Fluxomic approaches for Yeast metabolism

• Project/Area Number: 24510268
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Genome biology
• Research Institution: Keio University
• Principal Investigator: MURRAY Douglas 慶應義塾大学, 政策・メディア研究科(藤沢), 特任准教授 (50458965)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000); Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2013: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2012: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 国際研究者交流 / ドイツ:オーストリア:英 国 / 計算および実験結果の交換 / ドイツ：オーストリア：英国 / 国際的研究者交流 / Germany / Austria / UK / 計算上の結果と実験結果の交換 / ドイツ / オーストリア / 計測データや実験結果の交換

Outline of Final Research Achievements

Eukaryotic metabolism is a complex and highly dynamic process that can have a huge impact on the physiology of the organism. While we understand much about the major systems in metabolism a holistic view of how metabolic events impact metabolism remain elusive. In this project we developed experimental protocols, bioinformatic pipelines and computational tools to assist our understanding of how cellular respiration and bioenergetics influence metabolism. In particular, we concentrated on the the calculation and estimation of pathway fluxes. We applied these methods to precisely controlled continuous cultures of bakers' yeast to reveal nucleotide biosynthesis, large-scale mobilisation of lipids and carbon dioxide assimilation occurs during high respiration states. Currently, we are validating and integrating these data and plan to publish our findings in the public domain soon.

Research Products

• [Journal Article] Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program (2014)
  • Author(s): Cornelia Amariei, Rainer Machne, Viktor Stolc, Tomoyoshi Soga, Masaru Tomita and Douglas B. Murray
  • Journal Title: Microbial Cell Volume: 1 Pages: 279-288
  • DOI: 10.15698/mic2014.09.166
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Quantifying periodicity in omics data (2014)
  • Author(s): Cornelia Amariei, Masaru Tomita and Douglas B. Murray
  • Journal Title: Frontiers Cell Develepmantal Biology Volume: 2 Pages: 1-9
  • DOI: 10.3389/fcell.2014.00040
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Temporal Partitioning of the Yeast Cellular Network (2014)
  • Author(s): Douglas B. Murray, Cornelia Amariei, Kalesh Sasidharan, Rainer Machné, Miguel A. Aon, David Lloyd
  • Journal Title: Springer Series in Biophysics Volume: 16 Pages: 323-349
  • DOI: 10.1007/978-3-642-38505-6_12
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] The dynamics of cellular energetics during continuous yeast culture. (2013)
  • Author(s): Amariei C, Machne R, Sasidharan K, Gottstein W, Tomita M, Soga T, Lloyd D, Murray DB.
  • Journal Title: Conf Proc IEEE Eng Med Biol Soc. Volume: 2013 Pages: 2708-2711
  • DOI: 10.1109/embc.2013.6610099
  • Peer Reviewed
• [Journal Article] A yeast metabolite extraction protocol optimised for time-series analyses. (2012)
  • Author(s): Sasidharan K, Soga T, Tomita M, Murray DB.
  • Journal Title: PLoS One Volume: 7
  • DOI: 10.1371/journal.pone.0044283
  • Peer Reviewed
• [Journal Article] Rapid DNA, RNA and protein extraction protocols optimized for slow continuously growing yeast cultures. (2012)
  • Author(s): Sasidharan K, Amariei C, Tomita M, Murray DB.
  • Journal Title: Yeast Volume: 29 Pages: 311-322
  • DOI: 10.1002/yea.2911
  • Peer Reviewed
• [Presentation] Energetic feedback on chromatin state defines a system-wide reset point (2014)
  • Author(s): Douglas B. Murray
  • Organizer: Understanding Microbial Communities; Function, Structure and Dynamics
  • Place of Presentation: Isaac Newton Institute for Mathematical Science, Cambridge University (UK)
  • Year and Date: 2014-11-05
  • Invited
• [Presentation] Yeast Respiratory Oscillation: Fluxomic Approaches (2014)
  • Author(s): Douglas B. Murray
  • Organizer: Stoichiometric modelling (SM) of microbial metabolism
  • Place of Presentation: Isaac Newton Institute for Mathematical Science, Cambridge University (UK)
  • Year and Date: 2014-11-04
  • Invited
• [Presentation] Optimal metabolic dynamics resolved by cyclic FBA (2014)
  • Author(s): Sabrina Hoffmann, Willi Gottstein, Rainer Machne, Ralf Steuer, Douglas Murray
  • Organizer: Stoichiometric modelling (SM) of microbial metabolism
  • Place of Presentation: Isaac Newton Institute for Mathematical Science, Cambridge University (UK)
  • Year and Date: 2014-11-04
  • Invited
• [Presentation] Fluxomic approaches in Yeast (2014)
  • Author(s): Douglas B. Murray
  • Organizer: Metabolomics 2014
  • Place of Presentation: Tsuruoka (Yamagata, Japan)
  • Year and Date: 2014-06-23 – 2014-06-26
• [Presentation] The dynamics of cellular energetics during continuous yeast culture. (2013)
  • Author(s): Douglas Murray
  • Organizer: Engineering in Medicine and Biology Society (EMBC), 2013 35th Annual International Conference of the IEEE
  • Place of Presentation: Osaka, Japan
• [Book] Systems Biology of Metabolic and Signalling Networks (2013)
  • Author(s): Temporal Partitioning of the Yeast Cellular Network.
  • Total Pages: 375
  • Publisher: Douglas B. Murray, Cornelia Amariei, Kalesh Sasidharan, Rainer Machne´, Miguel A. Aon, and David Lloyd