Poster abstracts
Poster number 34 submitted by Peter Forstmeier
Computational discovery of novel functional RNAs in SARS-CoV-2
Peter C. Forstmeier (Department of Biochemistry and Molecular Biology - The Pennsylvania State University), McCauley O. Meyer (Department of Biochemistry and Molecular Biology - The Pennsylvania State University), Philip C. Bevilacqua (Pennsylvania State University, Department of Biochemistry and Molecular Biology, Department of Chemistry)
Abstract:
The global COVID-19 pandemic is caused by the positive-sense RNA virus SARS-CoV-2 (1). The genome of this virus is known to hold functional RNAs, a type of biologically essential RNA characterized by conserved sequence, conserved structure, and presence of a pseudoknot (2). Functional RNAs are also good therapeutic targets for antisense oligonucleotides (ASOs) or small molecules making the discovery of novel functional RNAs in SARS-CoV-2 a route for developing therapeutics to counter the disease (3). We built a computational pipeline that functions in two parts. The first part agnostically locates structured RNAs in the genome and determines which of those structures contain pseudoknots; those that contain pseudoknots continue through the pipeline. This part also eliminates terminators and known riboswitches and ribozymes. The second part of the pipeline uses thousands of viral genomic isolates to determine conservation of sequence, structure, and pseudoknots. A known functional RNA within the SARS-CoV-2 genome is a programmed (–1) ribosomal frameshifting element (FSE), which was also analyzed using the pipeline to establish a benchmark for a level of mutation that was acceptable (4). Pseudoknots that showed higher levels of conservation of sequence, secondary structure, and pseudoknot structure than the FSE were considered putatively functional. A final level of analysis was added to the pipeline that eliminated mutations that cause nonsense or missense non-conservative amino acid mutations. The rationale being that it is ambiguous whether the selective pressure acting on those mutations is due to RNA structure or the protein produced. Using this pipeline, seven putatively functional RNAs were identified in the SARS-CoV-2 genome that contain highly conserved sequence, secondary structure, and a pseudoknot. These RNAs are potential novel therapeutic targets.
References:
(1) Manfredonia, I.; Nithin, C.; Ponce-Salvatierra, A.; Ghosh, P.; Wirecki, T. K.; Marinus, T.; Ogando, N. S.; Snijder, E. J.; Hemert, M. J. van; Bujnicki, J. M.; Incarnato, D. Genome-Wide Mapping of Therapeutically-Relevant SARS-CoV-2 RNA Structures. bioRxiv 2020.
(2) Peselis, A.; Serganov, A. Structure and Function of Pseudoknots Involved in Gene Expression Control. Wiley interdisciplinary reviews. RNA. NIH Public Access November 1, 2014, pp 803–822.
(3) Crooke, S. T.; Witztum, J. L.; Bennett, C. F.; Baker, B. F. RNA-Targeted Therapeutics. Cell Metabolism. Cell Press April 3, 2018, pp 714–739.
(4) Sun, Y.; Abriola, L.; Surovtseva, Y. V; Lindenbach, B. D.; Guo, J. U. Restriction of SARS-CoV-2 Replication by Targeting Programmed −1 Ribosomal Frameshifting In Vitro. bioRxiv 2020.
Keywords: SARS-CoV-2, RNA, Pseudoknots