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Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.

Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R - Mol. Cell Proteomics (2013)

Bottom Line: The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances.Interestingly, the correlation was not equally tight for all functional categories ranging from r(s) >0.80 for proteins involved in translation to r(s) <0.45 for signal transduction proteins.In summary, the extensive and publicly available S. pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth, and quantitative proteomic studies on this microorganism.

View Article: PubMed Central - PubMed

Affiliation: Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, 61 Biopolis Drive, Singapore 138673.

ABSTRACT
We report a high quality and system-wide proteome catalogue covering 71% (3,542 proteins) of the predicted genes of fission yeast, Schizosaccharomyces pombe, presenting the largest protein dataset to date for this important model organism. We obtained this high proteome and peptide (11.4 peptides/protein) coverage by a combination of extensive sample fractionation, high resolution Orbitrap mass spectrometry, and combined database searching using the iProphet software as part of the Trans-Proteomics Pipeline. All raw and processed data are made accessible in the S. pombe PeptideAtlas. The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances. The high coverage of the PeptideAtlas allowed correlation with transcriptomic data in a system-wide manner indicating that post-transcriptional processes control the levels of at least half of all identified proteins. Interestingly, the correlation was not equally tight for all functional categories ranging from r(s) >0.80 for proteins involved in translation to r(s) <0.45 for signal transduction proteins. Moreover, many proteins involved in DNA damage repair could not be detected in the PeptideAtlas despite their high mRNA levels, strengthening the translation-on-demand hypothesis for members of this protein class. In summary, the extensive and publicly available S. pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth, and quantitative proteomic studies on this microorganism.

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Related in: MedlinePlus

Hierarchical clustering of protein levels of S. pombe genes and their orthologous genes in S. cerevisiae and humans. Protein clusters were subjected to GO-term enrichment analysis using DAVID (david.abcc.ncifcrf.gov). Only clusters with significant terms (p < 0.05) are displayed.
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Figure 5: Hierarchical clustering of protein levels of S. pombe genes and their orthologous genes in S. cerevisiae and humans. Protein clusters were subjected to GO-term enrichment analysis using DAVID (david.abcc.ncifcrf.gov). Only clusters with significant terms (p < 0.05) are displayed.

Mentions: In total, we found 1,758 genes with abundance values that map to all three species (supplemental Table S13) and compared their protein levels by hierarchical clustering (Fig. 5). We observed several protein clusters with common or specific protein expression patterns for the different species. Using enrichment analysis, we could identify four clusters with significantly enriched GO terms. As expected, proteins involved in cell cycle and nucleotide binding (cluster 1) are low abundant across all species, whereas the opposite is true for ribosomal proteins (cluster 4). Because S. cerevisiae has the lowest number of introns of the three organisms compared (0.04 introns/gene (1)), the expression of proteins involved in splicing is expected to be lowest in budding yeast, which can be confirmed in cluster 2. Accordingly, the expression of these proteins is higher in S. pombe (1 intron/gene (1)) and highest in the human cells (7.8 introns/gene (33)). Interestingly, proteins of the proteasome are specifically highly expressed in the human U2OS cell line compared with both yeast strains (cluster 3). This suggests that the human U2OS cells have higher proteasome activity and protein degradation rates compared with the two yeast strains.


Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.

Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R - Mol. Cell Proteomics (2013)

Hierarchical clustering of protein levels of S. pombe genes and their orthologous genes in S. cerevisiae and humans. Protein clusters were subjected to GO-term enrichment analysis using DAVID (david.abcc.ncifcrf.gov). Only clusters with significant terms (p < 0.05) are displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3675828&req=5

Figure 5: Hierarchical clustering of protein levels of S. pombe genes and their orthologous genes in S. cerevisiae and humans. Protein clusters were subjected to GO-term enrichment analysis using DAVID (david.abcc.ncifcrf.gov). Only clusters with significant terms (p < 0.05) are displayed.
Mentions: In total, we found 1,758 genes with abundance values that map to all three species (supplemental Table S13) and compared their protein levels by hierarchical clustering (Fig. 5). We observed several protein clusters with common or specific protein expression patterns for the different species. Using enrichment analysis, we could identify four clusters with significantly enriched GO terms. As expected, proteins involved in cell cycle and nucleotide binding (cluster 1) are low abundant across all species, whereas the opposite is true for ribosomal proteins (cluster 4). Because S. cerevisiae has the lowest number of introns of the three organisms compared (0.04 introns/gene (1)), the expression of proteins involved in splicing is expected to be lowest in budding yeast, which can be confirmed in cluster 2. Accordingly, the expression of these proteins is higher in S. pombe (1 intron/gene (1)) and highest in the human cells (7.8 introns/gene (33)). Interestingly, proteins of the proteasome are specifically highly expressed in the human U2OS cell line compared with both yeast strains (cluster 3). This suggests that the human U2OS cells have higher proteasome activity and protein degradation rates compared with the two yeast strains.

Bottom Line: The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances.Interestingly, the correlation was not equally tight for all functional categories ranging from r(s) >0.80 for proteins involved in translation to r(s) <0.45 for signal transduction proteins.In summary, the extensive and publicly available S. pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth, and quantitative proteomic studies on this microorganism.

View Article: PubMed Central - PubMed

Affiliation: Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, 61 Biopolis Drive, Singapore 138673.

ABSTRACT
We report a high quality and system-wide proteome catalogue covering 71% (3,542 proteins) of the predicted genes of fission yeast, Schizosaccharomyces pombe, presenting the largest protein dataset to date for this important model organism. We obtained this high proteome and peptide (11.4 peptides/protein) coverage by a combination of extensive sample fractionation, high resolution Orbitrap mass spectrometry, and combined database searching using the iProphet software as part of the Trans-Proteomics Pipeline. All raw and processed data are made accessible in the S. pombe PeptideAtlas. The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances. The high coverage of the PeptideAtlas allowed correlation with transcriptomic data in a system-wide manner indicating that post-transcriptional processes control the levels of at least half of all identified proteins. Interestingly, the correlation was not equally tight for all functional categories ranging from r(s) >0.80 for proteins involved in translation to r(s) <0.45 for signal transduction proteins. Moreover, many proteins involved in DNA damage repair could not be detected in the PeptideAtlas despite their high mRNA levels, strengthening the translation-on-demand hypothesis for members of this protein class. In summary, the extensive and publicly available S. pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth, and quantitative proteomic studies on this microorganism.

Show MeSH
Related in: MedlinePlus