Molecular basis of the action of Hfq-binding small RNA inEscherichia coli.

• Project/Area Number: 21247025
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Suzuka University of Medical Science
• Principal Investigator: AIBA Hiroji 鈴鹿医療科学大学, 薬学部, 教授 (20025662)
• Project Period (FY): 2009 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥29,250,000 (Direct Cost: ¥22,500,000、Indirect Cost: ¥6,750,000); Fiscal Year 2012: ¥9,750,000 (Direct Cost: ¥7,500,000、Indirect Cost: ¥2,250,000); Fiscal Year 2011: ¥9,750,000 (Direct Cost: ¥7,500,000、Indirect Cost: ¥2,250,000); Fiscal Year 2010: ¥9,750,000 (Direct Cost: ¥7,500,000、Indirect Cost: ¥2,250,000)
• Keywords: 小分子 RNA / Hfq / サイレンシング / 転写後制御 / 大腸菌 / 小分子RNA / 翻訳抑制 / 塩基対形成 / mRNA分解 / RNaseE / 転写終結シグナル / polyU tail / RNase E / RNAオリゴ / 試験管内翻訳

Research Abstract

Molecular basis of the function of Hfq-binding sRNA has been studied using SgrS as a model. The major findings are as follows. (1) The 14 nt region within SgrS is the minimum region required for base-pairing and translational repression of ptsG mRNA. (2) The region between 711 and 750 of RNase E is sufficient for the functional interaction with Hfq to support the rapid degradation of ptsG mRNA. (3) The polyU tail of rho-independent terminator is essential for Hfq action. (4) The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3’ poly(U) tail. (5) The synthetic Hfq-binding small RNAs to knock down desired mRNAs have been successfully designed.

Research Products

• [Journal Article] The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3'polyU tail. (2012)
  • Author(s): Ishikawa,H., Otaka,H., Maki,K., Morita, T.,and Aiba, H.
  • Journal Title: RNA Volume: 18 Pages: 1062-1074
• [Journal Article] The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3’ polyU tail. (2012)
  • Author(s): Ishikawa, H., Otaka, H., Maki, K., Morita, T., and Aiba, H.
  • Journal Title: RNA Volume: 18 Pages: 1062-1074
• [Journal Article] PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action. (2011)
  • Author(s): Hironori Otaka, Hirokazu Ishikawa, Teppei Morita, and Hiroji Aiba
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 108(32) Pages: 13059-13064
  • Peer Reviewed
• [Journal Article] 原核生物の制御RNA (2011)
  • Author(s): 森田鉄兵、饗場弘二
  • Journal Title: 医学のあゆみ Volume: 238(5) Pages: 394-399
• [Journal Article] A minimal base-pairing region of a bacterialsmall RNA SgrS required for translationalrepression of ptsG mRNA. (2011)
  • Author(s): Maki, K., Morita, T., Otaka, H., and Aiba, H.
  • Journal Title: Mol. Microbiol. Volume: 76 Pages: 782-792
  • Peer Reviewed
• [Journal Article] Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs inEscherichia coli. (2011)
  • Author(s): Ikeda, Y., Yagi, M., Morita, T., and Aiba, H.
  • Journal Title: Genes Dev. Volume: 79 Pages: 419-432
  • Peer Reviewed
• [Journal Article] RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria. (2011)
  • Author(s): Morita, T. and Aiba, H.
  • Journal Title: Genes Dev. Volume: 25 Pages: 294-298
  • Peer Reviewed
• [Journal Article] PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action (2011)
  • Author(s): Hironori Otaka, Hirokazu Ishikawa, Teppei Morita, Hiroji Aiba
  • Journal Title: Proc.Natl.Acad.Sci.USA Volume: 108(32) Issue: 32 Pages: 13059-13064
  • DOI: 10.1073/pnas.1107050108
  • Peer Reviewed
• [Journal Article] A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA (2011)
  • Author(s): Maki, K., Morita, T., Otaka, H., Aiba, H.
  • Journal Title: Mol.Microbiol. Volume: 76 Pages: 782-792
  • Peer Reviewed
• [Journal Article] Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli (2011)
  • Author(s): Ikeda, Y., Yagi, M., Morita, T., Aiba, H.
