We report a nearly complete mitochondrial genome (mitogenome) of Echinostoma caproni (Egyptian isolate), which was reassembled and thoroughly annotated from whole-genome sequencing data available from Sequence Read Archive (accession No. ERS055227). Although a mitogenome of E. caproni has previously been deposited in GenBank (accession No. AP017706), it represents a partial sequence lacking the transfer RNA (tRNA)-Ser2 and possessing only a short non-coding region. In contrast, the newly reconstructed mitogenome in this study is 14,549 bp in length and comprises 12 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and a 1,256 bp non-coding region containing 4 repeat units. The annotated sequence has been deposited in the Third Party Annotation database in GenBank (accession No. BK071757). Phylogenetic inference based on mitogenomic data indicates that E. caproni is closely related to E. miyagawai strains. This improved mitogenome provides a reliable genomic resource for comparative mitogenomic analyses and phylogenetic studies within the family Echinostomatidae.

Using an assay capable of detecting sequence-specific RNA/protein interactions in mammalian cells, we demonstrate that the poliovirus and rhinovirus 3C proteinases are able to bind structured target RNA sequences derived from their respective 5′ noncoding regions in vivo. Specific RNA binding by poliovirus 3C was found to be dependent on the integrity of stem-loop d of the RNA cloverleaf structure located at the 5′ end of poliovirus genomic RNA. In contrast, mutation of stem-loop b did not prevent this in vivo interaction. However, mutation of stem-loop b, which serves as the RNA binding site for a cellular co-factor important for efficient poliovirus replication, did significantly attenuate the efficiency of 3C RNA binding in vivo and 3CD RNA binding in vitro. This in vivo protein:RNA binding assay was also used to identify several residues in 3C that are critical for RNA binding, but dispensable for 3C proteinase activity. The mammalian cell-based RNA binding assay described in this study may have considerable potential utility in the future detection or analysis of in vivo RNA/protein interactions unrelated to the 3C/RNA interaction described here.