Identification of Host Factors that Bind to the 5’ End of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) RNA Genome

Viral RNA–host protein interactions contribute to different aspects of the viral life cycle. Middle East respiratory syndrome coronavirus (MERS-CoV), belonging to the Coronaviridae family, causes the Middle East respiratory syndrome (MERS) that is responsible for approximately 900 deaths most of which occur in the Arabian Peninsula. MERS-CoV has an enveloped positive-sense, single-stranded RNA genome that contains highly conserved RNA secondary structures at the 5ʹ and 3ʹ terminal regions. We conducted this study to identify the host factors that interact with the 5ʹ extremity of the MERS-CoV RNA genome. We performed RNA affinity chromatography followed by mass spectrometry and identified 59 host factors that bind to the 5ʹ end of the MERS-CoV RNA genome in Vero E6 cells. Most of the identified cellular proteins have been previously reported to interact with the genome of other RNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as STAU1, hnRNP A1, TRIM23, and NCAM. We also validated our mass spectrometry results using western blot analysis. Results suggested that the multifunctional dsRNA-binding protein STAU1 could interact specifically with the RNA stem-loop structure at the 5ʹ end of MERS-CoV and SARS-CoV-2. Protein–protein interaction network analysis revealed that the majority of the identified proteins could interact with each other, indicating that they could be functionally relevant. Altogether, these data enhance our knowledge about the viral RNA–host interactions of coronaviruses, which could thus serve as targets for developing antiviral therapeutics against MERS-CoV and SARS-CoV-2.Funding Information: This project was funded by the Ministry of Health, Saudi Arabia (Grant no. 826, on 20/04/2020).Declaration of Interests: None to declare.