Structural basis of circularly permuted group II intron self-splicing

Area of Science:

• Molecular Biology
• Structural Biology
• RNA Biology

Background:

• Circular RNAs (circRNAs) are increasingly recognized for their regulatory roles.
• The biogenesis of circRNAs by circularly permuted group II introns (CP introns) is not well understood.
• CP introns feature rearranged structural domains and tethered exons, leading to branched introns and circular exons.

Purpose of the Study:

• To elucidate the structural and mechanistic basis of circRNA generation by CP introns.
• To resolve the dynamic process of back-splicing in CP introns at high resolution.
• To identify unique structural features and molecular interactions involved in CP intron splicing.

Main Methods:

• Cryo-electron microscopy (cryo-EM) to determine high-resolution structures (2.5-2.9 Å).
• Analysis of a natural CP intron in multiple functional states.
• Comparative genomics to identify and analyze additional CP introns.

Main Results:

• Detailed cryo-EM structures reveal domain 6 conformational changes facilitating 3'-exon recognition and circularization.
• Unprecedented tertiary interactions were observed, compacting the catalytic triad and domain 6 for protein-independent splicing.
• A specific metal ion (M35) was identified to stabilize the 5'-exon during the splicing reaction.
• These unique features, distinct from canonical group II introns, are conserved in other CP introns.

Conclusions:

• The study elucidates the dynamic mechanism of CP intron back-splicing, revealing key structural adaptations for circRNA formation.
• Findings provide critical insights into the unique catalytic strategies of CP introns.
• The results have significant implications for understanding circRNA biogenesis and developing novel circRNA-based therapeutics.