  • Journal Title: Genes Dev. Volume: 79 Pages: 419-432
  • Peer Reviewed
• [Journal Article] RNase E action at a distance : degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria (2011)
  • Author(s): Morita, T., Aiba, H.
  • Journal Title: Genes Dev. Volume: 25 Pages: 294-298
  • Peer Reviewed
• [Journal Article] A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA. (2010)
  • Author(s): Maki, K., Morita, T., Otaka, H.,and Aiba, H.
  • Journal Title: Mol.Microbiol. Volume: 76 Pages: 782-792
  • Peer Reviewed
• [Journal Article] A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA (2010)
  • Author(s): Maki, K., Morita, T., Otaka, H., Aiba, H.
  • Journal Title: Mol.Microbiol. 76 Pages: 782-792
  • Peer Reviewed
• [Journal Article] Analysis of nonstop mRNA translation in the absence of tmRNA in Escherichia coli. (2009)
  • Author(s): Kuroha K., Horiguchi N., Aiba H., and Inada T.
  • Journal Title: Genes Cells Volume: 14 Pages: 739-749
  • Peer Reviewed
• [Journal Article] 歴史を遡るRNA研究. (2009)
  • Author(s): 饗場弘二
  • Journal Title: 遺伝子医学MOOK Volume: 15 Pages: 28-33
• [Journal Article] Analysis of nonstop mRNA translation in the absence of tmRNA in Escherichia coli. (2009)
  • Author(s): Kuroha K., Horiguchi N., Aiba H., Inada T.
  • Journal Title: Genes Cells 14 Pages: 739-749
  • Peer Reviewed
• [Journal Article] 歴史を遡るRNA研究 (2009)
  • Author(s): 饗場弘二
  • Journal Title: 遺伝子医学MOOK 15 Pages: 28-33
• [Presentation] Functional organization of Hfq-binding small RNAs (2013)
  • Author(s): 饗場弘二
  • Organizer: 第86回に本細菌学会総会(招待講演)
  • Place of Presentation: 幕張メッセ(千葉)
• [Presentation] Functional organization of Hfq-binding small RNAs (2013)
  • Author(s): 饗場弘二
  • Organizer: 第86回 日本細菌学会総会
  • Place of Presentation: 幕張メッセ（東京）
  • Invited
• [Presentation] Structual entity of functional hfq-binding module of bacterial base-pairing small RNAs (2012)
  • Author(s): Morita, T.,and Aiba, H.
  • Organizer: Cell Symposia Functional RNAs
  • Place of Presentation: Hotel Melia Sitges (Spain)
• [Presentation] 大腸菌小分子RNAの機能的Hfq結合モジュールの決定 (2012)
  • Author(s): 森田鉄兵、石川博一、大鷹弘紀、牧貴美香、饗場弘二
  • Organizer: 第14回日本RNA学会年会
  • Place of Presentation: 東北大学百周年記念会館(宮城)
• [Presentation] Functional organization of bacterial Hfq-binding small RNA、Furano Conference on (2012)
  • Author(s): 饗場弘二
  • Organizer: Advanced Bioregulation and RNA"、(招待講演)
  • Place of Presentation: ニュー富良野ホテル(北海道)
• [Presentation] 大腸菌小分子RNAにおける機能的Hfq結合モジュールの決定 (2012)
  • Author(s): 森田鉄兵、石川博一、大鷹弘紀、牧貴美香、饗場弘二
  • Organizer: 第9回 ２１世紀大腸菌研究会
  • Place of Presentation: 長浜ロイヤルホテル（滋賀）
• [Presentation] 大腸菌小分子RNAの機能的Hfq結合モジュールの決定 (2012)
  • Author(s): 森田鉄兵、石川博一、大鷹弘紀、牧貴美香、饗場弘二
  • Organizer: 第14回 日本RNA学会年会
  • Place of Presentation: 東北大学百周年記念会館（宮城）
• [Presentation] Structural entity of functional hfq-binding module of bacterial base-piaring small rnas (2012)
  • Author(s): 森田鉄兵、饗場弘二
  • Organizer: Cell Symposia Functional RNAs
  • Place of Presentation: Hotel Melia Sitges (Spain)
• [Presentation] Functional organization of bacterial Hfq-biading small RNA (2012)
