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Microbial production of artificial and functional RNAs and the use of the RNA producing microorganism

Research Project

Project/Area Number 25252017
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied microbiology
Research InstitutionToyohashi University of Technology

Principal Investigator

KIKUCHI Yo  豊橋技術科学大学, 研究推進アドミニストレーションセンター, 特命教授 (40273320)

Co-Investigator(Kenkyū-buntansha) UMEKAGE SO  豊橋技術科学大学, 大学院工学研究科, 講師 (30419436)
OHYAMA TAKASHI  早稲田大学, 教育・総合科学学術院, 教授 (60268513)
AOKI TAKASHI  早稲田大学, ナノ・ライフ創新研究機構, 招聘研究員 (00051805)
Project Period (FY) 2013-10-21 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥44,070,000 (Direct Cost: ¥33,900,000、Indirect Cost: ¥10,170,000)
Fiscal Year 2015: ¥14,950,000 (Direct Cost: ¥11,500,000、Indirect Cost: ¥3,450,000)
Fiscal Year 2014: ¥16,250,000 (Direct Cost: ¥12,500,000、Indirect Cost: ¥3,750,000)
Fiscal Year 2013: ¥12,870,000 (Direct Cost: ¥9,900,000、Indirect Cost: ¥2,970,000)
Keywords発酵 / 核酸 / 応用微生物学 / RNA生産 / RNAドラッグ / 細胞外核酸 / 光合成細菌 / 機能性RNA
Outline of Final Research Achievements

The purpose of this study is the development of an extracellular functional RNA production system using the marine bacterium Rhodovulum sulfidophilum. We had already succeeded a production of an RNA aptamer. In the present study, first, we could show the extracellular production of short hairpin RNAs those are known as strong inhibitors of gene expression. We also proceeded to basic study of this bacterium which is important for the safety assurance of this bacterium in the RNA drugs production in future. We discovered that this bacterium has the quorum sensing system and that the bacterium produces a new type of auto-inducer in the system. We also discovered the gene transfer agent of this bacterium which was thought to be a natural agent for horizontal gene transfer. Also, the total genome sequence of this bacterium has been completed using the next generation sequencer.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (42 results)

All 2016 2015 2014 2013 Other

All Journal Article (13 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 13 results,  Open Access: 13 results,  Acknowledgement Compliant: 7 results) Presentation (23 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results) Book (1 results) Remarks (3 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] Complete genome sequence of cyanobacterium Geminocystis sp. NIES-3708, which performs type II complementary chromatic acclimation2015

    • Author(s)
      Yuu Hirose, Mitsunori Katayama, Yoshiyuki Ohtsubo, Naomi Misawa, Erica Iioka, Wataru Suda, Kenshiro Oshima, Mitsumasa Hanaoka, Kan Tanaka, Toshihiko Eki, Masahiko Ikeuchi, Yo Kikuchi, Makoto Ishida, and Masahira Hattori
    • Journal Title

      Genome Announcement

      Volume: 3 Issue: 3 Pages: 1-2

    • DOI

      10.1128/genomea.00357-15

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Complete genome sequence of cyanobacterium Geminocystis sp. NIES-3709 that harbors phycoerythrin-rich phycobilisome2015

    • Author(s)
      Yuu Hirose, Mitsunori Katayama, Yoshiyuki Ohtsubo, Naomi Misawa, Erica Iioka, Wataru Suda, Kenshiro Oshima, Mitsumasa Hanaoka, Kan Tanaka, Toshihiko Eki, Masahiko Ikeuchi, Yo Kikuchi, Makoto Ishida, and Masahira Hattori
    • Journal Title

      Genome Announcement

      Volume: 3 Issue: 2 Pages: 1-2

    • DOI

      10.1128/genomea.00385-15

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Complete Genome Sequence of Rhodovulum sulfidophilum DSM 2351, an Extracellular Nucleic Acid-Producing Bacterium2015

    • Author(s)
      Nagao N, Hirose Y, Misawa N, Ohtsubo Y, Umekage S, Kikuchi Y.
    • Journal Title

      Genome Annoucements

      Volume: 3(2) e00388-15 Issue: 2 Pages: 1-2

    • DOI

      10.1128/genomea.00388-15

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Improved bioassay for detecting autoinducer of Rhodovulum sulfidophilum2015

    • Author(s)
      Terada, T., Kikuchi, Y., and Umekage, S.
    • Journal Title

      AIP Conference Proceedings

      Volume: 1649 Pages: 67-70

    • DOI

      10.1063/1.4913546

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Abnormal rapid non-linear RNA production induced by T7 RNA polymerase in the absence of an exogenous DNA template2015

    • Author(s)
      Kakimoto, Y. Fujinuma, A. Fujita, S. Kikuchi, Y. and Umekage S.
    • Journal Title

      AIP Conf. Proc.

