RNA catalyses nuclear pre-mRNA splicing

• Published in: Nature (London) 2013-11, Vol.503 (7475), p.229-234
• Main Authors: Fica, Sebastian M., Tuttle, Nicole, Novak, Thaddeus, Li, Nan-Sheng, Lu, Jun, Koodathingal, Prakash, Dai, Qing, Staley, Jonathan P., Piccirilli, Joseph A.
• Format: Article
• Language: English
• Subjects: 631/181/735; 631/337/1645/1792; 631/45/173; 631/45/500; Catalysis; Cell Nucleus - metabolism; Crystal structure; Editing; Experiments; Gene expression; Genetic research; Humanities and Social Sciences; Introns; Introns - genetics; Ligands; Messenger RNA; Metal catalysts; Metals; Metals - metabolism; Methods; Models, Biological; multidisciplinary; Physiological aspects; RNA Precursors - metabolism; RNA sequencing; RNA Splicing; RNA, Fungal - metabolism; RNA, Small Nuclear - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Science; Spliceosomes; Spliceosomes - metabolism; Yeasts
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature12734

In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a dynamic machine composed of both proteins and small nuclear RNAs (snRNAs). Over thirty years ago, after the discovery of self-splicing group II intron RNAs, the snRNAs were proposed to catalyse splicing. However, no definitive evidence for a role of either RNA or protein in catalysis by the spliceosome has been reported so far. By using metal rescue strategies in spliceosomes from budding yeast, here we show that the U6 snRNA catalyses both of the two splicing reactions by positioning divalent metals that stabilize the leaving groups during each reaction. Notably, all of the U6 catalytic metal ligands we identified correspond to the ligands observed to position catalytic, divalent metals in crystal structures of a group II intron RNA. These findings indicate that group II introns and the spliceosome share common catalytic mechanisms and probably common evolutionary origins. Our results demonstrate that RNA mediates catalysis within the spliceosome. The spliceosome is shown to catalyse splicing through the RNA and not the protein components of the spliceosome; pre-messenger RNA splicing requires U6 snRNA acting by a mechanism similar to that used by group II self-splicing introns. RNA/metal catalyst in the spliceosome The RNA- and protein-containing spliceosome complex excises introns from pre-mRNAs. On the basis of the existence of self-splicing group II introns, a type of ribozyme, it was hypothesized more than thirty years ago that the small nuclear RNAs (snRNAs) of the spliceosome would catalyse splicing. However, despite decades of research, no definitive evidence for a role of either RNA or protein in splicing catalysis has been reported. Now Joseph Piccirilli, Jonathan Staley and colleagues identify the metal-containing U6 snRNA as the catalyst. Moreover, the data strongly suggest a common evolutionary origin for the spliceosome and group II introns.