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; Jens Nielsen

doi:10.1038/ncomms1150

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 MensonidesAnja 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, Jens Nielsen

92 Citationer (Scopus)

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.

Originalsprog	Engelsk
Tidsskrift	Nature Communications
Vol/bind	1
Sider (fra-til)	145
ISSN	2041-1722
DOI	https://doi.org/10.1038/ncomms1150
Status	Udgivet - 2010
Udgivet eksternt	Ja

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10.1038/ncomms1150

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Canelas, A. B., Harrison, N., Fazio, A., Zhang, J., Pitkänen, J.-P., van den Brink, J., Bakker, B. M., Bogner, L., Bouwman, J., Castrillo, J. I., Cankorur, A., Chumnanpuen, P., Daran-Lapujade, P., Dikicioglu, D., van Eunen, K., Ewald, J. C., Heijnen, J. J., Kirdar, B., Mattila, I., ... Nielsen, J. (2010). Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nature Communications, 1, 145. https://doi.org/10.1038/ncomms1150

Canelas, AB, Harrison, N, Fazio, A, Zhang, J, Pitkänen, J-P, van den Brink, J, Bakker, BM, Bogner, L, Bouwman, J, Castrillo, JI, Cankorur, A, Chumnanpuen, P, Daran-Lapujade, P, Dikicioglu, D, van Eunen, K, Ewald, JC, Heijnen, JJ, Kirdar, B, Mattila, I, Mensonides, FIC, Niebel, A, Penttilä, M, Pronk, JT, Reuss, M, Salusjärvi, L, Sauer, U, Sherman, D, Siemann-Herzberg, M, Westerhoff, H, de Winde, J, Petranovic, D, Oliver, SG, Workman, CT, Zamboni, N & Nielsen, J 2010, 'Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains', Nature Communications, bind 1, s. 145. https://doi.org/10.1038/ncomms1150

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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.",

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AU - Canelas, André B

AU - Harrison, Nicola

AU - Fazio, Alessandro

AU - Zhang, Jie

AU - Pitkänen, Juha-Pekka

AU - van den Brink, Joost

AU - Bakker, Barbara M

AU - Bogner, Lara

AU - Bouwman, Jildau

AU - Castrillo, Juan I

AU - Cankorur, Ayca

AU - Chumnanpuen, Pramote

AU - Daran-Lapujade, Pascale

AU - Dikicioglu, Duygu

AU - van Eunen, Karen

AU - Ewald, Jennifer C

AU - Heijnen, Joseph J

AU - Kirdar, Betul

AU - Mattila, Ismo

AU - Mensonides, Femke I C

AU - Niebel, Anja

AU - Penttilä, Merja

AU - Pronk, Jack T

AU - Reuss, Matthias

AU - Salusjärvi, Laura

AU - Sauer, Uwe

AU - Sherman, David

AU - Siemann-Herzberg, Martin

AU - Westerhoff, Hans

AU - de Winde, Johannes

AU - Petranovic, Dina

AU - Oliver, Stephen G

AU - Workman, Christopher T

AU - Zamboni, Nicola

AU - Nielsen, Jens

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N2 - 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.

AB - 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.

KW - Saccharomyces cerevisiae/classification

KW - Systems Biology/methods

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DO - 10.1038/ncomms1150

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SN - 2041-1722

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SP - 145

JO - Nature Communications

JF - Nature Communications

ER -

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

Abstract

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