      Volume: 1649 Pages: 113-115

    • DOI

      10.1063/1.4913554

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Evidence for RNA template-directed elongation2015

    • Author(s)
      Kakimoto, Y. Fujinuma, A. Sakamoto, T. Kikuchi, Y. and Umekage S.
    • Journal Title

      AIP Conf. Proc.

      Volume: 1649 Pages: 116-120

    • DOI

      10.1063/1.4913555

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Functional analyses of carnivorous plant-specific amino acid residues in S-like ribonucleases2015

    • Author(s)
      Arai, N., Nishimura, E., Kikuchi, Y., and Ohyama, T.
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 465 Issue: 1 Pages: 108-112

    • DOI

      10.1016/j.bbrc.2015.07.139

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The gene transfer agent-like particle of the marine phototrophic bacterium Rhodovulum sulfidophilum2015

    • Author(s)
      Nagao, N., Yamamoto, J., Komatsu, H., Suzuki, H., Hirose, Y., Umekage, S., Ohyama, T., and Kikuchi, Y.
    • Journal Title

      Biochemistry and Biophysics Reports

      Volume: 4 Pages: 369-374

    • DOI

      10.1016/j.bbrep.2015.11.002

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Complete genome sequence of cyanobacterium Geminocystis sp. NIES-3708, which performs type II complementary chromatic acclimation2015

    • Author(s)
      Hirose, Y., Katayama, M., Ohtsubo, Y., Misawa, N., Iioka, E., Suda, W., Oshima, K., Hanaoka, M., Tanaka, K., Eki, T., Ikeuchi, M., Kikuchi, Y., Ishida, M., Hattori, M.
    • Journal Title

      Genome Announcements

      Volume: 未定

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Complete genome sequence of cyanobacterium Geminocystis sp. NIES-3709 that harbors phycoerythrin-rich phycobilisome2015

    • Author(s)
      Hirose, Y., Katayama, M., Ohtsubo, Y., Misawa, N., Iioka, E., Suda, W., Oshima, K., Hanaoka, M., Tanaka, K., Eki, T., Ikeuchi, M., Kikuchi, Y., Ishida, M., Hattori, M.
    • Journal Title

      Genome Announcements

      Volume: 未定

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Complete genome sequence of Rhodovulum sulfidophilum DSM 2351, an extracellular nucleic acids producing bacterium2015

    • Author(s)
      Nagao, N., Hirose, Y., Misawa, N., Ohtsubo, Y., Umekage, S., Kikuchi, Y
    • Journal Title

      Genome Announcements

      Volume: 未定

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Short hairpin RNAs of designed sequences can be extracellularly produced by the marine bacterium <i>Rhodovulum sulfidophilum</i>2014

    • Author(s)
      Nagao, N., Suzuki, H., Numano, R., Umekage, S., Kikuchi, Y.
    • Journal Title

      The Journal of General and Applied Microbiology

      Volume: 60 Issue: 6 Pages: 222-226

    • DOI

      10.2323/jgam.60.222

    • NAID

      130004802274

    • ISSN
      0022-1260, 1349-8037
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Melanopsin resets circadian rhythms in cells by inducing clock gene Period12013

    • Author(s)
      Shuhei Yamashita, Tomoe Uehara, Minako Matsuo, Yo Kikuchi and Rika Numano
    • Journal Title

      AIP Conference Proceedings

      Volume: 1585 Pages: 24-25

    • DOI

      10.1063/1.4866616

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Emergence of RNA self-replication cycle through RNA template-directed RNA polymerisation by DNA dependent RNA polymerase2015

    • Author(s)
      Kakimoto Y., Fujinuma A., Kikuchi Y. and Umekage S.
    • Organizer
      The International Chemical Congress of Pacific Basin Societies 2015
    • Place of Presentation
      Honolulu, USA(アメリカ合衆国)
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Agarose binding RNA aptamer2015

    • Author(s)
      Umekage S. and Kikuchi Y.
    • Organizer
      The International Chemical Congress of Pacific Basin Societies 2015
    • Place of Presentation
      Honolulu, USA(アメリカ合衆国)
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RNAの凝集化が引き起こすRNA安定化によるRNAワー ルド仮説の補強2015

