Specialized ribosomes in yeast as a response to oxidative stress

The yeast genome contains a substantial amount of duplicated ribosomal protein genes. Functional characterization of deletion strains of individual paralogs show that the phenotypes upon deletion are not the same for a given paralog pair, suggesting that ribosomal protein paralog genes have distinct functions and thus are not redundant. Here we aimed to explore the differential function of RPL22A and RPL22B in protein synthesis. For this aim, we compared the ribosome-bound mRNAs found in different polysomal fractions: monosome, polysomal low (2-3ribosomes/mRNA), and polysomal high (>3ribosomes/mRNA), relative to total mRNA, for 3 different yeast strains: ∆RPL22A, ∆RPL22B and wild-type. Our results show that the use of one or the other specific ribosomal paralog affects the protein synthesis rates of specific transcripts, suggesting that each ribosomal protein paralog is optimized for decoding a subset of transcripts. We also find that the ratio of these paralogs changes upon oxidative stress, and propose that ribosome heterogeneity might be employed as a strategy to tune protein translation upon oxidative stress. For each strain (WT, ∆RPL22A, ∆RPL22B), 4 RNA pools were sequenced (input total mRNA, monosome fraction, polysome low fraction, polysome high fraction), giving a total of 24 samples. Biological duplicates were produced. The 24 samples were sequenced in two HiSeq2500 lanes, and reads containing the same barcode from the two lanes were merged.