Study on the genes that promote bacterial colony formation

• Project/Area Number: 15K14688
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Applied microbiology
• Research Institution: The University of Tokyo
• Principal Investigator: Masaki Haruhiko 東京大学, 大学院農学生命科学研究科(農学部), 教授 (50134515)
• Project Period (FY): 2015-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• Keywords: cAMP / CRP / CyaA / コロニー / RpoS / 飢餓ストレス / VBNC / RNA-seq / RNA-Seq / 大腸菌 / 飢餓応答 / ASKA

Outline of Final Research Achievements

On exposure to cold starvation, Escherichia coli falls into a viable but non-culturable state, where colony formation is lost in spite of retaining signs of viability. We hypothesized that, during cold starvation, specific gene expressions important for colony formation are diminished and that boosting such gene functions would restrain cells from falling into the low-colony state. From the ASKA library containing all E. coli ORFs, we screened such genes restoring the diminished functions.
When seven such candidate clones are put in competition in the ability to survive against cold starvation, the winner was cpdA, encoding cAMP phosphodiesterase, suggesting that cAMP is a negative regulator in colony formation. In fact, cyaA or crp mutants kept high colony formation for 30 days in starvation. Assuming that a critical gene determining colony formation is under the control of cAMP-CRP, we are seeking it by RNA-seq, though too many genes change their expressions in response to cAMP-CRP

Research Products

• [Journal Article] Detection of diastereomer peptides as the intermediates generating D-amino acids during acid hydrolysis of peptides (2016)
  • Author(s): Miyamoto, T., Sekine, M., Ogawa, T., Hidaka, M., Watanabe, H., Homma, H., Masaki, H.
  • Journal Title: Amino Acids Volume: 48 Issue: 11 Pages: 2683-2692
  • DOI: 10.1007/s00726-016-2304-2
  • Peer Reviewed / Open Access
• [Journal Article] Transfer-messenger RNA and SmpB mediate bacteriostasis in Escherichia coli cells against tRNA cleavage. (2015)
  • Author(s): Sakai, F., Sugita,R., Chang, J.-W., Ogawa, T., Hidaka, M., Masaki, H.
  • Journal Title: Microbiology Volume: 161 Issue: 10 Pages: 2019-2028
  • DOI: 10.1099/mic.0.000144
  • Peer Reviewed
• [Journal Article] Origin of D-amino acids detected in the acid hydrolysates of purified Escherichia coli ß-galactosidase. (2015)
  • Author(s): Miyamoto, T., Sekine, M., Ogawa, T., Hidaka, M., Homma, H., Masaki, H.
  • Journal Title: J. Pharm. Biomed. Anal. Volume: 116 Pages: 105-108
  • DOI: 10.1016/j.jpba.2015.04.022
  • Peer Reviewed
• [Journal Article] Transition of serine residues to the D-form during the conversion of ovalbumin into heat stable S-ovalbumin. (2015)
  • Author(s): Miyamoto, T., Takahashi, N., Sekine, M., Ogawa, T., Hidaka, M., Homma, H., Masaki, H.
  • Journal Title: J. Pharm. Biomed. Anal. Volume: 116 Pages: 145-149
  • DOI: 10.1016/j.jpba.2015.04.030
  • Peer Reviewed
• [Presentation] 低温飢餓に曝された大腸菌のコロニー形成の制御に関わる遺伝子の解析 (2017)
  • Author(s): 西尾優宏、浅井健宏、小川哲弘、日髙真誠、正木春彦
  • Organizer: 日本農芸化学会2017年度大会
  • Place of Presentation: 京都女子大学（京都府京都市）
  • Year and Date: 2017-03-17
• [Presentation] 低温飢餓条件でのコロニー形成能の低下を抑える大腸菌遺伝子の解析解析 (2016)
  • Author(s): 福嶋凡子，西尾優宏，髙丸玲子，小川哲弘，日髙真誠，正木春彦
  • Organizer: 日本農芸化学会2016年度大会
  • Place of Presentation: 札幌市
  • Year and Date: 2016-03-27
• [Presentation] 大腸菌のコロニー形成能における遺伝子関与 (2015)
  • Author(s): 正木春彦
  • Organizer: 日本微生物生態学会第30回土浦大会
  • Place of Presentation: 土浦市
  • Year and Date: 2015-10-17
  • Int'l Joint Research / Invited
• [Presentation] コロニー形成における脂肪酸合成の重要性重要性 (2015)
  • Author(s): 納庄一樹，三井智玄，池端佑仁，小川哲弘，日髙真誠，正木春彦
  • Organizer: 日本微生物生態学会第30回土浦大会
  • Place of Presentation: 土浦市
  • Year and Date: 2015-10-17