RT Journal Article
SR Electronic
T1 Self-assembly Controls Self-cleavage of HHR from ASBVd(-): a Combined SANS and Modeling Study
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 045054
DO 10.1101/045054
A1 Fabrice Leclerc
A1 Giuseppe Zaccai
A1 Jacques Vergne
A1 Martina Řìhovà
A1 Anne Martel
A1 Marie-Christine Maurel
YR 2016
UL http://biorxiv.org/content/early/2016/03/23/045054.abstract
AB 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.