RNA-mediated activity-based protein profiling reveals dihydrouridine modification on human mRNA

ABSTRACT: Epitranscriptomic RNA modifications can regulate RNA activity, however there remains a major gap in our understanding of the scope of mRNA chemistry present in biological systems. Here, we develop RNA-mediated activity-based protein profiling (RNABPP), a chemoproteomic strategy relying upon metabolic RNA labeling with the mechanism-based inhibitor 5-fluorocytidine, mRNA interactome capture, and quantitative proteomics, to investigate pyrimidine-modifying enzymes in human cells. In addition to profiling 5-methylcytidine (m5C) methyltransferase activity on mRNA, metabolic deamination of 5-fluorocytidine to 5-fluorouridine allowed us to show that 5-methyluridine (m5U) is present on human mRNA and demonstrate that its formation is primarily mediated by the tRNA-modifying enzyme TRMT2A. Further, our approach uncovered DUS3L, the mammalian homolog of the yeast tRNA-dihydrouridine synthase DUS3, as a novel 5-fluoropyrimidine-reactive protein. We investigate the mechanism of protein-RNA crosslinking, which involves the conserved catalytic Cys residue, and use genetic knockdown combined with quantitative LC-MS/MS analysis to establish that DUS3L installs dihydrouridine (DHU) on human mRNA and small RNA. Finally, we find that DUS3L is important for cell proliferation and protein translation. Taken together, our work provides a general approach for profiling RNA modifying enzyme activity in vivo, and reveals the existence of new pathways for the epitranscriptomic regulation of mRNA behavior in human cells.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Thao Nguyen  

LAB HEAD: Martin Wuhr

PROVIDER: PXD022645 | Pride | 2021-07-16

REPOSITORIES: Pride