Analysis: Cell-cycle-regulated proteins are more abundant in haploid relative to diploid cells

Two days ago, Matthias Mann’s group published a paper in Nature in which they compare the level of individual proteins in haploid relative to diploid budding yeast cells:

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

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.

Although the paper focuses on the larger amount of cell-wall proteins and proteins involved in pheromone response in haploid cells, the supplementary tables reveal similar biases for many other functional classes, including nucleosomes and cyclin-dependent kinase inhibitors. As many of these proteins are regulated during the cell cycle, I suspected that cell-cycle-regulated proteins might be more abundant in haploid cells relative to diploid cells.

To test this hypothesis, I divided the proteins quantified by the Mann group into two classes: dynamic proteins, which are encoded by genes that are periodically expressed during the cell cycle, and static proteins, which are encoded by genes that are expressed at a constant level (de Lichtenberg et al., 2005). For each class, I plotted the log2-ratios of the protein levels in haploid and diploid cells:

The plot reeals a quite strong shift of dynamic proteins toward higher log-ratios; this difference is highly significant according to the Mann-Whitney U test (P < 10-12). Proteins encoded by cell-cycle-regulated genes are thus in general more abundant in haploid budding yeast cells than in diploid cells.

Full disclosure: I currently collaborate with Matthias Mann and members of his group, and we will soon be colleagues a the Novo Nordisk Foundation Center for Protein Research.

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One thought on “Analysis: Cell-cycle-regulated proteins are more abundant in haploid relative to diploid cells

  1. Lars Juhl Jensen Post author

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    Thomas Lemberger, Bill Hooker, Deepak Singh and Pedro Beltrao liked this.

    The coverage they got is impressive. I would be more interested in post-translational modifications at this points :) – Pedro Beltrao

    I agree, the coverage is excellent but it would have been even more interesting if one could compare PTMs between the conditions. Also, I would have liked to see microarray data for the exact same samples; I wonder how much that would improve the agreement between mRNA and protein levels. – Lars Juhl Jensen

    Did a few tests for correlation of haploid/diploid ratio with other properties: CDK substrates, phosphoproteins, ubiquitinated proteins, D box motifs, KEN box motifs, PEST regions, and phenotype screens. Found weak correlations for ubiquitinated proteins and PEST containing proteins, but these correlations are not statistically significant after correction for multiple testing. – Lars Juhl Jensen

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