Nature 503, 229–234 (2013)

Credit: SEBASTIAN FICA

Ribozymes have often been considered vestigial catalytic RNAs from an earlier era. However, protein translation by the ribosome, one of the most highly conserved biosynthetic processes in the cell, is catalyzed by RNA. Fica et al. now establish that the spliceosome, the machinery that catalyzes pre-mRNA splicing, is fundamentally a metalloenzyme made of RNA. The spliceosome catalyzes removal of introns from eukaryotic pre-mRNAs in a two-step transesterification process that is mechanistically analogous to the one used by self-splicing group II introns. Previous structural and biochemical parallels between the spliceosome and the group II intron have led to the hypothesis that U6 small nuclear RNA (snRNA) may function as the metal-dependent catalytic core of the spliceosome. To identify potential metal binding sites, Fica et al. replaced key oxygen atoms at specific sites of the phosphate backbone of yeast U6 snRNA with sulfur atoms and looked for positions where splicing was inhibited by the substitution but could be rescued with a thiophilic metal ion such as Cd2+. The analysis revealed five nucleotides that served as metal ligands in U6 snRNA, which are functionally analogous to those observed in crystal structures of group II introns. Further mechanistic investigations showed that the U6 snRNA assembles a single two-metal active site within the core of the spliceosome that catalyzes both steps of intron removal.