Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions

• Ribosomal protein modifications were quantified for yeast in different phases of growth.
• Of 27 confidently identified methylated and acetylated peptides, two change significantly.
• Methylated ribosomal protein (RP) S1B decreases 1.9-fold, inviting further investigation.
• Dimethylated RP S2 increases 10-fold, suggesting a role in regulating ribosome synthesis.
• Mass spectrometry is useful for investigating the role of post-translational modifications.

Ribosomes, as the center of protein translation in the cell, require careful regulation via multiple pathways. While regulation of ribosomal synthesis and function has been widely studied on the transcriptional and translational “levels,” the biological roles of ribosomal post-translational modifications (PTMs) are largely not understood. Here, we explore this matter by using quantitative mass spectrometry to compare the prevalence of ribosomal methylation and acetylation for yeast in the log phase and the stationary phase of growth. We find that of the 27 modified peptides identified, two peptides experience statistically significant changes in abundance: a 1.9-fold decrease in methylation for k(Me)VSGFKDEVLETV of ribosomal protein S1B (RPS1B), and a 10-fold increase in dimethylation for r(DiMe)GGFGGR of ribosomal protein S2 (RPS2). While the biological role of RPS1B methylation has largely been unexplored, RPS2 methylation is a modification known to have a role in processing and export of ribosomal RNA. This suggests that yeast in the stationary phase increase methylation of RPS2 in order to regulate ribosomal synthesis. These results demonstrate the utility of mass spectrometry for quantifying dynamic changes in ribosomal PTMs.