Analysis of cellular network during the death phase of stationary phase.

2012 Fiscal Year Final Research Report

• Project/Area Number: 22241050
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: System genome science
• Research Institution: Nara Institute of Science and Technology
• Principal Investigator: MORI Hirotada 奈良先端科学技術大学院大学, バイオサイエンス研究科, 教授 (90182203)
• Co-Investigator(Kenkyū-buntansha): YAMADA Mamoru 山口大学, 医学研究科, 教授 (30174741) ; MATSUNO Hiroshi 山口大学, 理工学研究科, 教授 (10181744) ; MAKI Yasushi 大阪医科大学, 医学部, 講師 (60401733)
• Project Period (FY): 2010 – 2012
• Keywords: molecular bar-code / single gene deletion library / stationary phase / population dynamics / cell death

Research Abstract

Organisms in nature spend most of their life time instationary growing phase. Cellular metabolisms in stationary phase are largely different to those in log phase. During long-term stationary phase, organisms might survive against variety of stresses, such as starvation of nutrient. To clear the physiological network during stationary phase, we have constructed the comprehensive bar-coded single gene deletion library of E. coli. Using this new resource, we have developed the method to quantitatively monitor the population dynamics of each of deletion strains during long-term stationary phase.

Research Products

• [Journal Article] The tRNA Thiolation Pathway Modulates the Intracellular Redox State in Escherichia coli. (2013)
  • Author(s): NakayashikiT., Saito N., Takeuchi R., Kadokura H., Nakahigashi K., Wanner B. L., & Mori H.
  • Journal Title: J Bacteriol Volume: 195 Pages: 2039-2049
  • DOI: DOI:10.1128/JB.02180-12
  • Peer Reviewed
• [Journal Article] Genome-wide screening with hydroxyurea reveals a link between nonessential ribosomal proteins and reactive oxygen species production (2013)
  • Author(s): NakayashikiT. & Mori H
  • Journal Title: J Bacteriol Volume: 195 Pages: 1226-1235
  • DOI: DOI:10.1128/JB.02145-12
  • Peer Reviewed
• [Journal Article] Crucial Roles of MicA and RybB as Vital Factors for sigma-Dependent Cell Lysis in Escherichia coli Long-Term Stationary Phase (2013)
  • Author(s): Nagamitsu H., Murata M., Kosaka T., Kawaguchi J., Mori H., & Yamada M
  • Journal Title: J Mol Microbiol Biotechnol Volume: 23 Pages: 227-232
  • DOI: DOI:10.1159/000350370
  • Peer Reviewed
• [Journal Article] Glycogen is the primary source of glucose during the lag phase of E. coli proliferation (2012)
  • Author(s): Yamamotoya T., Dose H., Tian Z., Faure A., Toya Y., Honma M., Igarashi K., Nakahigashi K., Soga T., Mori H., & Matsuno H
  • Journal Title: Biochim Biophys Acta Volume: 1824 Pages: 1442-1448
  • DOI: DOI:10.1016/j.bbapap.2012.06.010
  • Peer Reviewed
• [Journal Article] Investigating the effects of perturbations to pgi and enogene expression on central carbon metabolism in Escherichia coli using (13)C metabolic flux analysis (2012)
  • Author(s): Usui Y., Hirasawa T., Furusawa C., Shirai T., Yamamoto N., Mori H., & Shimizu H
  • Journal Title: Microb Cell Fact Volume: 11:87 Pages: 1475-2859-11-87
  • DOI: DOI:10.1186/1475-2859-11-87
  • Peer Reviewed
• [Journal Article] Novel pathway directed by sigma E to cause cell lysis in Escherichia coli (2012)
  • Author(s): Murata M., Noor R., Nagamitsu H., Tanaka S., & Yamada M
