SARS-CoV-2 ORF3a impairs mRNA nuclear export to facilitate immune evasion

Xiang, Chengyu (2026): SARS-CoV-2 ORF3a impairs mRNA nuclear export to facilitate immune evasion. Dissertation, LMU München: Faculty of Medicine

Abstract

Viruses employ diverse strategies to suppress host gene expression and immune re-sponses to facilitate their replication. One common strategy is the inhibition of host mRNA nuclear export. SARS-CoV-2, the causative agent of severe acute respiratory syndrome, similarly disrupts mRNA export from the nucleus. Identifying viral proteins that interfere with host translation is critical for developing effective antiviral therapies. In this study, the SARS-CoV-2 accessory protein ORF3a is identified as a key factor that disrupts mRNA export and represses protein synthesis. ORF3a induces nuclear accu-mulation of poly(A)+ RNA, thereby preventing mRNA from reaching the cytoplasm for translation. Although ORF3a localizes primarily to the cytoplasm, including the endo-plasmic reticulum and Golgi apparatus, it does not directly impair ribosomal translation. Mechanistically, ORF3a interacts with the mRNA binding proteins UAP56 and ALY/REF, promoting the cytoplasmic mislocalization of UAP56 and disrupting its association with ALY/REF. Moreover, ORF3a interferes directly with the binding of mRNA to both UAP56 and ALY/REF. Amino acid (a.a.) 1–132 of ORF3a is identified as the critical functional region responsible for these interactions. This region binds to a.a. 256–428 of UAP56 and full-length ALY/REF. Additionally, it interacts with the FG-repeat–containing domain of Nup62, a nuclear pore complex component essential for mRNA export, thereby direct-ly impairing the association between the mRNA export complex and the nuclear pore. Importantly, overexpression of Nup62 rescues the ORF3a-induced translational repres-sion. Beyond its role in mRNA export, ORF3a suppresses host antiviral responses through multiple mechanisms. It recruits TRIM25 and inhibits TRIM25-mediated ubiquitination of RIG-I, without affecting TRIM25-mediated MAVS degradation, thereby blocking down-stream immune signaling activation. ORF3a also impairs the nuclear translocation and transcriptional activity of p53, and interferes with antigen presentation by reducing HLA class I surface expression. Functionally, both SARS-CoV-2 ORF3a and the host factor ALY/REF are required for efficient viral replication. Taken together, our findings show that ORF3a disrupts host mRNA export through mul-tiple mechanisms, broadly suppressing antiviral protein synthesis and immune response. Furthermore, it enhances viral replication by hijacking ALY/REF. Targeting ORF3a-mediated disruption of mRNA export may represent a promising therapeutic strategy to restore antiviral gene expression during SARS-CoV-2 infection.

• Item Type: Theses (Dissertation, LMU Munich)
• Subjects: 600 Technology, Medicine; 600 Technology, Medicine > 610 Medical sciences and medicine
• Faculties: Faculty of Medicine
• Language: English
• Date of oral examination: 19. February 2026
• 1. Referee: Brunn, Albrecht von
• Signature of the printed copy: 0700/UMD 22730