Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

André B. Canelas, Nicola Harrison, Alessandro Fazio, Jie Zhang, Juha-Pekka Pitkänen, Joost van den Brink, Barbara M. Bakker, Lara Bogner, Jildau Bouwman, Juan I. Castrillo, Ayca Cankorur, Pramote Chumnanpuen, Pascale Daran-Lapujade, Duygu Dikicioglu, Karen van Eunen, Jennifer C. Ewald, Joseph J. Heijnen, Betul Kirdar, Ismo Mattila, Femke I. C. Mensonides, Anja Niebel, Merja Penttilä, Jack T. Pronk, Matthias Reuss, Laura Salusjärvi, Uwe Sauer, David Sherman, Martin Siemann-Herzberg, Hans Westerhoff, Johannes de Winde, Dina Petranovic, Stephen G. Oliver, Christopher T. Workman, Nicola Zamboni and Jens Nielsen ()
Additional contact information
André B. Canelas: Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
Nicola Harrison: University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
Alessandro Fazio: Center for Biological Sequence Analysis, Technical University of Denmark
Jie Zhang: Chalmers University of Technology
Juha-Pekka Pitkänen: VTT Technical Research Centre of Finland, PO Box 1000, Espoo FI-02044 VTT, Finland.
Joost van den Brink: Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
Barbara M. Bakker: Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands.
Lara Bogner: Institut für Bioverfahrenstechnik, University of Stuttgart, Allmandring 31, Stuttgart D-70569, Germany.
Jildau Bouwman: Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands.
Juan I. Castrillo: University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
Ayca Cankorur: Bogazici University, Bebek, Istanbul 34342, Turkey.
Pramote Chumnanpuen: Chalmers University of Technology
Pascale Daran-Lapujade: Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
Duygu Dikicioglu: Bogazici University, Bebek, Istanbul 34342, Turkey.
Karen van Eunen: Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands.
Jennifer C. Ewald: Institute for Molecular Systems Biology, ETH Zürich
Joseph J. Heijnen: Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
Betul Kirdar: Bogazici University, Bebek, Istanbul 34342, Turkey.
Ismo Mattila: VTT Technical Research Centre of Finland, PO Box 1000, Espoo FI-02044 VTT, Finland.
Femke I. C. Mensonides: Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands.
Anja Niebel: Institut für Bioverfahrenstechnik, University of Stuttgart, Allmandring 31, Stuttgart D-70569, Germany.
Merja Penttilä: VTT Technical Research Centre of Finland, PO Box 1000, Espoo FI-02044 VTT, Finland.
Jack T. Pronk: Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
Matthias Reuss: Institut für Bioverfahrenstechnik, University of Stuttgart, Allmandring 31, Stuttgart D-70569, Germany.
Laura Salusjärvi: VTT Technical Research Centre of Finland, PO Box 1000, Espoo FI-02044 VTT, Finland.
Uwe Sauer: Institute for Molecular Systems Biology, ETH Zürich
David Sherman: Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800, France.
Martin Siemann-Herzberg: Institut für Bioverfahrenstechnik, University of Stuttgart, Allmandring 31, Stuttgart D-70569, Germany.
Hans Westerhoff: Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands.
Johannes de Winde: Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
Dina Petranovic: Chalmers University of Technology
Stephen G. Oliver: University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
Christopher T. Workman: Center for Biological Sequence Analysis, Technical University of Denmark
Nicola Zamboni: Institute for Molecular Systems Biology, ETH Zürich
Jens Nielsen: Chalmers University of Technology

Nature Communications, 2010, vol. 1, issue 1, 1-8

Abstract: Abstract The field of systems biology is often held back by difficulties in obtaining comprehensive, high-quality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae, a widely used model organism that is also used in the production of fuels, chemicals, food ingredients and pharmaceuticals. With the current focus on biofuels and sustainability, there is much interest in harnessing this species as a general cell factory. In this study, we characterized two yeast strains, under two standard growth conditions. We ensured the high quality of the experimental data by evaluating a wide range of sampling and analytical techniques. Here we show significant differences in the maximum specific growth rate and biomass yield between the two strains. On the basis of the integrated analysis of the high-throughput data, we hypothesize that differences in phenotype are due to differences in protein metabolism.

Date: 2010
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DOI: 10.1038/ncomms1150

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