Viroids are the smallest known plant pathogens, composed of non-coding, single-stranded RNA. Despite their molecular simplicity, they cause serious diseases in many economically important plant species. Unlike viruses, viroids rely entirely on the host's cellular machinery for their replication, transport, and systemic spread. Their life cycle involves specific interactions with host proteins such as Virp1, IMPa4, TFIIIA-7ZF, RPL5 and RDR6, each participating in different stages of the infection. In this study, we identified and comparatively analyzed the sequences of these proteins across host species (potato, tomato, tobacco, hop, citrus) and non-host species (rice, cabbage, sunflower, bean) to elucidate their roles in viroid susceptibility or resistance. Homologous sequences were identified using BLAST alignments, followed by multiple sequence alignments and phylogenetic tree construction using RAxML. For structural analysis, we used AlphaFold 3 to predict the three-dimensional structures of candidate proteins and to model their interactions with the RNA of the Potato Spindle Tuber Viroid (PSTVd). The results reveal strong conservation of these proteins within the Solanaceae family and greater sequence divergence in more distantly related plant taxa. Virp1 and IMPa4 showed notable differences between host and non-host plants, which may reflect the role of selective nuclear import in host adaptation to viroid pressure. The protein–RNA interaction modeling yielded low confidence scores, highlighting methodological limitations in predicting interactions with highly structured viroid RNA. These findings contribute to our understanding of the molecular basis of viroid resistance and offer potential targets for the biotechnological development of viroid-resistant plant varieties.
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