What’s the difference between haploid and diploid yeast?

Another isotope based, high throughput mass spectrometry approach, they called it “Stable-isotope labelling by amino acids in cell culture (SILAC) quantification”

As said in a review in F1000:

Anne Osbourn
John Innes Centre, United Kingdom
Plant Biology

This paper reports the development and deployment of a proteomics method that enables deep coverage of the yeast proteome and further allows quantitative comparisons to be made between the protein complements of two different states of yeast (in this case haploid v diploid). The ability to comprehensively identify and quantify the yeast proteome in this way and to compare the proteomes of two different states opens up all kinds of new opportunities in systems biology.
The method, which involves high-resolution MS and advanced computational biology, relies on stable-isotope labelling by amino acids in cell culture (SILAC) and does not involve generating tagged versions of proteins. This method is likely to have considerable potential for comparative proteomes in other organisms. Many exciting and fundamental findings have emerged from this study. For example, De Godoy et al. found that the components of the pheromone pathway were amongst the top ten haploid-specific proteins, as expected. However, interestingly, not all components of this pathway were regulated equally. Some proteins remained unchanged in haploid and diploid cells, suggesting that these proteins have additional functions (known to be the case for several). These kinds of observations will enable predictions to be made about the level of commitment of proteins to particular functions and identification of those proteins that are likely to be “multi-tasking”. Another very interesting area is the potential for quantitative genome-wide comparisons at both the mRNA and protein levels. This paper will provide new insights into the components of the genome that are under post-transcriptional control.

Pubmed Abstract:

Nature. 2008 Oct 30;455(7217):1251-4. Epub 2008 Sep 28.

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast.

de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M.

Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

Mass spectrometry is a powerful technology for the analysis of large numbers of endogenous proteins. However, the analytical challenges associated with comprehensive identification and relative quantification of cellular proteomes have so far appeared to be insurmountable. Here, using advances in computational proteomics, instrument performance and sample preparation strategies, we compare protein levels of essentially all endogenous proteins in haploid yeast cells to their diploid counterparts. Our analysis spans more than four orders of magnitude in protein abundance with no discrimination against membrane or low level regulatory proteins. Stable-isotope labelling by amino acids in cell culture (SILAC) quantification was very accurate across the proteome, as demonstrated by one-to-one ratios of most yeast proteins. Key members of the pheromone pathway were specific to haploid yeast but others were unaltered, suggesting an efficient control mechanism of the mating response. Several retrotransposon-associated proteins were specific to haploid yeast. Gene ontology analysis pinpointed a significant change for cell wall components in agreement with geometrical considerations: diploid cells have twice the volume but not twice the surface area of haploid cells. Transcriptome levels agreed poorly with proteome changes overall. However, after filtering out low confidence microarray measurements, messenger RNA changes and SILAC ratios correlated very well for pheromone pathway components. Systems-wide, precise quantification directly at the protein level opens up new perspectives in post-genomics and systems biology.

PMID: 18820680

It is so cooooooooooooool. Same genetic material, just one copy vs. two copies. The protein expression can be very different!

Why it is a nature paper? As they said in the text, “In summary, a combination of SILAC labelling, high-resolution MS and sophisticated computational proteomics allows accurate quantitative analysis of an entire proteome. Among several tested strategies, in-solution digest of unfractionated cell lysate followed by simple isoelectric focusing of the peptides proved most powerful.”