  • Author(s): 饗場弘二
  • Organizer: Furano Conference on "Advanced Bioregulation and RNA"
  • Place of Presentation: ニュー富良野ホテル(北海道)
• [Presentation] PolyU tail of rho-independent terminator of bacterial small RNAs acts as an essential Hfu-bindine site for riboreeulation (2011)
  • Author(s): 饗場弘二
  • Organizer: ASM Conference on Regulating with RNA in Bacteria
  • Place of Presentation: San Juan, Puerto Rico
  • Year and Date: 2011-03-08
• [Presentation] Functional organization of Hfq-binding regulatory RNA、IUMS2011 The Unlimited World Microbes (2011)
  • Author(s): 饗場弘二
  • Organizer: 国際微生物学連合2011、(招待講演)
  • Place of Presentation: 札幌コンベンションセンター(北海道)
• [Presentation] Poly tail of rho-independent terminator of bacterial small RNA acts an essentialHfq-binding site for riboregulation. The 16thAnnual meeting of the RNA society (2011)
  • Author(s): 大鷹弘紀、石川博一、森田鉄兵、饗場弘二
  • Organizer: 第13回日本RNA学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] Identification of Hfq binding sites on RNase E in E. coli. (2011)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、金井昭夫、饗場弘二
  • Organizer: The 16 Annual meeting of the RNA society, 第13回日本 RNA 学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] Both polyU tail and the upstream region of rho-independent terminator are required for the functional interaction of SgrS with Hfq. (2011)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: The 16^<th> Annual meeting of the RNA society, 第13回日本RNA学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] Generation of functional E. coli DicF small RNA and the role of the 3' polyU stretch in Hfq binding. (2011)
  • Author(s): 森田鉄兵、飯田芳文、饗場弘二
  • Organizer: The 16th Annual meeting of the RNA society, 第13回日本 RNA 学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] PolyU tail of rho-independent terminator of bacterial small RNAs acts as an essential Hfq-binding site for riboregulation. (2011)
  • Author(s): 饗場弘二
  • Organizer: ASM Conference on Regulating with RNA in Bacteria.(招待講演)
  • Place of Presentation: San Juan (Puerto Rico)
• [Presentation] Functional organization of Hfq-binding regulatory RNA (2011)
  • Author(s): 饗場弘二
  • Organizer: IUMS2011 The Unlimited world Microbes-国際微生物学連合2011-
  • Place of Presentation: 札幌コンベンションセンター(北海道)
• [Presentation] 遺伝子発現制御機構における大腸菌低分子RNA3'末端ポリU配列の役割 (2011)
  • Author(s): 大鷹弘紀、石川博一、森田鉄兵、饗場弘二
  • Organizer: 第8回21世紀大腸菌研究会
  • Place of Presentation: ホテル木曽路(長野)
• [Presentation] 大腸菌小分子RNAのHfq作用領域の解析:塩基対形成領域と転写終結領域間の役割 (2011)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: 第8回21世紀大腸菌研究会
  • Place of Presentation: ホテル木曽路(長野)
• [Presentation] Poly tail of rho-independent terminator of bacterial small RNA acts an essential Hfq-binding site for riboregulation (2011)
  • Author(s): 大鷹弘紀、石川博一、森田鉄兵、饗場弘二
  • Organizer: The 16^<th> Annual meeting of the RNA society,第13回日本RNA学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] Identification of Hfq binding sites on RNase E in E. coli (2011)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、金井昭夫、饗場弘二
