Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.
André B Canelas
(1)
,
Nicola Harrison
(2)
,
Alessandro Fazio
(3)
,
Jie Zhang
(4, 5)
,
Juha-Pekka Pitkänen
(6)
,
Joost van den Brink
(1)
,
Barbara M Bakker
(7)
,
Lara Bogner
(8)
,
Jildau Bouwman
(7)
,
Juan I Castrillo
(2)
,
Ayca Cankorur
(9)
,
Pramote Chumnanpuen
(5)
,
Pascale Daran-Lapujade
(1)
,
Duygu Dikicioglu
(9)
,
Karen van Eunen
(7)
,
Jennifer C Ewald
(10)
,
Joseph J Heijnen
(1)
,
Betul Kirdar
(9)
,
Ismo Mattila
(6)
,
Femke I C Mensonides
(7)
,
Anja Niebel
(8)
,
Merja Penttilä
(6)
,
Jack T Pronk
(1)
,
Matthias Reuss
(8)
,
Laura Salusjärvi
(6)
,
Uwe Sauer
(10)
,
David James Sherman
(11, 12)
,
Martin Siemann-Herzberg
(8)
,
Hans Westerhoff
(7)
,
Johannes de Winde
(1)
,
Dina Petranovic
(5)
,
Stephen G Oliver
(2)
,
Christopher T Workman
(3)
,
Nicola Zamboni
(10)
,
Jens Nielsen
(5)
1
Department of Biotechnology [Delft]
2 CSBC - Cambridge Systems Biology Centre & Department of Biochemistry
3 DTU - Danmarks Tekniske Universitet = Technical University of Denmark
4 CWIND - Centre for Wireless Network Design
5 Chalmers University of Technology [Göteborg]
6 Technical Research Centre of Finland
7 Department of Molecular Cell Physiology [VU Amsterdam]
8 University of Stuttgart
9 ChE - Department of Chemical Engineering [Bogazici]
10 IMSB - Institute for Molecular Systems Biology [ETH Zurich]
11 MAGNOME - Models and Algorithms for the Genome
12 MABIOVIS - Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations;
2 CSBC - Cambridge Systems Biology Centre & Department of Biochemistry
3 DTU - Danmarks Tekniske Universitet = Technical University of Denmark
4 CWIND - Centre for Wireless Network Design
5 Chalmers University of Technology [Göteborg]
6 Technical Research Centre of Finland
7 Department of Molecular Cell Physiology [VU Amsterdam]
8 University of Stuttgart
9 ChE - Department of Chemical Engineering [Bogazici]
10 IMSB - Institute for Molecular Systems Biology [ETH Zurich]
11 MAGNOME - Models and Algorithms for the Genome
12 MABIOVIS - Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations;
Jie Zhang
- Function : Author
- PersonId : 763033
- ORCID : 0000-0002-0530-3954
David James Sherman
- Function : Author
- PersonId : 1356
- IdHAL : david-james-sherman
- ORCID : 0000-0002-2316-1005
- IdRef : 09147101X
Jens Nielsen
- Function : Author
- PersonId : 758788
- ORCID : 0000-0002-9955-6003
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.