High-content image-based screening reveals vaccinia virus membrane proteins as potential regulators of LC3 lipidation

Abstract

Autophagy is a catabolic process used for the degradation of organelles and proteins, and it also functions as a cellular defense mechanism, known as xenophagy, during infection. Vaccinia virus (VACV), the prototypic poxvirus, replicates exclusively in the cytoplasm of host cells. It is known that VACV infection causes LC3 lipidation while preventing autophagosome formation, yet the viral protein(s) responsible have not been identified. Using infection time-course Western blotting and a phospholipase D band-shift assay, we show that VACV drives genuine LC3-II formation, rather than a block in pro-LC3 cleavage, and that this depends on early viral gene expression. To identify the gene(s) involved, we generated a dsRed-LC3-I-GFP reporter cell line and developed an image-based screening approach based on single-cell LC3 granularity, which we applied to 80 early VACV genes. The screen revealed that VACV-induced lipidation is regulated in both directions. Follow-up validation identified H3 as a negative regulator and the membrane proteins A14, L5, and G5 as positive contributors to LC3 lipidation. These findings provide the first systematic map of VACV genes affecting LC3 lipidation and suggest that the interplay between VACV and autophagy is more directed than previously thought. IMPORTANCE: Poxviruses, including vaccinia virus and the closely related monkeypox virus, remain a significant public health concern and are increasingly exploited as vaccine and cancer immunotherapy vectors. Understanding how these viruses manipulate host defenses is therefore important for both antiviral and biotechnology applications. Autophagy is a key cellular defense pathway, and vaccinia virus is known to trigger lipidation of the autophagy protein LC3 while blocking productive autophagy, although the viral genes driving this remained unknown. Using an image-based screening strategy, we identify several early vaccinia virus genes that increase or decrease LC3 lipidation, showing that the virus actively regulates this process in both directions. These findings reveal a more targeted interaction between vaccinia virus and host autophagy than previously recognized and provide a broadly applicable screening approach for studying virus-autophagy interactions.