  • Organizer: The 16^<th> Annual meeting of the RNA society,第13回日本RNA学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] Both polyU tail and the upstream region of rho-independent terminator are required for the functional interaction of SgrS with Hfq (2011)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: The 16^<th> Annual meeting of the RNA society,第13回日本RNA学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] Generation of functional E. coli DicF small RNA and the role of the 3'polyU stretch in Hfq binding (2011)
  • Author(s): 森田鉄兵、飯田芳文、饗場弘二
  • Organizer: The 16^<th> Annual meeting of the RNA society,第13回日本RNA学会総会合同会
  • Place of Presentation: 京都国際会議場(京都)
• [Presentation] 遺伝子発現制御機構における大腸菌低分子RNA3'末端ポリU配列の役割 (2011)
  • Author(s): 大鷹弘紀、石川博一、森田鉄兵、饗場弘二
  • Organizer: 第5回細菌学若手コロッセウム
  • Place of Presentation: 桂浜荘(高知)
• [Presentation] 大腸菌小分子RNAのHfq作用領域の解析:塩基対形成領域と転写終結領域間の役割 (2011)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: 第5回細菌学若手コロッセウム
  • Place of Presentation: 桂浜荘(高知)
• [Presentation] 遺伝子発現制御機構における大腸菌低分子RNA3'末端ポリU配列の役割 (2011)
  • Author(s): 大鷹弘紀、石川博一、森田鉄兵、饗場弘二
  • Organizer: RNAフロンティアミーティング2011
  • Place of Presentation: あいち健康プラザ(愛知)
• [Presentation] 大腸菌小分子RNAの3'末端の役割 (2011)
  • Author(s): 森田鉄兵、大鷹弘紀、石川博一、饗場弘二
  • Organizer: 第5回日本ゲノム微生物学会若手の会
  • Place of Presentation: ろうきん研修所富士センター(静岡)
• [Presentation] Implication of spacer length between base-pairing and Hfq-binding region in bacterial small RNA function. (2010)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: The 11th Asian and Oceanian Conference on Transcription.
  • Place of Presentation: 沖縄県国頭郡
• [Presentation] 大腸菌RNase E/Hfqの結合領域の同定 (2010)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、饗場弘二
  • Organizer: 第7回21世紀大腸菌研究会
  • Place of Presentation: 熊本県阿蘇郡
• [Presentation] 大腸菌sRNAであるSgrSの機能領域の解析 (2010)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: 第7回21世紀大腸菌研究会
  • Place of Presentation: 熊本県阿蘇郡
• [Presentation] Identification of Hfq binding sites onRNase E in E.coli (2010)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、饗場弘二
  • Organizer: The 11^<th> Asian and Oceanian Conference on Transcription
  • Place of Presentation: 沖縄県国頭郡
• [Presentation] Implication of spacer length between base-pairing and Hfq-binding region in bacterial small RNA function (2010)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: The 11^<th> Asian and Oceanian Conference on Transcription
  • Place of Presentation: 沖縄県国頭郡
• [Presentation] SgrS3'末端のポリU配列はRNA抑制機能に重要な役割を果たす (2010)
  • Author(s): 大鷹弘紀、石川博一、森田鉄兵、饗場弘二
  • Organizer: 第12回日本RNA学会年会
  • Place of Presentation: 東京都千代田区
• [Presentation] 大腸菌小分子RNAの作用機構の解析:塩基対形成領域とHfq結合領域間の距離の重要性 (2010)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: 第12回日本RNA学会年会
  • Place of Presentation: 東京都千代田区
• [Presentation] Heterogeneity of RNA degradosome of Escherichia coli : RNase E forms several distinct complexes with partner proteins (2010)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、饗場弘二