    • Author(s)
      梅影創、菊池洋
    • Organizer
      第38回日本分子生物学会年会(BMB 2015)
    • Place of Presentation
      神戸
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] RNA分解酵素耐性を示す天然型RNA配列の解析2015

    • Author(s)
      藤沼輝、柿本恭宏、坂本泰一、菊池洋、梅影創
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2015-07-15
    • Related Report
      2015 Annual Research Report
  • [Presentation] DNA鋳型依存的RNAポリメラーゼによるRNA鋳型依存的なRNA合成反応は急激なRNAの増幅を引き起こす2015

    • Author(s)
      柿本恭宏、藤沼輝、菊池洋、梅影創
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2015-07-15
    • Related Report
      2015 Annual Research Report
  • [Presentation] 環状RNAと直鎖状 RNA を分離する方法2015

    • Author(s)
      黒木 大海、菊池 洋、梅影 創
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2015-07-15
    • Related Report
      2015 Annual Research Report
  • [Presentation] Enhanced floc forming mutants of Rhodovulum sulfidophilum obtained by UV mutagenesis2015

    • Author(s)
      Umekage, S., Noda,A., and Kikuchi, Y.
    • Organizer
      FEMS 2015
    • Place of Presentation
      Maastricht, The Netherlands(オランダ)
    • Year and Date
      2015-06-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 改良型バイオアッセイ法を用いたRhodovulum sulfidophilumのN-アシルホモセリンラクトン(AHL)生産の検証2015

    • Author(s)
      寺田岳史、沖見卓哉、菊池 洋、梅影 創
    • Organizer
      日本農芸化学会2015年度大会
    • Place of Presentation
      岡山
    • Year and Date
      2015-03-26 – 2015-03-29
    • Related Report
      2014 Annual Research Report
  • [Presentation] Rhodovulum sulfidophilum T7 RNAポリメラーゼ発現株を用いた細胞外RNA生産系2015

    • Author(s)
      長尾信義、米川千夏、梅影 創、菊池 洋
    • Organizer
      日本農芸化学会2015年度大会
    • Place of Presentation
      岡山
    • Year and Date
      2015-03-26 – 2015-03-29
    • Related Report
      2014 Annual Research Report
  • [Presentation] 紅色光合成細菌 Rhodovulum sulfidophilum DSM1374株および DSM2351株のゲノム配列解析とその比較2015

    • Author(s)
      長尾信義、広瀬 侑、梅影創、菊池 洋
    • Organizer
      第9回日本ゲノム微生物学会年会
    • Place of Presentation
      神戸
    • Year and Date
      2015-03-06 – 2015-03-08
    • Related Report
      2014 Annual Research Report
  • [Presentation] Strong floc forming mutants of Rhodovulum sulfidophilum obtained by UV mutagenesis2014

    • Author(s)
      Noda, A, Kikuchi, Y., Umekage, S
    • Organizer
      The Irago Conference 2014
    • Place of Presentation
      つくば
    • Year and Date
      2014-11-06 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] Improved bioassay for detecting autoinducers of Rhodovulum sulfidophilum2014

    • Author(s)
      Terada, T., Kikuchi, Y., Umekage, S.
    • Organizer
      The Irago Conference 2014
    • Place of Presentation
      つくば
    • Year and Date
      2014-11-06 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] Pseudoknot folding is essential for agarose aptamer binding2014

    • Author(s)
      Koto, T., Sakashita, J., Kikuchi, Y., Umekage, S.
    • Organizer
      The Irago Conference 2014
    • Place of Presentation
      つくば
    • Year and Date
      2014-11-06 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] Abnormal rapid non-linear RNA production by T7 RNA polymerase in the absence of a DNA template2014

    • Author(s)
      Kakimoto, Y., Fujinuma, A., Fujita, S., Kikuchi, Y., Umekage, S.
    • Organizer
      The Irago Conference 2014
    • Place of Presentation
      つくば
    • Year and Date
      2014-11-06 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] Evidence for RNA template-directed elongation induced by binding T7 RNA polymerase2014

    • Author(s)
      Kakimoto, Y., Fujinuma, A., Sakamoto, T., Kikuchi, Y., Umekage, S.
    • Organizer
      The Irago Conference 2014
    • Place of Presentation
      つくば
    • Year and Date
      2014-11-06 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] Utilization of RNase III activity for functional RNA production by a marinephototrophic bacterium, Rhodovulum sulfidophilum2014

