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TitleStructures of a natural circularly permuted group II intron reveal mechanisms of branching and backsplicing.
Journal, issue, pagesNat Struct Mol Biol, Vol. 32, Issue 6, Page 1101-1110, Year 2025
Publish dateFeb 27, 2025
AuthorsXiaobin Ling / Yuqi Yao / Jinbiao Ma /
PubMed AbstractCircularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5' end and have reversed splice sites (SSs), leading to backsplicing and circular RNA ...Circularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5' end and have reversed splice sites (SSs), leading to backsplicing and circular RNA formation. In this study, we present multiple high-resolution cryo-electron microscopy structures of a natural CP group II intron from Comamonas testosteroni KF-1 (Cte 1), elucidating the molecular mechanisms of branching and backsplicing. During branching, the 5' SS is positioned by an auxiliary sequence (AUX)-enhanced interaction between the exon-binding site and intron-binding site (IBS) and stacks on the branch-site adenosine within D6, allowing the attacking 2'-OH group to coordinate with a metal ion in the active center. In backsplicing, the 3' SS is aligned with the branching step, leaving IBS in the active center, stabilized by base pairing with the AUX, which enables the free 3'-end hydroxyl group to directly attack the scissile phosphate of 3' SS. Furthermore, a groove in Cte 1 may stabilize the circular RNA. These findings highlight a conserved catalytic mechanism for canonical group II introns, albeit facilitated by the versatile AUX, opening avenues for designing potent ribozymes producing circular RNAs.
External linksNat Struct Mol Biol / PubMed:40016344
MethodsEM (single particle)
Resolution2.63 - 3.06 Å
Structure data

38173

8x9k

EMDB-38173, PDB-8x9k:
Cte_Branching,Ca,inactive
Method: EM (single particle) / Resolution: 2.63 Å

38174

8x9l

EMDB-38174, PDB-8x9l:
Cte-U537ins_Branch Intermediate,Ca,active
Method: EM (single particle) / Resolution: 3.04 Å

38175

8x9m

EMDB-38175, PDB-8x9m:
Cte-Branch Product, Mg, post
Method: EM (single particle) / Resolution: 2.78 Å

38176

8x9n

EMDB-38176, PDB-8x9n:
Cte_A695U_Branch Intermediate,Mg,inactive
Method: EM (single particle) / Resolution: 3.01 Å

38177

8x9o

EMDB-38177, PDB-8x9o:
Cte-U537ins-Branching,Ca,inactive
Method: EM (single particle) / Resolution: 3.06 Å

38182

8x9q

EMDB-38182, PDB-8x9q:
Cte-A695U-branching,Mg,active
Method: EM (single particle) / Resolution: 3.04 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

Source
  • comamonas testosteroni kf-1 (bacteria)
KeywordsRNA / SPLICING / CP group ii intron / Cte / back-splicing / circular RNA / Cryo-EM / Cte-branching / cirular RNA

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