  • Journal Title: Genes to cells : devoted to molecular & cellular mechanisms Volume: 17 Pages: 234-247
  • DOI: DOI:10.1111/j.1365-2443.2012.01585.x
  • Peer Reviewed
• [Journal Article] Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli (2011)
  • Author(s): Shinhara A., Matsui M., Hiraoka K., Nomura W., Hirano R., Nakahigashi K., Tomita M., Mori H., & Kanai A
  • Journal Title: BMC Genomics Volume: 12 Pages: 428
  • DOI: DOI:10.1186/1471-2164-12-428
  • Peer Reviewed
• [Journal Article] Environmental dependency of gene knockouts on phenotype microarray analysis in Escherichia coli (2010)
  • Author(s): Tohsato Y., Baba T., Mazaki Y., Ito M., Wanner B. L., & Mori H.
  • Journal Title: J Bioinform Comput Biol 8 Suppl Volume: 1 Pages: 83-99
  • DOI: DOI:S021972001000521X
  • Peer Reviewed
• [Presentation] FunctionalProfiling of the E. coli Genes in Long-Term Stationary Phase (2012)
  • Author(s): Y. Otsuka, R. Takeuchi, H. Dose, H-C. Huang, H-F. Juan, M. Yamada, H. Matsuno, B. L. Wanner, H. Mori1
  • Organizer: ASM meeting San Francisco
  • Place of Presentation: CA
  • Year and Date: 20120616-19
• [Presentation] Keio collectionを使ったHydroxyurea感受性株の解析 (2012)
  • Author(s): 中屋敷徹、森浩禎
  • Organizer: 第6回日本ゲノム微生物学会年会
  • Place of Presentation: 立教大学池袋キャンパス
  • Year and Date: 20120310-12
• [Presentation] Functional Profiling of the E. coli (2012)
  • Author(s): Y. Otsuka1, R. Takeuchi1, H. Dose1, H-C. Huang2, H-F. Juan3, M. Yamada4, H. Matsuno5, B. L. Wanner6, H. Mori1.
  • Organizer: Genes in Long-Term Stationary Phase 第6回日本ゲノム微生物学会年会
  • Place of Presentation: 立教大学池袋キャンパス.
  • Year and Date: 20120310-12
• [Presentation] Keio collection を使ったHydroxyurea 感受性株の解析 (2012)
  • Author(s): 中屋敷徹、森浩禎
  • Organizer: 第6回日本ゲノム微生物学会年会
  • Place of Presentation: 東京
  • Year and Date: 20120000
• [Presentation] Functional Profiling of the E. coli Genes in Long-Term Stationary Phase (2012)
  • Author(s): Y. Otsuka1, R. Takeuchi1, H.Dose1, H-C. Huang2,H-F. Juan3, M. Yamada4, H. Matsuno5, B. L. Wanner6, H.Mori1
  • Organizer: 第6回日本ゲノム微生物学会
  • Place of Presentation: 東京
  • Year and Date: 20120000
• [Presentation] Towards complete understanding of cellularnetwork in Escherichia coli K-12 (2012)
  • Author(s): Hirotada Mori
  • Organizer: School of Biological Science
  • Place of Presentation: University of Reading, UK
  • Year and Date: 20120000
• [Presentation] バクテリア接合伝達のゲノム操作への可能性 (2012)
  • Author(s): 森浩禎
  • Organizer: 農芸化学会シンポジウム
  • Place of Presentation: 京都
  • Year and Date: 20120000
• [Presentation] 次世代型シーケンサーがもたらす大腸菌像;「大量シーケンスと網羅解析から、モデル生物大腸菌を見直す」 (2012)
  • Author(s): 森浩禎
  • Organizer: 第6回日本ゲノム微生物学会年会ワークショップ
  • Place of Presentation: 東京
  • Year and Date: 20120000
• [Presentation] Towards complete understanding of cellular network in Escherichia coli K-12 (2011)
  • Author(s): Hirotada Mori
  • Organizer: School of Biological Science
  • Place of Presentation: University of Cambridge, UK
  • Year and Date: 20110000
• [Presentation] ゲノム微生物学から遺伝学へのインパクト (2011)
  • Author(s): 森浩禎
  • Organizer: 日本遺伝学会
  • Place of Presentation: 京都大学, 京都
  • Year and Date: 20110000
• [Presentation] Perspective of network biology in Escherichia coli (2011)
  • Author(s): Hirotada Mori
  • Organizer: UK-JP systems biology symposium
