Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot

Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV causing SARS, and SARS-CoV-2 causing COVID-19, use a mechanism known as −1 programmed ribosomal frameshifting (−1 PRF) to replicate. SARS-CoV-2 possesses a unique RNA pseudoknotted structure that stimulates −1 PRF. Targeting −1 PRF in SARS-CoV-2 to impair viral replication can improve patients’ prognoses. Crucial to developing these therapies is understanding the structure of the SARS-CoV-2 −1 PRF pseudoknot. Our goal is to expand knowledge of −1 PRF structural conformations. Following a structural alignment approach, we identify similarities in −1 PRF pseudoknots of SARS-CoV-2, SARS-CoV, and MERS-CoV. We provide in-depth analysis of the SARS-CoV-2 and MERS-CoV −1 PRF pseudoknots, including reference and noteworthy mutated sequences. To better understand the impact of mutations, we provide insight on −1 PRF pseudoknot sequence mutations and their effect on resulting structures. We introduce Shapify, a novel algorithm that given an RNA sequence incorporates structural reactivity (SHAPE) data and partial structure information to output an RNA secondary structure prediction within a biologically sound hierarchical folding approach. Shapify enhances our understanding of SARS-CoV-2 −1 PRF pseudoknot conformations by providing energetically favourable predictions that are relevant to structure-function and may correlate with −1 PRF efficiency. Applied to the SARS-CoV-2 −1 PRF pseudoknot, Shapify unveils previously unknown paths from initial stems to pseudoknotted structures. By contextualizing our work with available experimental data, our structure predictions motivate future RNA structure-function research and can aid 3-D modeling of pseudoknots.