Yeast's Protein Arsenal Catalogued - Max Planck scientists' experiment reveals proteome of baker's yeast

September 29, 2008

Scientists have tried to determine the entirety of proteins (the proteome) in a given organism for more than 30 years. Until recently, technological limits made this impossible. But researchers at the Max Planck Institute of Biochemistry in Martinsried have now been able to identify a total of 4399 different proteins in baker’s yeast. The scientists furthermore showed how the set of proteins in yeast changed in different cellular states. In another publication, the scientists introduced a method with which proteins regulated by a gene are markedly easier to spot than with the traditional microarray method. (Nature Online, September 29th, 2008 and Molecular Cell, September 5th, 2008).

Since the sequencing of the human genome in 2001 it has been known that the analysis of genes alone will not be sufficient for understanding life. Scientists, instead, are trying to identify the entirety of proteins in an organism – the proteome. This is the entire stock of proteins in a living being. The researchers hope to better understand the development and workings of organisms as well as the causes of diseases. This knowledge would provide a foundation on which specific therapeutics could be developed.

Yeast as an ideal test object

Yeast, alongside fruit flies, zebra fish and mice, is one of the model organisms that cell biologists use. Yeast cells, like human cells, possess complementary chromosomes. As its proteins are very similar to those of mammalian cells, yeast is used in biotechnology for the production of biomaterials. During its vegetative growth, yeast cells, like human egg- and sperm cells, have just a simple – haploid – chromosome complement: the cells posses just one copy of each chromosome type. Yeast is also able to reproduce sexually, and possesses diploid chromosome complements during its sexually reproductive phase. Yeast was the first eukaryote to have its genome sequenced. It is now also the first eukaryote to have its proteome discovered.

Identical genes; different set of proteins

The scientists compared the proteome of haploid with diploid yeast cells. They found that the proteins of the pheromone signal pathways are prominent in haploid cells. In diploid cells, however, the ability to make this chemical messenger was not found. Yeast cells need pheromones for coupling and produce them only when they are ready to mate. The Max Planck researchers identified further differences in the two cell phases. The comparison is interesting because the cells possess identical genes yet need a variety of different proteins for their functions. Liver- and muscle cells in humans, too, have an identical genetic composition even though their functions in the body are not the same.

“We have proven that it is possible to reveal the entire proteome of an organism using our approach. Now we need to fine-tune our methods and expand our analysis to decipher other proteomes,” says Matthias Mann. The comparison of the proteome of the two different stages – diploid and haploid – allows for new insights into the regulation of cell differentiation, the development of tissues and the causes for diseases.

Heavy and light proteins

The SILAC-method (Stable Isotope Labeling by Amino Acids in Cell Culture), developed by Matthias Mann, which was used to identify the proteome of yeast, has also been applied to Drosophila fruit flies. The method involves marking organism food or specific amino acids of proteins in the growth culture of cells with heavy isotopes. This allows comparison between the proteomes of cells or organisms through the observation of the ratios between heavy and light proteins which are created. Alongside this quantitative analysis of the Drosophila proteome, the Martinsried scientists and their colleagues at the University of Munich blocked the translation of specific genes into proteins. This allowed them, for example, to investigate the regulation of the ISWI gene which plays an important role in the differentiation of egg cells in higher organisms.

Changes in protein samples

The researchers identified 4100 proteins in the cells of the fruit fly. After purposefully disabling the ISWI gene, the synthesis of more than 300 proteins changed. These changes in the protein samples did not correlate with the results achieved by using the traditional microarray method. “The results indicate that our approach is better suited for understanding the regulation of individual genes in different organisms such as fruit fly, mouse or human being,” says Matthias Mann.

The scientists now want to integrate existing data with the data obtained by their new techniques. This could lead them closer to their goal of understanding the human proteome.


Recently an international consortium in the area of proteomics was created under the leadership of Matthias Mann. This is the largest EU research project in the area. The project, named PROSPECTS (Proteomics specification in Time and Space), will be sponsored through the seventh European Framework Program for Research and Technological Development by a total of nearly 12 million euros. The PROSPECTS consortium plans to advance current proteomics research through the development of new instruments and technologies. PROSPECTS will lead to new insights into the cellular function of proteins and their change during disease, which can be used in biomedicine.

Original publications:

Lyris M. F. de Godoy, Jesper V. Olsen, Jürgen Cox, Michael L. Nielsen, Nina C. Hubner, Florian Fröhlich,Tobias C. Walther & Matthias Mann: "Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast". Nature. 2008 Oct 30;455(7217):1251-4.

Tiziana Bonaldi, Tobias Straub, Jürgen Cox, Chanchal Kumar, Peter B. Becker, Matthias Mann: "Combined use of RNAi and quantitative proteomics to study gene function in Drosophila". Mol Cell. 2008, Sep 5;31(5):762-72.


Prof. Dr. Matthias Mann


Eva-Maria Diehl, Public Relations

Max Planck Institute of Biochemistry, Martinsried near Munich

phone: +49 89 8578-2824, Email:

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