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Published Erratum
. 2015 Oct 26;11(10):833.
doi: 10.15252/msb.156513.

Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

Brian T Weinert, Vytautas Iesmantavicius, Tarek Moustafa, Christian Schölz, Sebastian A Wagner, Christoph Magnes, Rudolf Zechner, Chunaram Choudhary
Published Erratum

Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

Brian T Weinert et al. Mol Syst Biol. .
No abstract available

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Figures

Figure 5
Figure 5
Most acetylation sites are modified with a low stoichiometry

  1. The majority of yeast acetylation sites are highly sensitive to partial chemical acetylation by AcP. The histogram shows the distribution of SILAC L/H ratios for the indicated samples.

  2. AcP caused substantially increased acetylation at a majority of sites. The histogram shows acetylation changes induced by 100 mM AcP in two experimental replicates, and only sites that were independently identified in cells without AcP treatment are shown.

  3. Acetylation stoichiometry is inversely proportional to AcP sensitivity. The scatterplot shows the relationship between AcP sensitivity (SILAC ratio L/H 100 mM AcP) and acetylation stoichiometry (Log10 stoichiometry) as determined by AQUA analysis (Table 1). The Spearman's correlation (ρ) and the significance by two-tailed test (P-value) are shown.

  4. Most acetylation occurs with a low stoichiometry. Absolute acetylation site stoichiometries were estimated based on relative abundance changes (SILAC ratio L/H) after treatment with 100 mM AcP and using an estimate that AcP treatment caused < 1% chemical acetylation.

  5. For comparison, previously determined phosphorylation site stoichiometries are shown *(Wu et al, 2011).

  6. iBAQ-based abundance corrected acetylated peptide intensity (I/iBAQ-A) is proportional to AcP sensitivity. The box plots show the distributions of I/iBAQ-A values for the indicated classes of acetylation sites. AcP-insensitive sites had a significantly (P) higher distribution of I/iBAQ-A values by Wilcoxon test.

  7. Sites without SILAC ratios are highly sensitive to AcP. The minimum ratio of increased acetylation was determined by calculating the increased intensity of AcP-treated “light” peptides relative to an empirically determined detection limit for “heavy” SILAC peptides.

  8. Absolute acetylation stoichiometry of sites without SILAC ratios was estimated to be very low. Stoichiometry was estimated by the same method used to estimate stoichiometry of sites with SILAC ratios in (D) using the minimum ratios of increased acetylation shown in (G).

Figure 6
Figure 6
Functional analysis of high stoichiometry acetylation sites

  1. AcP-insensitive acetylation sites occur on proteins associated with nuclear processes. Gene Ontology (GO) term enrichment was performed by comparing proteins with AcP-insensitive acetylation sites (ratio L/H < 2) to all acetylated proteins. The bar graph shows the percentage of AcP-insensitive sites occurring on proteins associated with the indicated GO terms. P-values (P) indicate the statistical significance of GO term enrichment by Fishers exact test.

  2. AcP-insensitive acetylation sites occur on nuclear proteins. The histogram shows the distribution of SILAC L/H ratios occurring on proteins localized to the indicated subcellular compartments.

  3. Acetylated peptides from mitochondrial proteins have a significantly higher median I/iBAQ-A value compared to acetylated peptides from cytoplasmic proteins. The box plots show the iBAQ-based abundance-corrected peptide intensity (I/iBAQ-A) distributions for the indicated classes of peptides occurring on mitochondrial (Mito.) or cytoplasmic (Cyto.) proteins. Significance (P) was determined by Wilcoxon test.

  4. AcP-insensitive sites (SILAC Ratio < 2) have a significantly different subcellular distribution. Sites without SILAC ratios (No ratio) have a similar subcellular distribution to AcP-sensitive sites (SILAC Ratio > 2). The bar graph shows the fraction of sites localized to the indicated subcellular compartments: mitochondria (Mito.), cytoplasm (Cyto.), or nucleus (Nuc.). Significance (P) was calculated by Fisher exact test.

  5. Detection of acetylation sites is biased to occur on abundant proteins, and this bias is more pronounced for sites with the lowest estimated stoichiometries. The histograms show the distributions of iBAQ protein abundances for observed proteins (n = 3,104). The distributions of the indicated classes of acetylation sites occurring exclusively in the indicated subcellular compartments are shown in red. The numbers of acetylated proteins are shown in parenthesis, and the median Log10 iBAQ abundance for these acetylated proteins is shown.

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References

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