The Ptch/SPOUT1 methyltransferase deposits an m(3)U modification on 28S rRNA for normal ribosomal function in flies and humans.

The ribosomal RNA (rRNA) is one of the most heavily modified RNA species in nature. Although we have advanced knowledge of the sites, functions, and the enzymology of many of the rRNA modifications from all kingdoms of life, we lack basic understanding of many of those that are not universally present. A single N(3) modified uridine base (m(3)U) was identified to be present on the 28S rRNA from humans and frogs but absent in bacteria or yeast. Here, we show that the equivalent m(3)U is present in Drosophila and that the Ptch/CG12128 enzyme and its human homolog SPOUT1 are both necessary and sufficient for carrying out the modification. The Ptch-modified U is at a functional center of the large ribosomal subunit, and, consistently, ptch-mutant cells suffer loss of ribosomal functions. SPOUT1, suggested to be the most druggable RNA methyltransferases in humans, represents a unique target where ribosomal functions could be specifically compromised in cancer cells.