Investigating SARS-CoV-2 ORF3a binding to human TRAF2 and TRAF3

Abstract

Abstract Severe COVID-19, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is characterized by widespread inflammation and cytokine storm. A number of viral proteins are capable of inducing inflammatory responses, one of which is open reading frame 3a (ORF3a). ORF3a from SARS-CoV shares 73% homology with SARS-CoV-2 ORF3a and was shown to stimulate NF-κB signaling and inflammasome activation in a manner dependent on TNF receptor-associated factor 3 (TRAF3). TRAF family proteins regulate NF-κB activation and thereby influence inflammatory responses. Both ORF3a homologs contain a TRAF-binding consensus sequence, and SARS-CoV ORF3a has been shown to bind to human TRAFs 2, 3, and 6. We therefore investigated the binding of SARS-CoV-2 ORF3a to TRAF proteins as a potential mechanism through which SARS-CoV-2 may activate inflammatory signaling. TRAF-C domains from TRAFs 2 and 3 were purified and co-crystallized with a peptide from ORF3a containing the TRAF-binding sequence (PIQAS). Fluorescence polarization (FP) was used to assess binding affinity between TRAF-C domains and ORF3a peptide, and dual-luciferase assays were used to measure NF-κB activation in cells transfected with wildtype ORF3a or ORF3a in which the TRAF-binding sequence was mutated to alanines. X-ray crystallography revealed that the ORF3a peptide is able to bind to the TRAF-C domain of TRAFs 2 and 3, and FP indicated that the binding affinity for these interactions is low. When we compared NF-κB activation in HEK293T cells expressing WT vs mutant ORF3a, there was no significant difference. Therefore, while ORF3a has the potential to bind to TRAFs, this interaction does not significantly contribute to inflammatory signaling through NF-κB in our assay. This work is supported by NIH grants R01GM127609 and P01AI141350.