Self-assembly Controls Self-cleavage of HHR from ASBVd (−): a Combined SANS and Modeling Study

Fabrice Leclerc (1, 2) , Giuseppe Zaccai (3, 4) , Jacques Vergne (5) , Martina Řìhovà (6, 5) , Anne Martel (3) , Marie-Christine Maurel (5)

1 I2BC - Institut de Biologie Intégrative de la Cellule
2 CEA - Commissariat à l'énergie atomique et aux énergies alternatives
3 ILL - Institut Laue-Langevin
4 IBS - UMR 5075 - Institut de biologie structurale
5 ISYEB - Institut de Systématique, Evolution, Biodiversité
6 Institute of Physics [Prague]

In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (−) RNAs thus generated are processed by cleavage to unit-length where ASBVd (−) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (−) and its derived 79-nt HHR (−). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (−) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (−) though with a remoter region from an extension of the HI domain.

Mots clés: Catalytic RNA; Molecular modelling; Ribozymes; Thermodynamics; Computational models

Domaines: Biologie cellulaire

Fabrice Leclerc, Giuseppe Zaccai, Jacques Vergne, Martina Řìhovà, Anne Martel, et al.. Self-assembly Controls Self-cleavage of HHR from ASBVd (−): a Combined SANS and Modeling Study. Scientific Reports, 2016, 6 (30287), ⟨10.1038/srep30287⟩. ⟨hal-01357443⟩