Long-distance RNA–RNA interactions shape dynamic RNA architectures and functional states in plant positive-strand RNA viruses

Abstract

The genomes of positive-strand RNA [(+)ssRNA] viruses function as dynamic RNA molecules that participate in multiple, sometimes competing, processes during infection, including translation, genome replication, subgenomic RNA (sgRNA) transcription, and genome packaging. These distinct processes require viral RNAs to adopt different conformational states, which are influenced by RNA–RNA interactions and associated viral or host factors. Therefore, understanding how viral RNAs undergo structural remodeling in space and time, and how they transition between different functional states, represents a central question in the regulation of positive-strand RNA virus gene expression. Recent studies of diverse plant positive-strand RNA viruses have revealed that long-distance RNA–RNA interactions (LDRIs) serve as important regulatory mechanisms that shape viral RNA higher-order structures and functional states. This review summarizes recent advances in understanding how LDRI-mediated RNA conformational transitions contribute to the formation of higher-order viral RNA structures and support diverse viral RNA functions. We propose that LDRIs should be viewed not only as physical connections between distant RNA regions, but also as dynamic structural elements embedded within viral RNA folding landscapes, where they contribute to transitions between alternative RNA conformations and functional states.