Functional analysis of noncoding RNAs in Bacillus subtilis.

• Project/Area Number: 16380055
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Applied microbiology
• Research Institution: University of Tsukuba
• Principal Investigator: NAKAMURA Kouji University of Tsukuba, Graduate school of Life and Environmental Sciences, Associate Professor (40212097)
• Project Period (FY): 2004 – 2006
• Project Status: Completed (Fiscal Year 2006)
• Budget Amount: ¥6,900,000 (Direct Cost: ¥6,900,000); Fiscal Year 2006: ¥2,000,000 (Direct Cost: ¥2,000,000); Fiscal Year 2005: ¥2,000,000 (Direct Cost: ¥2,000,000); Fiscal Year 2004: ¥2,900,000 (Direct Cost: ¥2,900,000)
• Keywords: RNomics / noncoding RNA / riboswitch / Bacillus subtilis / Clostridium perfringens / 非翻訳型RNA / 遺伝子発現制御 / ポストゲノム解析 / 非翻訳型 / アテニュエーター / non-coding RNA / 翻訳制御 / ストレス応答 / 糖代謝 / 転写制御 / リボ制御 / BS190RNA / T-ボックス

Research Abstract

Genomes from all organisms known to date express both messenger RNAs (mRNAs) that are translated into proteins and non-messenger RNAs, which function at the RNA level and do not serve as templates for translation. Therefore, the latter is referred to as non-coding RNAs. Most of these can be defined as regulatory molecules that apparently fine-tune cellular responses to stress by integrating environmental signals into global regulation. We isolated and characterized a novel small RNA from Bacillus subtilis and called it BS203 RNA based on the length of its mature-form (203 nt). We then located the corresponding gene at the yocI-yocJ intergenic region on the B. subtilis genome. Northern blotting revealed that BS203 RNA is transcribed in vegetative growing cells and that the amount of it decreased in the middle of the vegetative phase. A computer-aided prediction of the secondary structure of BS203 RNA revealed three characteristic stem-loop structures. Despite active expression during the vegetative phase, BS203 RNA depletion did not affect the growth of knockout mutants by A phylogenetic comparison of the sequences of BS203 RNA and other Bacillus species including B. cereus and B. halodurans C-125, or with that of Clostridium perfringens suggested that the sequence is unique to Bacillus subtilis. Computational Rnomics predicted that over 100 intergenic regions encode small non-coding RNAs. We experimentally identified 8 novel small RNAs and analyzed their functions in B. subtilis.

Research Products

• [Journal Article] Bacillus subtilis genome factory : effective utilization of microbial genome information. (2007)
  • Author(s): Ara, K., Ozaki, K, Nakamura, K., Yamane, K., Sekiguchi, Ogasawara, N.
  • Journal Title: Biotechnol. Appl. Biochem. 46 Pages: 169-178
• [Journal Article] A Bacillus subtilis DEAD protein YdbR possesses ATPase, RNA Binding and RNA unwinding activities (2006)
  • Author(s): Ando, Y. and Nakamura, K.
  • Journal Title: Bioscience, Biotechnology, and Biochemistry 70 Pages: 1606-1615
  • NAID: 10018528883
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A Bacillus subtilis DEAD protein YdbR possesses ATPase, RNA binding and RNA unwinding activities. (2006)
  • Author(s): Ando, S., Nakamura, K.
  • Journal Title: Bioscience, Biotechnology, and Biochemistry 70
  • NAID: 10018528883
• [Journal Article] Expression of galectin-3, glutathione S-transferase A2 and peroxiredoxin-1 by nonypehnol-induced Caco-2 cells and reduction in transepithelial electrical resistance by nonyphenol. (2006)
  • Author(s): Nakamura, K., Isoda, H.ほか3名
  • Journal Title: Toxlcology in Vitro 20 Pages: 63-70
• [Book] RNA工学の最前線 (2005)
  • Author(s): 中村義一, 大内将司監修
  • Total Pages: 268
  • Publisher: シーエムシー出版