UKRI/BBSRC-NSF/BIO: Deciphering the RNA structure code for viroid infections

Viral agents constantly threaten humans, livestock, and crops. Many viruses have RNA genomes. In the most extreme case, noncoding RNAs alone (i.e., viroids) can infect crops leading to production losses. For instance, consider the cases of oil palm and coconut palm; approximately 40 million palms were killed by viroids between 1980 to 2007 due to the lack of effective treatments. Climate change is projected to increase cross-species viral transmission risks and pose risks of new viroid and virus outbreaks. Thus, it is imperative to explore potential solutions for sustainable agriculture. Unfortunately, there is no effective measure available to combat viral or viroid diseases in crops. Given that RNA structures are often the functional basis for infectious RNAs (i.e., RNA viruses and viroids) to achieve a successful infection, understanding those RNA structures with functional implications will likely provide targets for blocking infection. Based on recent breakthroughs from the research team, this proposal will develop state-of-the-art technologies to outline a comprehensive atlas of viroid RNA structures in plant cells and improve understanding of structure-based viroid infection. The knowledge gained here will ultimately lay the foundation for screening structure-targeting anti-viroid drugs to combat viroid diseases. Moreover, next-generation scientists, including undergraduate, graduate students, and postdoc researchers, will receive high-quality training. It is well-known that RNA structures exhibit dynamic folding patterns in cellular environment for exerting functions. However, current understanding of most RNAs was based on thermodynamic modeling or limited in vitro probing data. The research group will characterize both spatial and temporal landscapes of viroid RNA structures in living plant cells using a comprehensive experimental design. By employing cutting-edge chemical probing techniques and computational algorithms, this project will determine the in vivo RNA structure landscapes of viroids in different subcellular locations and the potential biological significance. The study will span multiple time points to create a comprehensive atlas of viroid structurome dynamics throughout the infection process. In particular, understanding in vivo RNA structure features in regulating the intracellular movement of viroids will be a major goal. Notably, warm temperatures lead to more severe foliage symptoms and significant potato yield loss by viroid infection. The risk of new outbreaks of viroid diseases is projected based on global climate change. Hence, this project will also outline viroid RNA structural alterations in response to high temperatures. The research tools developed in this project will aid the broader RNA biology research community. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.