Regulation of translation by methylation multiplicity of 18S rRNA

SUMMARY: N(6)-methyladenosine (m(6)A) is a conserved ribonucleoside modification that regulates many facets of RNA metabolism. Using quantitative mass spectrometry, we find that the universally conserved tandem adenosines at the 3′ end of 18S rRNA, thought to be constitutively di-methylated (m(6)(2)A), are also mono-methylated (m(6)A). Although present at substoichiometric amounts, m(6)A at these positions increases significantly in response to sulfur starvation in yeast cells and mammalian cell lines. Combining yeast genetics and ribosome profiling, we provide evidence to suggest that m(6)A-bearing ribosomes carry out translation distinctly from m(6)(2)A-bearing ribosomes, featuring a striking specificity for sulfur metabolism genes. Our work thus reveals methylation multiplicity as a mechanism to regulate translation. IN BRIEF: Ribosome heterogeneity has become increasingly evident. Liu et al. report an example in the form of rRNA methylation. They show two conserved adenosines in the 18S rRNA are modified with varying numbers of methyl groups. Differentially methylated ribosomes translate differently, suggesting methylation multiplicity as a mechanism to regulate translation.