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Transcriptional activation mechanism by the memory effect of single RNA polymerase-promoter complex molecules

Research Project

Project/Area Number 12480203
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionNational Institute of Genetics

Principal Investigator

SHIMAMOTO Nobuo  National Institute of Genetics, Structural Biology Center, Professor, 構造遺伝学研究センター, 教授 (20127658)

Co-Investigator(Kenkyū-buntansha) SOGAWA Kumiko  National Institute of Genetics, Structural Biology Center, Assistant Professor, 構造遺伝学研究センター, 助手 (20291073)
Project Period (FY) 2000 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥15,400,000 (Direct Cost: ¥15,400,000)
Fiscal Year 2002: ¥6,100,000 (Direct Cost: ¥6,100,000)
Fiscal Year 2001: ¥6,500,000 (Direct Cost: ¥6,500,000)
Fiscal Year 2000: ¥2,800,000 (Direct Cost: ¥2,800,000)
KeywordsRNA polymerase / promoter / abortive initiation / moribund complex / molecular memory / GreAGreB / RNA切断因子
Research Abstract

The mechanism of transcription initiation has been assumed to be a sequence of three essential steps: formation of a complex between RNA polymerase and a promoter (closed complex), formation of another complex with partially melted DNA duplex to form phosphodiester bonds (open complex and chemical reaction), and escape of RNA polymerase from the promoter associated with the progress of RNA elongation (promoter clearance). There is a process called "abortive initiation", an iterative synthesis and release of oligo-RNA molecules, and is often excluded from the mainstream of the mechanism. Altough this process has been observed in vitro with all prokaryotic and eukaryotic RNA polymerases so far isolated, its role as well as its occurrence in vivo has been unknown.
We have been clarifying for several years that this sequential mechanism is not the case and the initiation follows branched pathways, one of which contains the moribund complex, being defined as a complex that produces only abor … More tive and no full-length transcripts. Followings are its characteristics. 1.The moribund complex, as well as the productive complex that synthesizes full-length product, are formed from the same homogeneous fraction of enzyme molecules, and dissociation of the molecules from the promoter DNA cancels any difference between them. 2.Structural differences between these complexes have been demonstrated. 3.At some promoters, a moribund complex is converted into a dead-end complex that still retains a short transcript but has no elongation activity. Therefore, the initiation pathway is branched into the conventional productive pathway and the abortive pathway that can lead towards a dead end. 4.The fates of a moribund complex are either inactivation as a dead-end complex, dissociation from the DNA, or direct conversion into a productive complex, and the rates of these reactions vary with the promoter. 5. There are factors that affect the fate of the moribund complex in a manner that depends on the promoter.
To examine the existence and significance of the branched pathway in vivo, we selected GreA and GreB for clues. At the lP_RAL promoter these factors enhance conversion of the moribund complex into the productive one, in the presence of high concentrations of initiating nucleoside triphosphate in vitro. If the branched mechanism exists in vivo, absence of the Gre factors should result in reduction of productive transcription from promoters at which the moribund complex is susceptible to these factors. We constructed a double-disruptant of E.coli, DgreA DgreB, and then arbitrarily selected 10 genes from among those whose levels of transcripts in the mutant strain were found to be lower than those in the parental greA^+greB^+ strain. Finally, the promoter for three of these genes, atpC (uncC), cspA, and rpsA, passed a further conventional test which confirmed that they displayed a branched initiation pathway in a reconstituted transcription system composed of purified components. The results obtained prove that the branched initiation pathway exists in vivo and is utilized in regulation of transcription initiation from some promoters, through modulation of the fraction of polymerase-promoter complexes entering each branch of the pathway. The determination of the level of GreB was observed to be constitutive. The level of GreA remained the same through the growth phase, and did not respond much to the richness of the culture media. However, it decreased into half in aerobic conditions, indicating that some genes are regulated by GreA. Therefore, the regulatory circuit responding to the levels of proteins involving GreA, namely the branched pathway mechanism, is working in cells. Less

Report

(4 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (29 results)

All 2004 2003 2002 2001 Other

All Journal Article (8 results) Book (2 results) Patent(Industrial Property Rights) (1 results) Publications (18 results)

  • [Journal Article] RNA polymerase can track a DNA groove during promoter search.2004

    • Author(s)
      Sakata-Sogawa, K., Shimamoto, N.
    • Journal Title

      Proc.Nat.Sci.U.S.A. 101

      Pages: 14731-14735

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Journal Article] RNA polymerase can track a DNA groove during promoter search2004

    • Author(s)
      Sakata-Sogawa, K., Shimamoto, N.
    • Journal Title

      Proc.Nat.Sci.U.S.A. 101

      Pages: 14731-14735

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Journal Article] Movements of RNA polymerase along DNA2003

    • Author(s)
      Shimamoto, N.
    • Journal Title

      Methods Enzymology 371

      Pages: 50-70

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Journal Article] Movement of RNA polymerase along DNA2003