  • Organizer: International symposium on Biodiversity Sciences 2010
  • Place of Presentation: 愛知県名古屋市
• [Presentation] Implication of spacer length between base-pairing and Hfq-binding region in bacterial small RNA function (2010)
  • Author(s): 石川博一、大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: International symposium on Biodiversity Sciences 2010
  • Place of Presentation: 愛知県名古屋市
• [Presentation] The 3' terminator poly-U tract of SgrS plays a crucial role in Hfq-dependent gene silencing (2010)
  • Author(s): 大鷹弘紀、石川博一、森田鉄兵、饗場弘二
  • Organizer: International symposium on Biodiversity Sciences 2010
  • Place of Presentation: 愛知県名古屋市
• [Presentation] 大腸菌小分子RNAであるSgrSの機能解析 (2010)
  • Author(s): 森田鉄兵、牧貴美香、大鷹弘紀、石川博一、饗場弘二
  • Organizer: 第4回細菌学・若手コロッセウム
  • Place of Presentation: 修善寺(静岡県伊豆市)
• [Presentation] 大腸菌小分子RNAであるSgrSの機能解析 (2010)
  • Author(s): 森田鉄兵、牧貴美香、大鷹弘紀、.石川博一、饗場弘二
  • Organizer: 第4回日本ゲノム微生物学会若手の会
  • Place of Presentation: 兵庫県神戸市
• [Presentation] Identification of Hfq binding sites on RNase E in E.coli (2010)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、饗場弘二
  • Organizer: 第33回日本分子生物学会年会
  • Place of Presentation: 兵庫県神戸市
• [Presentation] ptsG mRNAの翻訳抑制に重要なSgrS最小領域の同定 (2009)
  • Author(s): 牧貴美香、森田鉄兵、饗場弘二
  • Organizer: 第46回日本細菌学会中部支部会
  • Place of Presentation: 名城大学(愛知県名古屋市)
  • Year and Date: 2009-10-23
• [Presentation] 大腸菌RNase E/Hfqの結合領域の同定 (2009)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、饗場弘二
  • Organizer: 第46回日本細菌学会中部支部会
  • Place of Presentation: 名城大学(愛知県名古屋市)
  • Year and Date: 2009-10-23
• [Presentation] 合成RNAによるptsG mRNAの翻訳抑制 (2009)
  • Author(s): 牧貴美香、森田鉄兵、饗場弘二
  • Organizer: 第11回日本RNA学会年会
  • Place of Presentation: 朱鷺メッセ(新潟)
  • Year and Date: 2009-07-27
• [Presentation] 遺伝子発現抑制機能におけるSgrS3'末端領域の役割 (2009)
  • Author(s): 大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: 第11回日本RNA学会年会
  • Place of Presentation: 朱鷺メッセ(新潟)
  • Year and Date: 2009-07-27
• [Presentation] 合成RNAによるptsG mRNAの翻訳抑制 (2009)
  • Author(s): 牧貴美香、森田鉄兵、饗場弘二
  • Organizer: 第11回日本RNA学会年会
  • Place of Presentation: 朱鷺メッセ(新潟県新潟市)
  • Year and Date: 2009-07-27
• [Presentation] 遺伝子発現抑制機能におけるSgrS3'末端領域の役割 (2009)
  • Author(s): 大鷹弘紀、森田鉄兵、饗場弘二
  • Organizer: 第11回日本RNA学会年会
  • Place of Presentation: 朱鷺メッセ(新潟県新潟市)
  • Year and Date: 2009-07-27
• [Presentation] sRNAによるポリシストロニックなmRNAの発現抑制の解析 (2009)
  • Author(s): 石川博一、森田鉄兵、饗場弘二
  • Organizer: 第11回日本RNA学会年会
  • Place of Presentation: 朱鷺メッセ(新潟県新潟市)
  • Year and Date: 2009-07-27
• [Presentation] 大腸菌RNase E/Hfqの結合領域の同定 (2009)
  • Author(s): 池田幸樹、八木美江子、森田鉄兵、饗場弘二
  • Organizer: 第11回日本RNA学会年会
  • Place of Presentation: 朱鷺メッセ(新潟県新潟市)
  • Year and Date: 2009-07-27
• [Presentation] 遺伝子発現抑制機能におけるSgrS3'末端領域の重要性の解析 (2009)
  • Author(s): 大鷹弘紀、森田鉄兵、本間道夫、饗場弘二
  • Organizer: 第6回21世紀大腸菌研究会
  • Place of Presentation: KKRホテル熱海
  • Year and Date: 2009-06-11
• [Presentation] sRNAによるポリシストロニックなmRNAの発現抑制の解析 (2009)
  • Author(s): 石川博一、森田鉄兵、本間道夫、饗場弘二
  • Organizer: 第6回21世紀大腸菌研究会
  • Place of Presentation: KKRホテル熱海
  • Year and Date: 2009-06-11