Structural and functional studies on RNases in the RNA degradation system

• Project/Area Number: 19770083
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: Osaka University
• Principal Investigator: NAKAGAWA Noriko Osaka University, 大学院・理学研究科, 助教 (50379278)
• Project Period (FY): 2007 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥3,960,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥660,000); Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2008: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2007: ¥1,100,000 (Direct Cost: ¥1,100,000)
• Keywords: RNA / RNA分解 / 酵素反応 / 立体構造 / トランスクリプトーム解析 / 相互作用解析 / 高度好熱菌 / 立体構造解析

Research Abstract

Degradation of mRNA plays an essential role in regulation of gene expression in all organisms. Defects in this process lead to potentially fatal defects. mRNA degradation is mediated by the concerted action of several ribonucleases including β-CASP family proteins. This study revealed the mechanism of RNA degradation by β-CASP family proteins and found a novel pathway that involves these proteins.

Research Products

• [Journal Article] Crystal Structure of An Archaeal Cleavage and Polyadenylation Specificity Factor Subunit from Pyrococcus horikoshii (2010)
  • Author(s): Nishida, Y., Ishikawa, H., Baba, S., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: Proteins (in press)
  • Peer Reviewed
• [Journal Article] A Novel Single-Stranded DNA-Specific 3′-5′Exonuclease, Thermus thermophilus Exonuclease I, Is Involved in Several DNA Repair Pathways (2010)
  • Author(s): Shimada, A., Masui, R., Nakagawa, N., Takahata, Y., Kim, K., Kuramitsu, S., Fukui, K.
  • Journal Title: Nucleic Acids Res. (in press)
  • Peer Reviewed
• [Journal Article] The First Crystal Structure of An Archaeal Metallobeta- Lactamase Superfamily Protein; ST1585 from Sulfolobus tokodai (2010)
  • Author(s): Shimada, A., Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: Proteins (in press)
  • Peer Reviewed
• [Journal Article] Structure of RecJ Exonuclease Defines Its Specificity for Single-Stranded DNA (2010)
  • Author(s): Wakamatsu, T., Kitamura, Y., Kotera, Y., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: J. Biol. Chem. Vol.285,No.13 Pages: 9762-9769
  • Peer Reviewed
• [Journal Article] Structure of RecJ Exonuclease Defines Its Specificity for Single-stranded DNA. (2010)
  • Author(s): Wakamatsu, T.
  • Journal Title: J.Biol.Chem. 285 Pages: 9762-9769
  • Peer Reviewed
• [Journal Article] Characterization of DNA Polymerase X from Thermus thermophilus HB8 Reveals the POLXc and PHP Domains are both Required for 3'-5' Exonuclease Activity (2009)
  • Author(s): Nakane, S., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: Nucleic Acids Res. Vol.37,No.6 Pages: 2037-2052
  • Peer Reviewed
• [Journal Article] Structure of TTHA1623, A Novel Metallo-betalactamase Superfamily protein from Thermus thermophilus HB8 (2009)
  • Author(s): Yamamura, A., Okada, A., Kameda, Y., Ohtsuka, J., Nakagawa, N., Ebihara, A., Nagata, K., Tanokura, M.
  • Journal Title: Acta Cryst. Vol.F65,No.5 Pages: 455-459
  • Peer Reviewed
• [Journal Article] Structure of TTHA1623, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8. (2009)
  • Author(s): Yamamura, A.
  • Journal Title: Acta Cryst. F65 Pages: 455-459
  • Peer Reviewed
• [Journal Article] Insights into Different Dependence of dNTP Triphosphohydrolase on Metal Ion Species from Intracellular Ion Concentrations in Thermus thermophilus (2008)
  • Author(s): Kondo, N., Nishikubo, T., Wakamatsu, T., Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: Extremophiles Vol.12,No.2 Pages: 217-223
  • Peer Reviewed
• [Journal Article] Crystal Structure of TTHA1429, A Novel Metallobeta- lactamase Superfamily Protein from Thermus thermophilus HB8 (2008)
  • Author(s): Yamamura, A., Ohtsuka, J., Kubota, K., Agari, Y., Ebihara, A., Nakagawa, N., Nagata, K., Tanokura, M.
  • Journal Title: Proteins Vol.73,No.4 Pages: 1953-1057
  • Peer Reviewed
• [Journal Article] Bound Nucleotide Controls the Endonuclease Activity of Mismatch Repair Enzyme MutL (2008)
  • Author(s): Fukui, K., Nishida, M., Nakagawa, N., Masui, R., Kuramitsu, S.
  • Journal Title: J. Biol. Chem. Vol.283,No.18 Pages: 12136-12145
  • Peer Reviewed
• [Journal Article] An O6-Methylguanine-DNA Methyltransferase-Like Protein from Thermus thermophilus Interacts with A Nucleotide Excision Repair Protein (2008)
  • Author(s): Morita, R., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: J. Biochem. Vol.144,No.2 Pages: 267-277
  • NAID: 10024911935
  • Peer Reviewed