    • Author(s)
      Shimamoto, N.
    • Journal Title

      Methods Enzymology 371

      Pages: 50-70

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Journal Article] Generality of the Branched Pathway in Transcription Initiation by E.coli RNA Polymerase..2002

    • Author(s)
      Susa, M., Sen, R., Shimamoto, N.
    • Journal Title

      J.Biol.Chem. 277

      Pages: 15407-15412

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Journal Article] Generality of the Branched Pathway in Transcription Initiation by E.coli RNA Polymerase..2002

    • Author(s)
      Susa, M., Sen, R., Shimamoto, N.
    • Journal Title

      J.BIol.Chem. 277

      Pages: 15407-15412

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Journal Article] Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated by elongation factors GreA and GreB.2001

    • Author(s)
      Sen, R., Nagai, H., Shimamoto, N.
    • Journal Title

      Gene.Cells 6

      Pages: 389-402

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Journal Article] スライディングによるDNA結合のアンテナ効果:1分子観察により発見された分子効果2001

    • Author(s)
      嶋本伸雄
    • Journal Title

      細胞工学 20

      Pages: 666-671

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Book] 分子生物学・免疫学キーワード辞典 第2版(リボ核酸、RNAポリメラーゼ、転写開始、エロンゲーション(転写の)、メッセンジヤーRNA)2003

    • Author(s)
      嶋本伸雄
    • Total Pages
      1035
    • Publisher
      医学書院
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Book] ナノバイオマシン創製のための技術及び市場性に関する調査研究2003

    • Author(s)
      嶋本伸雄
    • Total Pages
      250
    • Publisher
      バイオインダストリー協会調査委員会(嶋本伸雄委員長)
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Patent(Industrial Property Rights)] 特許2003

    • Inventor(s)
      嶋本 伸雄, 須佐 太樹, 福島 和久
    • Industrial Property Rights Holder
      国立遺伝学研究所所長, 横河電機
    • Filing Date
      2003-12-16
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Shimamoto, N: "Movements of RNA polymerase along DNA in Methods of Enzymology"Methods of Enzymology. (in press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Susa, M., Sen, R., Shimamoto, N.: "Generality of the branched pathway in transcription initiation by Escherichia coli RNA polymerase"J.Biol.Chem.. 277. 15407-15412 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 嶋本伸雄: "分子レベルで見たタンパク質とDNAとの結合"総研大ジャーナル. 1. 42-47 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 嶋本伸雄: "ナノバイオマシン〜世界が血眼の次世代デバイスの代表"NIF NEWS. 12月号. 2-2 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 嶋本伸雄: "分子生物キーワード辞典第2版(RNA、RNAポリメラーゼ、(転写の)イニシエーション、(転写の)エロンゲーション、mRNA、)"羊土社(in press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] 嶋本伸雄: "わかる実験医学(原核生物の転写反応)"羊土社(in press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Sen, R., Nagai, H., Shimamoto.N.: "Generality of the Branched Pathway in Transcription Initiation by E. coli RNA Polymerase"J. Biol. Chem.. (in press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Sen, R., Nagal, H., Shimamoto, N.: "Conformational switching of Escherichia coli RNA polymemse-promoter binary complex is facilitated by elongation factors GreA and GreB."Gene. Cells. 6. 389-402 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 嶋本伸雄: "スライディングによるDNA結合のアンテナ効果:1分子観察により発見された分子効果"細胞工学. 20. 666-671 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 嶋本伸雄: "スライディングによるDNA結合のアンテナ効果:1分子観察により発見された分子効果"細胞工学. 20. 666-671 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 嶋本伸雄: "分子生物学・免疫学キーワード辞典第2版"医学書 院編者:永田和宏, 長野 敬, 宮坂信之, 宮坂昌之. (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 嶋本伸雄: "Bioscience新用語ライブラリー第二版"羊土社 編者:田村隆明, 山本雅之, 安田国男. (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Sen,R.,Nagai,H.and Shimamoto.N.: "Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated by elongation factors GreA and GreB."Gene. Cells. 6(in press). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Sen,R.,Nagai,H.and Shimamoto.N.: "polymerase-arrest at the λP_R promoter during transcription initiation."J.Biol.Chem.. 275. 10899-10904 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Harada,Y.,Ohara,O.,Takatsuki,A.,Itoh,H.,Shimamoto,N.and Jr.,K.K.: "Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase."Nature. 409. 113-115 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Yamamoto,T.,Kurosawa,O.,Kabata,H.,Shimamoto,N.and Washizu,M.: "Molecular surgery of DNA based on electrostatic micromanipuration."IEEE Trans. on Indst.Appl.. 36. 1010-1017 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Matsumoto,T., Morimoto,Y.,Shibata,N.,Kinebuchi,T.,Shimamoto,N.,Tsukihara,T.and Yasuoka,N.: "Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-ray structure."J.Biochem.. 127. 329-335 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Muramatsu,H.,Hamma,K.,Yamamoto,N.,Wang,J.,Sakata-Sogawa,K.and Shimamoto,N.: "Imaging of DNA molecules by scanning near-field microscope."Mater.Sci.Eng.. C12. 29-32 (2000)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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