Properties of a novel satellite RNA associated with tomato bushy stunt virus infections

The biological and molecular properties of a new satellite RNA (satRNA L) associated with Tomato bushy stunt virus (TBSV) are described. satRNA L consists of a linear single-stranded RNA 615 nucleotides in size, lacks significant open reading frames and has no sequence homology with the helper genome other than in the 5’-proximal seven nucleotides and in a central region that is also conserved in all tombusvirus genomic, defective interfering (DI) and satellite RNAs. Secondary structure analysis showed the presence of high order domains similar to those described for other tombusvirus RNAs. Shorter-than-unit-length molecules were shown not to be related to a silencing mechanism. satRNA L did not modify the symptoms induced by TBSV at all temperature conditions tested. A full-length cDNA clone was constructed and used in coinoculations with transcripts of Carnation Italian ringspot virus (CIRV) and Cymbidium ringspot virus (CymRSV). CIRV, but not CymRSV, supported the replication of satRNA L. Using CIRV/CymRSV hybrid infectious clones, two regions were identified as possible determinants of the different ability to support satRNA L replication. The first region is in the 5’-untranslated region, which folds differently in CymRSV in comparison with CIRV and TBSV; the second region is in the ORF 1-encoded protein where a more efficient satRNA L binding domain is suggested to be present in CIRV.