Cross-talk between orientation-dependent recognition determinants of a complex control RNA element, the enterovirus oriR

The coxsackie B3 virus oriR is an element of viral RNA thought to promote t he assembly of a ribonucleoprotein complex involved in the initiation of ge nome replication. The mutual orientation of its two helical domains X and Y is determined by a kissing interaction between the loops of these domains. Here, a genetic approach was worked out to identify spatial orientation-de pendent recognition signals in these helices. Spatial orientation changes ( due to linear and rotational shifts) were introduced by appropriate inserti ons/deletions of a single base pair into one or both of the domains, and ph enotypic consequences caused by these mutations were studied. The insertion of a base pair into domain Y caused a defect in viral reproduction that co uld be suppressed by a base-pair insertion into domain X. Similarly, a defe ct in viral replication caused by a base-pair deletion from domain X could be suppressed by a base-pair deletion from domain Y. Thus, certain areas of the two domains should cross-talk to one another in the sense that a chang e of space position of one of them required an adequate reply (change of sp ace position) from the other. Phenotypic effects of the local rotation of o ne or more base pairs land of some other mutations) in either domain X or d omain Y suggested that the two most distal base pairs of these domains serv ed as orientation-dependent recognizable signals. The results were also con sistent with the notion that the recognition of the distal base pair of dom ain Y involved a mechanism similar to the intercalation of an amino acid re sidue.