• [Journal Article] Crystal Structure of a Putative DNA Methylase TTHA0409 from Thermus thermophilus HB8 (2008)
  • Author(s): Morita, R., Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: Proteins Vol.73,No.1 Pages: 259-264
  • Peer Reviewed
• [Journal Article] Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8 (2008)
  • Author(s): Morita, R.
  • Journal Title: Proteins 73 Pages: 259-264
  • Peer Reviewed
• [Journal Article] Crystallization screening test for the whole-cell project on Thermus thermophilus HB8 (2008)
  • Author(s): Iino, H.
  • Journal Title: Acta crystallographica. Section F 64 Pages: 487-491
  • Peer Reviewed
• [Journal Article] Analysis of a Nuclease Activity of Catalytic Domain of Thermus thermophilus MutS2 by High-Accuracy Mass Spectrometry (2007)
  • Author(s): Fukui, K., Takahata, Y., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: Nucleic Acids Res. Vol.35,No.15
  • Peer Reviewed
• [Journal Article] Crystal Structure of Family 5 Uracil-DNA Glycosylase Bound to DNA (2007)
  • Author(s): Kosaka, H., Hoseki, J., Nakagawa, N., Kuramitsu, S., Masui, R.
  • Journal Title: J. Mol. Biol. Vol.373,No.4 Pages: 839-850
  • Peer Reviewed
• [Journal Article] UvrA and UvrB Enhance Mutations Induced by Oxidized Deoxyribonucleotides (2007)
  • Author(s): Hori, M., Ishiguro, C., Suzuki, T., Nakagawa, N., Nunoshiba, T., Kuramitsu, S., Yamamoto, K., Kasai, H., Harashima, H., Kamiya, H.
  • Journal Title: DNA Repair Vol.6,No.12 Pages: 1786-1793
  • NAID: 120000950256
  • Peer Reviewed
• [Journal Article] Transcription activation mediated by a cyclic AMP recptor protein from Thermus (2007)
  • Author(s): Shinkai, A.
  • Journal Title: Journal of Bacteriology 189 Pages: 3891-3901
  • Peer Reviewed
• [Journal Article] Crystal structure of farnily 5 uracil-DNA glycosylase bound to DAN. (2007)
  • Author(s): Kosaka, H.
  • Journal Title: Journal of Molecular Bolecular Biology 373 Pages: 839-850
  • Peer Reviewed
• [Presentation] Interaction analysis of a novel ribonuclease from Thermus thermophilus HB8 (2009)
  • Author(s): 大山礼雅, 石川大仁, 中川紀子, 増井良治, 倉光成紀
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-12
• [Presentation] Structural and functional analysis of TTHA0252, a novel RNase of the beta- CASP family (2009)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: 第82回日本生化学会大会
  • Place of Presentation: 神戸
  • Year and Date: 2009-10-22
• [Presentation] Structural and functional analysis of TTHA0252, a novel RNase of the beta-CASP family (2009)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-20
• [Presentation] Structural and functional analysis of TTHA0252, a novel RNase of the beta- CASP family (2008)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: 第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
  • Place of Presentation: 神戸
  • Year and Date: 2008-12-12
• [Presentation] Structural and functional analysis of TTHA0252, a novel RNase of the beta-CASP family (2008)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-12
• [Presentation] Structural Analysis of the Beta-CASP Family, A New Member of the Metallo-beta-lactamase Superfamily (2008)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: ISGO International Conference On Structural Genomics Oxford 2008 (ICSG2008)
  • Place of Presentation: イギリス・オックスフォード
• [Presentation] Structural and functional analysis of TTHA0252, a novel RNase of the beta-CASP family (2008)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: XXI Congress and Assembly of the International Union of Crystallography (IUCr2008)
  • Place of Presentation: 大阪
• [Presentation] Thermus thermophilusを用いた生物界に普遍的な新規RNA分解系の探求 (2008)
  • Author(s): 石川大仁, 若松泰介, 中川紀子, 倉光成紀, 増井良治
  • Organizer: 第2回日本ゲノム微生物学会年会
  • Place of Presentation: 大阪
• [Presentation] Functional identification of protein from Thermus thermophilus HB8:Structural and functional analysis of TTHA0252, a novel RNase of the beta-CASP family (2007)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: 第30回日本分子生物学会年会・第80回日本生化学会大会合同大会(BMB2007)
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-11
• [Presentation] Structural and functional analysis of TTHA0252 from Thermus thermophilus HB8, a novel RNase of the beta-CASP family (2007)
  • Author(s): 石川大仁, 中川紀子, 倉光成紀, 増井良治
  • Organizer: 第7回日本蛋白質科学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2007-05-26
• [Book] 酵素ハンドブック (2008)
  • Author(s): 中川紀子, 増井良治, 倉光成紀, 他
  • Publisher: 朝倉書店
• [Book] 構造生物学-ポストゲノム時代のタンパク質研究- (2007)
  • Author(s): 中川紀子, 他
  • Publisher: 共立出版
• [Remarks]
  • URL: http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/kuramitu/