RNA structure and viroid-plant protein interactions

Visit the ViroiDoc YouTube channel to watch a featured video lecture by Prof. Ying Wang, University of Florida, on fundamentals of RNA nucleotides, the RNA base-pair catalog, and examine the fascinating structures of viroid RNA.

In his lecture, prof. Wang started with the basic concepts of RNA nucleotides, the components, and the noncanonical edges in the RNA nucleotides. Unlike DNA nucleotides, all three edges of RNA nucleotides (i.e., hoogsteen, sugar, and Watson-crick edges) can be involved in base pairings. This feature makes RNA base pairings more flexible and complex. RNA base editing will likely mask the reactive nitrogen in the bases that will lead to changes in base pairings or interaction with other biological molecules. RNA structures range from primary sequences, secondary structures that mainly formed by helices, bulges, and loops, as well as tertiary structures that form by long-distance base pairings and interaction with other biological molecules. RNA helices are different from DNA helices based on angles, width of grooves, etc.

Then Prof. Wang introduced the RNA basepair catalog webpage that summarizes key features of base pairings, including the C1’-C1’ distance, etc. This tool is critical for designing structure-maintaining or structure-disruptive mutants. Another important summary is the modes of RNA-protein interactions. In these interactions, RNA-backbone binding with protein account for the most cases (41%), but this mode has less specificity. RNA-base to protein interaction account for 35.5%, the second most abundant. This binding mode confers specificity.

With the basic knowledge, we looked at viroid RNA structures. There are 27 loops/bulges in PSTVd (potato spindle tuber viroid). We discussed the structure-based interaction between PSTVd and host factors (e.g., Pol II, RPL5, TFIIIA-7ZF, etc).

Curious to learn more?

Visit the ViroiDoc YouTube channel to watch a featured video lecture by Prof. Ying Wang, recorded in September 2025 during the ViroiDoc Days of the EU-funded ViroiDoc project's training activities.

Ying Wang is an Associate Professor at the University of Florida, Department of Plant Pathology. Prof. Wang’s group is focusing on understanding plant-viroid interactions. They aim to understand how viroids using their RNA structures to exploit host machinery to achieve successful replication and spreading in plants, as well as the mechanism of viroid pathogenicity.

Explore more content on viroid research by visiting ViroiDoc YouTube channel.