragment on DNA polymerase reactions near a (6-4) photoproduct site"Photochem Photobiol. 69. 226-230 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Komatsu, Y.: "Investigation of the recognition of an important uridine in an internal loop of a hairpin ribozyme prepared using post-synthetically modified oligonucleotides"Nucleic Acids Res.. 27. 4314-4323 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Komatsu, Y.: "Conformational multiplicity of the antibody combining site of a monoclonal antibody specific for a (6-4) photoproduct"J. Mol. Biol.. 290. 731-740 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Komatsu, Y.: "DNA binding mode of the Fab fragment of a monoclonal antibody specific for cyclobutane pyrimidine dimer"Nucleic Acids Res. 28. 944-951 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] Taira, K.: "tRNA Val-heterodimeric maxizymes with high potential as gene-inactivating agent : simultaneous cleavage at two sites in HIV-1 tat mRNA in cultured cells"Proc. Natl. Acad. Sci. USA. 96. 1886-1891 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Taira, K.: "Extremely high and specific activity of DNA enzymes in cells with a Philadelphia chromosome"Chem. Biol.. 6. 237-250 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Taira, K.: "CTAB-mediated enrichment for active forms of novel dimeric maxizymes"FEBS Lett.. 448. 67-74 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Taira, K.: "Specificity of novel allosterically trans- and cis-activated connected maxiz ymes that are designed to suppress BCR-ABL expression"FEBS Lett.. 461. 77-85 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Tokio Tani: "Characterization of the ptr6+ gene in fission yeast : A possible involvement of a transcriptional coactivator TAF in nucleocytoplasmic transport of mRNA"Genetics. 152. 869-880 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Tokio Tani: "A "G" to "A" transition at the last nucleotide of exon 6 of the gc gene (868G-A) may result in either a splice or missensemutation in patients with X-linked severe combined immunodeficiency"Human Genet.. 104. 36-42 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] 谷時雄: "実験医学増刊「核-細胞質間輸送と小胞輸送」"mRNAの核外輸送機構. 52 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] 谷時雄: "蛋白質核酸酵素、増刊号「細胞核研究の最先端」"mRNAの核外輸送に関与する遺伝子群. 9 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Ikawa,Y.: "Trans-activation of the Tetrahymena ribozyme by its P2-2.1 domains" J.Biochem. 123. 528-533 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Naito,Y.: "P5abc of the Tetrahymena ribozyme consists of three functionally independent elements" RNA. 4. 837-846 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Ikawa,Y.: "Trans-activation of the Tetrahymena group I intron ribozyme via a non-native RNA-RNA interaction" Nucleic Acids Research. 27・7 (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Ikawa,Y.: "A conserved motif in group IC3 introns is a new class of GNRA receptor" Nucleic Acids Research. 27・8 (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Komatsu,Y.: "Modification and application of self-trimming hairpin ribozymes to targeting a transcribed RNA in vitro." J.Biochem. 124・5. 986-991 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Koizumi,M.: "Design and anti-HIV-1 activity of hammerhead and hairpin ribozymes containing a stable loop." Nucleosides & Nucleotides. (in press).

    • Related Report
      1998 Annual Research Report
  • [Publications] Kobayashi,H: "Effets of a high-affinity antibody fragment on DNA polymerase reactions near a (6-4) photoproduct site." Photochem.& Photobio.69・2. 226-230 (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Ota,N.: "Determination of interactions between structured nucleic acids by fluorescence resonance energy transfer (FRET): selection of target sites for functional nucleic acids" Nucleic Acids Res.26. 735-743 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kawasaki,H.: "p300 and ATF-2 are components of the DRF complex, which regulates retinoicacid-and E1A-mediated transcription of the c-jun gene in F9 cells." Genes & Dev.12. 233-245 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kawasaki,H.: "Distinct roles of the co-activators p300 and CBP in retinoic-acid-induced F9-cell differentiation." Nature. 393. 284-289 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Ota,N.: "Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity" Nucleic Acids Res.26. 3385-3391 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kuwabara,T.: "Formation of a catalytically active dimer by tRNA Val-driven short ribozymes" Nature Biotechnology. 16. 961-965 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kuwabara,T.: "A novel nallosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo." Mol.Cell. 2. 617-627 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kuwabara,T.: "tRNA Val-heterodimeric maxizymes with high potential as gene-inactivating agent: simultaneous cleavage at two sites in HIV-1tat mRNA in cultured cells." Proc.Natl.Acad.Sci.USA96. 1886-1891 (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Shibuya,T.: "Characterization of the ptr6+ gene in fission yeast: A possible involvement of a transcriptional coactivator TAF in nucleocytoplasmic transport of mRNA" Genetics. in press (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kanai,N.: "A “G" to “A" transition at the last nucleotide of exon 6 of the gene(868G-A) may result in either a splice or missense mutation in patients with X-linked severe combined immunodeficiency" Human Genet.104. 36-42 (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] Habara,Y.: "The fission yeast prp10+ gene involved in pre-mRNA splicing encodes a homologue of highly conserved splicing factor, SAP155" Nucleic Acids Res.26・24. 5662-5669 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Imamura,O: "Cloning and characterization of a human DEAH-box RNA helicase, a functional homolog of fission yeast Cdc28/Prp8." Nucleic Acids Res.26. 2063-2068 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Nitta,I.: "Possible involvement of Escherichia coli 23S ribosomal RNA in peptide bond formation." RNA. 4. 257-267 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Nitta,I.: "Reconstitution of peptide bond formation with Escherichia coli 23S ribosomal RNA domains." Science. 281. 666-669 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Nitta,I.: "A novel cell-free system for peptide synthesis driven by pyridine." Biol.Chem.379. 819-829 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kimoto,M.: "RNA aptamers that specifically bind to the Ras-binding domain of Raf-1" FEBS Letters. 441. 322-326 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kiga,D.: "An RNA aptamer to the xanthine/guanine base with a distictive mode of purine recognition" Nucleic Acids Research. 26・7. 1755-1760 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Seio,K.: "Chemical synthesis and properties of conformationally fixed diuridine monophosphates as builiding blocks of the RNA turn motif" Journal of Organic Chemistry. 63・5. 1429-1443 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Ikawa,Y.: "Long-range interaction between the P2.1 and P9.1 peripheral domains of the Tetrahymena ribozyme." Nucleic Acids Research. 25. 1761-1765 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Ikawa,Y.: "Idertification of the nucleotides in the A-rich bulge of the Tetrahymena ribozyme responsible for an efficient self-splicing." J.Biochem. 122. 878-882 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Ikawa,Y.: "Trans-activation of the Tetrahymena ribozyme by its P2-2.1 domains" J.Biochem. 123. 528-533 (1998)

