Abstract
Ribosome heterogeneity arises via the differential incorporation of ribosomal protein (RP) paralogs, post-transcriptionally modified rRNA, post-translationally modified RPs, and ribosome-associated proteins (RAPs) into ribosomes. This has led to the hypothesis that heterogeneous or “specialized” ribosomes, which translate specific mRNA subsets, confer key roles in cell growth and development. While proven examples of functional ribosome heterogeneity in eukaryotes exist, there is no comprehensive analysis of specialized ribosome formation. We employed yeast RP paralog deletion libraries and high-throughput screening to investigate the functional specificity and redundancy between paralogs under various growth conditions. Composition and translatome analyses verified paralog specificity in the assembly and function of ribosomes specialized for growth on different carbon sources, and identified a novel RAP required for the efficient translation of peroxisomal proteins. Importantly, we also show that the mechanism by which specific RP paralogs incorporate into ribosomes requires their unique 3’-untranslated regions to yield ribosomes that differ in composition and function.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
The revision includes minor changes to the manuscript. First, 4 out of 114 yeast deletion strains tested for growth on different carbon source/stress conditions (shown in the original Figure 2) were removed, as genomic analysis revealed these were not bona fide deletion strains. Hierarchal phenotype cluster mapping (revised Figure 2) was repeated with the remaining 110 strains, and showed only minor differences in co-clustering between the two experiments shown Figure 2A and 2B, respectively. Correspondingly, Supplementary Figure 1 has been revised as well. Second, the original Supplementary Figure 3 and Figure 9B were replaced with a revised Figure 9B that comprehensively demonstrates rescue of the RPL12B paralog deletion strain (RPL12A rpl12b delta) by replacement of the RPL12A 3'UTR (at the genomic RPL12A locus) with the RPL12B 3'UTR instead. This rescue is equivalent to that seen upon RPL12A paralog overexpression, although in the case of the 3'UTR switch there is no paralog overexpression. This experiment further substantiates our results showing that paralog specificity is important for translational control in yeast and that the mechanism for conferring specificity is determined by the 3'UTRs of the ribosomal protein paralogs.
