Ribosomal RNA (rRNA) modifications, including ribose, base methylations and pseudouridines, are important players in the ribosome biogenesis process and translation. In my work, I combine mass spectrometry (MS) with stable isotope labeling to quantitatively monitor rRNA modifications in bacteria , yeast and human cells. For example, by looking at the ribosome assembly intermediates isolated from the wild type E. coli cells, this technique enabled me to characterize the relative order of individual modification events along the ribosome biogenesis pathway of the small and large subunits. Additionally, using mutant strains lacking the specific assembly factors RimP and SrmB we observe functional crosstalk between modifications and other assembly steps. More recently, I extended quantitative MS application for studies of rRNA from S. Cerevisiae, where successfully identified and quantified 80% of over 100 modified nucleosides present in both 18S and 28S RNA. The broad goal of this research is to map rRNA modifications on to the existing framework for ribosome assembly, and to explain how modification steps may assist in maintaining the speed and accuracy of the fundamental to life ribosome biogenesis process. Aside from answering mechanistic questions, we dig into the clinical importance of rRNA modifications. I am actively trying to characterize the heterogeneity of the modification patterns found in rRNA from different human tissues and disease states, including hereditary disorders and cancer.
1. Popova A.M. and Williamson J.R., Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry, J. Am. Chem. Soc., 2014, 136, 2058-2069.