    • Related Report
      1997 Annual Research Report
  • [Publications] Y.Naito: "P5abc of the Tetrahymena ribozyme consists of three functionally independent elements" RNA. (in press).

    • Related Report
      1997 Annual Research Report
  • [Publications] Komatsu,Y.: "A new type of hairpin ribozyme consisting of three domains." Biochemistry. 36. 9935-9940 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Komatsu,Y.: "Construction of hairpin ribozymes with a three-way junction." Bioorg.Med.Chem.5. 11063-11069 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Urushiyama,S.: "The prp1+gene required for pre-mRNA splicing in Schizosaccharomyces pombe encodes a protein that contains TPR motifs and is similar to Prp6p of budding yeast." Genetics. 147. 101-115 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] J-H.Park: "Structure and expression of the gsa-1 gene encoding a G protein a (s) subunit in C. elegans" Gene. 194. 183-190 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] A.K.Azed: "Isolation and molecular characterization of mRNA transport mutants in Schizosaccharomyces pombe" Mol.Biol.Cell. 8. 825-841 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Nitta,I.: "Possible involvement of Escherichia coli 23S ribosomal RNA in peptide bond formation." RNA. 4・3. 257-267 (1998)

    • Related Report
      1997 Annual Research Report
  • [Publications] Nitta,I.: "A novel cell-free system for peptide synthesis driven by pyridine." Bio.Chem.(in press).

    • Related Report
      1997 Annual Research Report
  • [Publications] D.Kiga,: "An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition" Nucleic Acids Research. (in press).

    • Related Report
      1997 Annual Research Report
  • [Publications] Koizumi,M.: "Design and anti-HIV-1 activity of hammerhead and hairpin ribozymes containing a stable loop." Nucleosides & Nucleotides. (in press).

    • Related Report
      1997 Annual Research Report
  • [Publications] Warashina,M.: "Entropically driven enhancement of cleavage activity of aDNA-armed hammerhead ribozyme : mechanism of action of hammerhead ribozymes." J.Org.Chem.62. 9138-9147 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Fujita,S.: "Discrimination of a single base change in a ribozyme using the gene for dihydrofolate reductase as a selective marker in Escherichia coli." Proc.Natl.Acad.Sci.USA. 94. 391-396 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Zhou,D.-M.: "Explanation by thedouble-metal-ion mechanism of catalysis for the differential metal ion effects on the cleavage rates of 5'-oxy and 5'-thio substrates by a hammerhead ribozyme." Proc.Natl.Acad.Sci.USA. 94. 14343-14348 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Kuwabara,T.: "Comparison of the specificities and catalytic activities of hammerhead ribozymes and DNA enzymes with respect to the cleavage of BCR-ABL chimeric L6 (b2a2) mRNA." Nucleic Acids Res.25. 3074-3082 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Imamura,O.: "Cloning and characterization of a human DEAH-box RNA helicase,a functional homolog of fission yeast Cdc28/Prp8." Nucleic Acids Res.(in press).

    • Related Report
      1997 Annual Research Report
  • [Publications] 新田至, 上田卓也, 渡辺公綱: "リボソームとRNAワールド" 化学と生物 36(4), 92 (1998)

    • Related Report
      1997 Annual Research Report

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Published: 1997-04-01   Modified: 2016-04-21  

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