Organelle remodeling across infection time: Cytomegalovirus-host protein interactions viewed through the lens of Inter-ViSTA

Nearly all biological processes rely on the finely-tuned coordination of protein interactions across cellular space and time. Accordingly, generating protein interactome datasets has become routine in biological studies, yet effectively interpreting these datasets remains computationally challenging. Here, we describe the development of Inter-ViSTA, a computational web platform for protein Interaction Visualization in Space and Time Analysis. Inter-ViSTA enables users to quickly build animated interaction networks by automatically synthesizing information on protein abundances, functional annotations, multiprotein complexes, and subcellular localizations. We then leverage Inter-ViSTA, in conjunction with quantitative mass spectrometry and molecular virology, to define the virus-host protein interactions of the human cytomegalovirus (HCMV) anti-apoptotic protein, pUL37x1 (vMIA). We find that spatially and temporally controlled protein interactions underly pUL37x1 functions during infection, facilitating the pro-viral remodeling of both mitochondria and peroxisomes. Reciprocal isolations, microscopy, and CRISPR-based genetic tools further characterize these associations, revealing new mechanisms at the core of the pUL37x1 manipulation of mitochondrial integrity, such as interactions with the MICOS and SAMM50 complexes. Finally, we show that pUL37x1 activates the peroxisomal protein PEX11ß to regulate peroxisome fission during infection, a key metabolic aspect of virus assembly and spread.