    • Author(s)
      Nagao, N., Umekage, S., and Kikuchi, Y.
    • Organizer
      The Irago Conference 2014
    • Place of Presentation
      つくば
    • Year and Date
      2014-11-06 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] 改良型バイオアッセイ法による海洋性光合成細菌 Rhodovulum sulfidophilum の N-acylhomoserine lactone(AHL)生産の検証2014

    • Author(s)
      寺田岳史、沖見卓哉、梅影 創、菊池 洋
    • Organizer
      環境微生物系学会合同大会
    • Place of Presentation
      浜松
    • Year and Date
      2014-10-21 – 2014-10-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] 紅色光合成細菌Rhodovulum sulfidophilumのGTA (gene transfer agent)の解析2014

    • Author(s)
      1)山本絢也、長尾信義、、広瀬 侑、梅影 創、菊池 洋
    • Organizer
      第8回日本ゲノム微生物学会 若手の会
    • Place of Presentation
      小山(静岡)
    • Year and Date
      2014-09-28 – 2014-09-29
    • Related Report
      2014 Annual Research Report
  • [Presentation] アガロースに結合するRNAアプタマーの機能解析2014

    • Author(s)
      向當健司、坂下 淳、梅影 創、菊池 洋
    • Organizer
      第16回日本RNA学会年会(名古屋)
    • Place of Presentation
      名古屋
    • Year and Date
      2014-07-23 – 2014-07-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] 夢の薬RNAの微生物生産と豊橋技科大の先端農業・バイオリサーチセンター2014

    • Author(s)
      菊池 洋
    • Organizer
      中部大学開学50周年記念夢構想事業 中部大学応用生物学部第2回夢構想フォーラム「バイオ支援型持続可能社会の実現に向けて」
    • Place of Presentation
      春日井(愛知)
    • Year and Date
      2014-06-28
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 夢の薬 RNA を微生物に作らせる2014

    • Author(s)
      菊池 洋
    • Organizer
      第55回日本放線菌学会学術講演会
    • Place of Presentation
      東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Bacillus cereusu細菌を標的としたDNAアプタマーの構築2014

    • Author(s)
      海谷慎一、梅影 創、菊池 洋
    • Organizer
      日本農芸化学会2014年度大会
    • Place of Presentation
      川崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] Melanopsin resets circadian rhythms in cells by inducing clock gene period12013

    • Author(s)
      Yamashita, S, Uehara, T., Matsuo, M., Kikuchi, Y., Numano, R.
    • Organizer
      Irago Conference
    • Place of Presentation
      田原(愛知県)
    • Related Report
      2013 Annual Research Report
  • [Book] ベーシックマスター分子生物学 改訂2版2013

    • Author(s)
      菊池 洋 他 (東中川徹 他編)
    • Total Pages
      438
    • Publisher
      オーム社
    • Related Report
      2013 Annual Research Report
  • [Remarks] 豊橋技術科学大学教員の研究紹介

    • URL

      http://www.tut.ac.jp/university/faculty/rac/362.html

    • Related Report
      2015 Annual Research Report
  • [Remarks] 豊橋技術科学大学 教員紹介

    • URL

      http://www.tut.ac.jp/university/faculty/rac/362.html

    • Related Report
      2014 Annual Research Report
  • [Remarks] 研究紹介 菊池洋

    • URL

      http://www.tut.ac.jp/teach/main.php?mode=detail&article=362

    • Related Report
      2013 Annual Research Report
  • [Patent(Industrial Property Rights)] 偽環状二重鎖ポリヌクレオチドと、それを用いた遺伝子発現阻害剤2016

    • Inventor(s)
      梅影創、菊池洋
    • Industrial Property Rights Holder
      豊橋技術科学大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2016-028988
    • Filing Date
      2016-02-03
    • Related Report
      2015 Annual Research Report
  • [Patent(Industrial Property Rights)] RNA分子にヌクレアーゼ耐性能を付与する方法、ヌクレアーゼ耐性能を有するキメラRNA分子2013

    • Inventor(s)
      梅影創、藤田隼輔、藤沼輝、菊池洋
    • Industrial Property Rights Holder
      国立大学法人豊橋技術科学大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2013-256425
    • Filing Date
      2013-12-11
    • Related Report
      2013 Annual Research Report

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Published: 2013-10-24   Modified: 2019-07-29  

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