  • Place of Presentation: University of Surrey, UK
  • Year and Date: 20110000
• [Presentation] Towards complete understanding of cellular systems (2011)
  • Author(s): Hirotada Mori
  • Organizer: 5th International IECAconference
  • Place of Presentation: Mexico
  • Year and Date: 20110000
• [Presentation] Towards complete understanding of cellular systems (2011)
  • Author(s): 森浩禎
  • Organizer: モデル生物丸ごと一匹シンポジウム
  • Place of Presentation: 兵庫
  • Year and Date: 20110000
• [Presentation] Genetic network in Escherichia coli K-12 (2011)
  • Author(s): 森浩禎
  • Organizer: KEGG シンポジウム
  • Place of Presentation: 京都
  • Year and Date: 20110000
• [Presentation] Towards complete understanding of cellular network in E. coli (2011)
  • Author(s): 森浩禎
  • Organizer: International E.coli Alliance (IECA)
  • Place of Presentation: Sapporo
  • Year and Date: 20110000
• [Presentation] Towards complete elucidation of genetic interaction of E. coli and its application (2010)
  • Author(s): Hirotada Mori, Tkeuchi, R., and Wanner, B. L
  • Organizer: 5th International Conference on Microbiology of Food, Health and Environment:Problems and Prospects in Developing Countries
  • Place of Presentation: Dhaka, Bagladesh
  • Year and Date: 20100000
• [Presentation] New era for network analysis of Escherichia coli. (2010)
  • Author(s): Mori, H
  • Organizer: International E.coli Alliance (IECA)
  • Place of Presentation: West Lafeyette, USA.
  • Year and Date: 20100000
• [Presentation] Keio collectionを使ったHydroxyurea感受性株の解析 (2010)
  • Author(s): 中屋敷徹
  • Organizer: 第5回日本ゲノム微生物学会年会
  • Place of Presentation: 宮城
  • Year and Date: 20100000
• [Presentation] Keio collectionを使ったHydroxyurea感受性株のスクリーニング (2010)
  • Author(s): 中屋敷徹
  • Organizer: 第7回21世紀大腸菌研究会
  • Place of Presentation: 福岡
  • Year and Date: 20100000
• [Presentation] Towards complete understanding of cellular system (2010)
  • Author(s): 森浩禎
  • Organizer: 日印転写シンポジウム
  • Place of Presentation: 沖縄
  • Year and Date: 20100000
• [Presentation] New era for network biology of Escherichia coli. (2010)
  • Author(s): 森浩禎
  • Organizer: Spring8
  • Place of Presentation: 兵庫
  • Year and Date: 20100000
• [Presentation] Elucidation of physiological cellular network and potentialities towards genomic design (2010)
  • Author(s): 森浩禎
  • Organizer: 第62回日本生物工学会大会
  • Place of Presentation: 宮崎
  • Year and Date: 20100000
• [Presentation] 細胞内ネットワークの全体像解明に向けて (2010)
  • Author(s): 森浩禎
  • Organizer: 岡山大学・理学部
  • Place of Presentation: 岡山
  • Year and Date: 20100000
• [Presentation] Systems biology resources and their applications. (2010)
  • Author(s): 森浩禎
  • Organizer: National Cheng Kung University
  • Place of Presentation: Taiwan
  • Year and Date: 20100000
• [Book] In Escherichia coli and Bacillus subtilis; The Frontiers of Molecular Microbiology Revisited (2012)
  • Author(s): Masayuki Murata
  • Publisher: Research Signpost
• [Book] INTECH (2012)
  • Author(s): Naoko Fujimoto
  • Publisher: Naoko Fujimoto, Chemical Biology
• [Book] 生命誌年間号遊ぶ (2012)
  • Author(s): 森浩禎
  • Publisher: 新曜社
• [Book] 微生物を活用した新世代の有用物質生産技術 (2012)
  • Author(s): 森浩禎
  • Publisher: シーエムシー出版
• [Book] システム生物学におけるリソースの重要性 (2012)
  • Author(s): 森浩禎
  • Publisher: シーエムシー出版
• [Book] 大腸菌網羅的変異株ライブラリーの創成と活用 (2012)
  • Author(s): 森浩禎
  • Publisher: シーエムシー出版