Differential Stoichiometry among Core Ribosomal Proteins.
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.
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: email@example.com.Show MeSH
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Mentions: Next, we tested the differential RPs stoichiometry and its phenotypic consequences by independent fitness measurements. Our observation that the RP stoichiometry depends on the number of ribosomes bound per mRNA parallels measurements of higher translational activity of polysomes compared to monosomes (Warner et al., 1963, Goodman and Rich, 1963); some studies have even reported that the translational activity per ribosome increases with the number of ribosomes bound per mRNA (Noll et al., 1963, Wettstein et al., 1963), but this finding has not been widely reproduced. We therefore hypothesized that genetic deletions of RPs enriched in the more active ribosomes—as compared to RPs enriched in less active ribosomes—may result in a larger decrease of the translation rate and thus lower fitness. To test this hypothesis, we computed the correlation (Figure 4A) between the fitness of yeast strains with single RP gene deletions (Qian et al., 2012) and the corresponding relative RP levels measured in the tetra-ribosomal fraction (four ribosomes per mRNA). Consistent with our hypothesis, the fitness of strains lacking RP genes is inversely proportional to the relative levels of the corresponding RPs in the tetra-ribosomes (Figure 4A). Extending this correlation analysis to the RP levels in all sucrose fractions shown in Figure 3E results in a correlation pattern (Figure 4B) that further supports our hypothesis by showing the opposite dependence for fractions with fewer ribosomes per mRNA: the fitness of strains lacking RP genes is proportional to the relative levels of the corresponding RPs in fractions with fewer ribosomes per mRNA (Figure 4B). This correlation pattern holds both for ethanol and for glucose carbon sources. To mitigate possible artifacts in the fitness data due to potential chromosome duplications in the deletion strains, we computed the correlations between the RP levels and the fitness of the corresponding RP deletion strains only for RPs without paralogs (thus unlikely to be affected by chromosome duplication) and found much higher magnitudes of the correlations (Figures 4A and 4B). This result suggests that the differential RP stoichiometry is not limited to paralogous RPs substituting for each other.
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: firstname.lastname@example.org.