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

被引：84

作者：

Canelas, Andre B. ^{[2
]}

Harrison, Nicola ^{[3
]}

Fazio, Alessandro ^{[4
]}

Zhang, Jie ^{[1
]}

Pitkanen, Juha-Pekka ^{[5
]}

van den Brink, Joost ^{[2
]}

Bakker, Barbara M. ^{[6
]}

Bogner, Lara ^{[7
]}

Bouwman, Jildau ^{[6
]}

Castrillo, Juan I. ^{[3
]}

Cankorur, Ayca ^{[8
]}

Chumnanpuen, Pramote ^{[1
]}

Daran-Lapujade, Pascale ^{[2
]}

Dikicioglu, Duygu ^{[8
]}

van Eunen, Karen ^{[6
]}

Ewald, Jennifer C. ^{[9
]}

Heijnen, Joseph J. ^{[2
]}

Kirdar, Betul ^{[8
]}

Mattila, Ismo ^{[5
]}

Mensonides, Femke I. C. ^{[6
]}

Niebel, Anja ^{[7
]}

Penttila, Merja ^{[5
]}

Pronk, Jack T. ^{[2
]}

Reuss, Matthias ^{[7
]}

Salusjarvi, Laura ^{[5
]}

Sauer, Uwe ^{[9
]}

Sherman, David ^{[10
]}

Siemann-Herzberg, Martin ^{[7
]}

Westerhoff, Hans ^{[6
]}

de Winde, Johannes ^{[2
]}

Petranovic, Dina ^{[1
]}

Oliver, Stephen G. ^{[3
]}

Workman, Christopher T. ^{[4
]}

Zamboni, Nicola ^{[9
]}

Nielsen, Jens ^{[1
]}

机构：

[1] Chalmers Univ Technol, Dept Chem & Biol Engn, SE-41296 Gothenburg, Sweden

[2] Delft Univ Technol, Kluyver Ctr Genom Ind Fermentat, Dept Biotechnol, NL-2628 BC Delft, Netherlands

[3] Univ Cambridge, Cambridge Syst Biol Ctr, Cambridge CB2 1GA, England

[4] Tech Univ Denmark, Ctr Biol Sequence Anal, Dept Syst Biol, DK-2800 Lyngby, Denmark

[5] VTT Tech Res Ctr Finland, FI-02044 Espoo, Vtt, Finland

[6] Vrije Univ Amsterdam, Dept Mol Cell Physiol, NL-1081 HV Amsterdam, Netherlands

[7] Univ Stuttgart, Inst Bioverfahrenstech, D-70569 Stuttgart, Germany

[8] Bogazici Univ, Dept Chem Engn, TR-34342 Istanbul, Turkey

[9] ETH, Inst Mol Syst Biol, CH-8093 Zurich, Switzerland

[10] CNRS, UMR 5800, Lab Bordelais Rech Informat, F-75700 Paris, France

来源：

NATURE COMMUNICATIONS | 2010年 / 1卷

关键词：

SACCHAROMYCES-CEREVISIAE; MINIMUM INFORMATION; GLYCOLYTIC-ENZYMES; CHEMOSTAT CULTURES; FERMENTATIVE CAPACITY; QUANTITATIVE-ANALYSIS; EXTRACTION; SET;

D O I：

10.1038/ncomms1150

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：8

共 36 条

[1]

Baganz F, 1998, YEAST, V14, P1417, DOI 10.1002/(SICI)1097-0061(199811)14:15<1417::AID-YEA334>3.0.CO

[2]

2-N

[3] Systems biology as a foundation for genome-scale synthetic biology [J].

Barrett, Christian L. ;

Kim, Tae Yong ;

Kim, Hyun Uk ;

Palsson, Bernhard O. ;

Lee, Sang Yup .

CURRENT OPINION IN BIOTECHNOLOGY, 2006, 17 (05) :488-492

[4]

Brachmann CB, 1998, YEAST, V14, P115

[5] Minimum information about a microarray experiment (MIAME) - toward standards for microarray data [J].

Brazma, A ;

Hingamp, P ;

Quackenbush, J ;

Sherlock, G ;

Spellman, P ;

Stoeckert, C ;

Aach, J ;

Ansorge, W ;

Ball, CA ;

Causton, HC ;

Gaasterland, T ;

Glenisson, P ;

Holstege, FCP ;

Kim, IF ;

Markowitz, V ;

Matese, JC ;

Parkinson, H ;

Robinson, A ;

Sarkans, U ;

Schulze-Kremer, S ;

Stewart, J ;

Taylor, R ;

Vilo, J ;

Vingron, M .

NATURE GENETICS, 2001, 29 (04) :365-371

[6] A partnership between biology and engineering [J].

Brent, R .

NATURE BIOTECHNOLOGY, 2004, 22 (10) :1211-1214

[7] The nature of systems biology [J].

Bruggeman, Frank J. ;

Westerhoff, Hans V. .

TRENDS IN MICROBIOLOGY, 2007, 15 (01) :45-50

[8] Quantitative Evaluation of Intracellular Metabolite Extraction Techniques for Yeast Metabolomics [J].

Canelas, Andre B. ;

ten Pierick, Angela ;

Ras, Cor ;

Seifar, Reza M. ;

van Dam, Jan C. ;

van Gulik, Walter M. ;

Heijnen, Joseph J. .

ANALYTICAL CHEMISTRY, 2009, 81 (17) :7379-7389

[9] The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels [J].

Daran-Lapujade, Pascale ;

Rossell, Sergio ;

van Gulik, Walter M. ;

Luttik, Marijke A. H. ;

de Groot, Marco J. L. ;

Slijper, Monique ;

Heck, Albert J. R. ;

Daran, Jean-Marc ;

de Winde, Johannes H. ;

Westerhoff, Hans V. ;

Pronk, Jack T. ;

Bakker, Barbara M. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (40) :15753-15758

[10] A METHOD FOR THE DETERMINATION OF CHANGES OF GLYCOLYTIC METABOLITES IN YEAST ON A SUBSECOND TIME SCALE USING EXTRACTION AT NEUTRAL PH [J].

DEKONING, W ;

VANDAM, K .

ANALYTICAL BIOCHEMISTRY, 1992, 204 (01) :118-123

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