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Evaluation and properties of the budding yeast phosphoproteome

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Abstract
We have assembled a reliable phosphoproteomic data set for budding yeast Saccharomyces cerevisiae and have investigated its properties. Twelve publicly available phosphoproteome data sets were triaged to obtain a subset of high-confidence phosphorylation sites (p-sites), free of "noisy" phosphorylations. Analysis of this combined data set suggests that the inventory of phosphoproteins in yeast is close to completion, but that these proteins may have many undiscovered p-sites. Proteins involved in budding and protein kinase activity have high numbers of p-sites and are highly over-represented in the vast majority of the yeast phosphoproteome data sets. The yeast phosphoproteome is characterized by a few proteins with many p-sites and many proteins with a few p-sites. We confirm a tendency for p-sites to cluster together and find evidence that kinases may phosphorylate off-target amino acids that are within one or two residues of their cognate target. This suggests that the precise position of the phosphorylated amino acid is not a stringent requirement for regulatory fidelity. Compared with nonphosphorylated proteins, phosphoproteins are more ancient, more abundant, have longer unstructured regions, have more genetic interactions, more protein interactions, and are under tighter post-translational regulation. It appears that phosphoproteins constitute the raw material for pathway rewiring and adaptation at various evolutionary rates.
Keywords
PROTEIN-PHOSPHORYLATION SITES, MASS-SPECTROMETRY, SACCHAROMYCES-CEREVISIAE, GLOBAL ANALYSIS, SER/THR/TYR PHOSPHOPROTEOME, PROTEOMICS, REVEALS, KINASE, NETWORKS, EVOLUTION

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MLA
Amoutzias, Grigoris D., et al. “Evaluation and Properties of the Budding Yeast Phosphoproteome.” MOLECULAR & CELLULAR PROTEOMICS, vol. 11, no. 6, 2012, doi:10.1074/mcp.M111.009555.
APA
Amoutzias, G. D., He, Y., Lilley, K. S., Van de Peer, Y., & Oliver, S. G. (2012). Evaluation and properties of the budding yeast phosphoproteome. MOLECULAR & CELLULAR PROTEOMICS, 11(6). https://doi.org/10.1074/mcp.M111.009555
Chicago author-date
Amoutzias, Grigoris D, Ying He, Kathryn S Lilley, Yves Van de Peer, and Sthephen G Oliver. 2012. “Evaluation and Properties of the Budding Yeast Phosphoproteome.” MOLECULAR & CELLULAR PROTEOMICS 11 (6). https://doi.org/10.1074/mcp.M111.009555.
Chicago author-date (all authors)
Amoutzias, Grigoris D, Ying He, Kathryn S Lilley, Yves Van de Peer, and Sthephen G Oliver. 2012. “Evaluation and Properties of the Budding Yeast Phosphoproteome.” MOLECULAR & CELLULAR PROTEOMICS 11 (6). doi:10.1074/mcp.M111.009555.
Vancouver
1.
Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Evaluation and properties of the budding yeast phosphoproteome. MOLECULAR & CELLULAR PROTEOMICS. 2012;11(6).
IEEE
[1]
G. D. Amoutzias, Y. He, K. S. Lilley, Y. Van de Peer, and S. G. Oliver, “Evaluation and properties of the budding yeast phosphoproteome,” MOLECULAR & CELLULAR PROTEOMICS, vol. 11, no. 6, 2012.
@article{2971788,
  abstract     = {{We have assembled a reliable phosphoproteomic data set for budding yeast Saccharomyces cerevisiae and have investigated its properties. Twelve publicly available phosphoproteome data sets were triaged to obtain a subset of high-confidence phosphorylation sites (p-sites), free of "noisy" phosphorylations. Analysis of this combined data set suggests that the inventory of phosphoproteins in yeast is close to completion, but that these proteins may have many undiscovered p-sites. Proteins involved in budding and protein kinase activity have high numbers of p-sites and are highly over-represented in the vast majority of the yeast phosphoproteome data sets. The yeast phosphoproteome is characterized by a few proteins with many p-sites and many proteins with a few p-sites. We confirm a tendency for p-sites to cluster together and find evidence that kinases may phosphorylate off-target amino acids that are within one or two residues of their cognate target. This suggests that the precise position of the phosphorylated amino acid is not a stringent requirement for regulatory fidelity. Compared with nonphosphorylated proteins, phosphoproteins are more ancient, more abundant, have longer unstructured regions, have more genetic interactions, more protein interactions, and are under tighter post-translational regulation. It appears that phosphoproteins constitute the raw material for pathway rewiring and adaptation at various evolutionary rates.}},
  author       = {{Amoutzias, Grigoris D and He, Ying and Lilley, Kathryn S and Van de Peer, Yves and Oliver, Sthephen G}},
  issn         = {{1535-9476}},
  journal      = {{MOLECULAR & CELLULAR PROTEOMICS}},
  keywords     = {{PROTEIN-PHOSPHORYLATION SITES,MASS-SPECTROMETRY,SACCHAROMYCES-CEREVISIAE,GLOBAL ANALYSIS,SER/THR/TYR PHOSPHOPROTEOME,PROTEOMICS,REVEALS,KINASE,NETWORKS,EVOLUTION}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{13}},
  title        = {{Evaluation and properties of the budding yeast phosphoproteome}},
  url          = {{http://dx.doi.org/10.1074/mcp.M111.009555}},
  volume       = {{11}},
  year         = {{2012}},
}

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