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Differential Stoichiometry among Core Ribosomal Proteins.

Slavov N, Semrau S, Airoldi E, Budnik B, van Oudenaarden A - Cell Rep (2015)

Bottom Line: Testing such variability requires direct and precise quantification of RPs.Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes.Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, Northeastern University, Boston, MA 02115, USA; Department of Statistics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: nslavov@alum.mit.edu.

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Global Pattern of Differential Stoichiometry among Mouse RPs across Sucrose GradientsThe relative levels of core RPs in monosomes and polysomes were quantified by MS and found to vary depending on the number of ribosomes bound per mRNA. The measurement noise was estimated by (1) replica quantification of the monosomal fraction (by using different tandem mass tags reporter ions, 126 or 131) and by (2) estimating RP levels separately using either trypsin (T) or lys-C (L) digestion, as indicated at the bottom of each column. The log2 levels of each RP are shown relative to their mean.See also Figures S2 and S3 and Tables S1, S2, and S3.
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fig2: Global Pattern of Differential Stoichiometry among Mouse RPs across Sucrose GradientsThe relative levels of core RPs in monosomes and polysomes were quantified by MS and found to vary depending on the number of ribosomes bound per mRNA. The measurement noise was estimated by (1) replica quantification of the monosomal fraction (by using different tandem mass tags reporter ions, 126 or 131) and by (2) estimating RP levels separately using either trypsin (T) or lys-C (L) digestion, as indicated at the bottom of each column. The log2 levels of each RP are shown relative to their mean.See also Figures S2 and S3 and Tables S1, S2, and S3.

Mentions: The measured levels of a unique peptide (a peptide present in a single RP) reflect the levels of the corresponding RP, post-translational modifications (PTMs) of the peptide (if any), and measurement error. We quantify on average ten distinct RP peptides per RP (Figure S2A), and the levels of these peptides allow both the estimation of the RP levels and the consistency of these estimates. To depict both the estimates and their consistency, we display the full distributions of relative levels of all peptides unique to an RP as boxplots in Figures 1C and 1D. The RP levels across the sucrose gradient (estimated as the median of the levels of unique peptides) indicate that some RPs are enriched in monosomes (Figure 1C), while other RPs are enriched in polysomes (Figure 1D). Each RP group includes proteins from both the large (60S) and the small (40S) subunits of the ribosomes and thus differential loss of 40S or 60S cannot account for the RP levels displayed in Figures 1C and 1D. Indeed, normalizing for the total amount of 40S and 60S proteins in each fraction does not alter significantly the results. The RP enrichment in Figure 1 is substantially higher than the measurement noise, consistent across replicates and across distinct peptides, and highly statistically significant at false discovery rate (FDR) <10−6. The relative levels of all RPs with quantified unique peptides are displayed in Figure 2 to illustrate the global pattern of RP levels across monosomes and polysomes. This pattern shows more RPs whose variability is consistent across replicates and enzymatic digestions. In contrast, the levels of RPs buried in the core of the ribosomes remain constant, with estimates fluctuating within the tight bounds of the measurement noise, Figure 2. This fixed stoichiometry among RPs constituting the ribosomal core suggests that even ribosomes lacking some surface RPs likely have the same core structure.


Differential Stoichiometry among Core Ribosomal Proteins.

Slavov N, Semrau S, Airoldi E, Budnik B, van Oudenaarden A - Cell Rep (2015)

Global Pattern of Differential Stoichiometry among Mouse RPs across Sucrose GradientsThe relative levels of core RPs in monosomes and polysomes were quantified by MS and found to vary depending on the number of ribosomes bound per mRNA. The measurement noise was estimated by (1) replica quantification of the monosomal fraction (by using different tandem mass tags reporter ions, 126 or 131) and by (2) estimating RP levels separately using either trypsin (T) or lys-C (L) digestion, as indicated at the bottom of each column. The log2 levels of each RP are shown relative to their mean.See also Figures S2 and S3 and Tables S1, S2, and S3.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4644233&req=5

fig2: Global Pattern of Differential Stoichiometry among Mouse RPs across Sucrose GradientsThe relative levels of core RPs in monosomes and polysomes were quantified by MS and found to vary depending on the number of ribosomes bound per mRNA. The measurement noise was estimated by (1) replica quantification of the monosomal fraction (by using different tandem mass tags reporter ions, 126 or 131) and by (2) estimating RP levels separately using either trypsin (T) or lys-C (L) digestion, as indicated at the bottom of each column. The log2 levels of each RP are shown relative to their mean.See also Figures S2 and S3 and Tables S1, S2, and S3.
Mentions: The measured levels of a unique peptide (a peptide present in a single RP) reflect the levels of the corresponding RP, post-translational modifications (PTMs) of the peptide (if any), and measurement error. We quantify on average ten distinct RP peptides per RP (Figure S2A), and the levels of these peptides allow both the estimation of the RP levels and the consistency of these estimates. To depict both the estimates and their consistency, we display the full distributions of relative levels of all peptides unique to an RP as boxplots in Figures 1C and 1D. The RP levels across the sucrose gradient (estimated as the median of the levels of unique peptides) indicate that some RPs are enriched in monosomes (Figure 1C), while other RPs are enriched in polysomes (Figure 1D). Each RP group includes proteins from both the large (60S) and the small (40S) subunits of the ribosomes and thus differential loss of 40S or 60S cannot account for the RP levels displayed in Figures 1C and 1D. Indeed, normalizing for the total amount of 40S and 60S proteins in each fraction does not alter significantly the results. The RP enrichment in Figure 1 is substantially higher than the measurement noise, consistent across replicates and across distinct peptides, and highly statistically significant at false discovery rate (FDR) <10−6. The relative levels of all RPs with quantified unique peptides are displayed in Figure 2 to illustrate the global pattern of RP levels across monosomes and polysomes. This pattern shows more RPs whose variability is consistent across replicates and enzymatic digestions. In contrast, the levels of RPs buried in the core of the ribosomes remain constant, with estimates fluctuating within the tight bounds of the measurement noise, Figure 2. This fixed stoichiometry among RPs constituting the ribosomal core suggests that even ribosomes lacking some surface RPs likely have the same core structure.

Bottom Line: Testing such variability requires direct and precise quantification of RPs.Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes.Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, Northeastern University, Boston, MA 02115, USA; Department of Statistics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: nslavov@alum.mit.edu.

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Related in: MedlinePlus