A new role for PHYHD1 and related dioxygenases: demethylation of 2′- <i>O</i> -methylated nucleosides

Nucleoside 2'-O-methylation is a widespread RNA modification found across diverse RNA types in all domains of life. Although considerable progress has been made in mapping 2'-O-methylation sites and elucidating their biological roles, the enzymatic pathways responsible for the catabolism of 2'-O-methylated nucleosides remain largely unexplored. Here, we report a previously unidentified 2'-O-methylated nucleoside demethylation reaction catalyzed by a metagenome-derived bacterial dioxygenase named FJS. We further show that FJS-related enzymes, including human phytanoyl-CoA dioxygenase domain-containing protein 1 (PHYHD1), catalyze the 2-oxoglutarate-dependent demethylation of a broad range of ribose-methylated nucleosides, but do not act on modified nucleotides or 3'-terminal 2'-O-methylated RNA substrates. To determine whether the loss of PHYHD1 function affects 2'-O-methylation levels of RNA-incorporated or free nucleosides, we generated a phyhd1 knockout zebrafish line. While RNA modification levels remained unchanged, the amount of free 2'-O-methylated nucleosides was significantly elevated in both phyhd1 knockout embryos and adult zebrafish. These findings indicate that PHYHD1 does not directly demethylate RNA but instead functions in the turnover of free 2'-O-methylated nucleosides. Together, our study identifies a previously unrecognized metabolic pathway for 2'-O-methylated nucleosides and defines PHYHD1 as the key dioxygenase involved in their demethylation, providing new insights into the catabolism of modified nucleosides.