Dynamically Restructured ER-mitochondria Contacts in Herpesvirus-Driven Modulation of the Mitophagy-Metabolism Axis

Abstract

Viruses remodel organelles to subvert host defenses and reprogram cellular functions for virus replication. This is exemplified by human cytomegalovirus (HCMV), a prevalent beta-herpesvirus with significant health burden in infants and immunocompromised patients. A hallmark of HCMV infection is the dynamic regulation of mitochondria, whereby mitochondria are highly fragmented yet, surprisingly, exhibit upregulated metabolism necessary for virus production. This poses a conundrum, as in other contexts (e.g., neurodegeneration, other virus infections), fragmentation is coupled with decreased cellular respiration and precedes targeted mitochondrial degradation via mitophagy. It is unknown how HCMV circumvents mitophagy to meet the bioenergetic demands of the replication cycle. Infection-induced mitochondrial features are reminiscent of functions controlled by ER-mitochondria membrane contact sites (MCSs), nanometer regions of apposition between organelles that are fundamental to mitochondrial health and dynamics, enabling biomolecule transfer and coordinated regulation of function. These regions are mediated by tethering proteins, such as the protein tyrosine phosphatase interacting protein 51 (PTPIP51) and vesicle associated membrane protein-associated protein B (VAPB), which have not been investigated during HCMV infection despite their essential roles in mitochondrial calcium homeostasis, ATP production, and autophagy. Here, we integrate quantitative proteomics, super-resolution microscopy, live-cell metabolic assays, and molecular virology to uncover the temporally controlled regulation of ER-mitochondria contacts during HCMV infection. Specifically, we discover that infection induces the formation of a stabilized and asymmetric ER-mitochondria contact structure, which we term mitochondria-ER encapsulations (MENCs). MENCs sequentially recruit VAPB and then PTPIP51, increasing their protein abundances and tethering interactions throughout infection. We show that PTPIP51 is required for virus production and go on to define its dynamic protein interactome, revealing its role as a temporal scaffold in the pro-viral mitochondrial remodeling. PTPIP51 recruitment to MENCs is accompanied by time-sensitive protein interactions with the mitochondrial respiratory complexes. In agreement with this finding, we discover that PTPIP51 drives virus-induced metabolic upregulation. We also find that PTPIP51 interacts with the crucial autophagy complex ATG12-ATG5-ATG16, potentially mediating suppression of autophagosome assembly around mitochondria. Altogether, our work reveals pro-viral restructuring of ER-mitochondria contacts that recruit PTPIP51 and its interactors for a temporal modulation of mitophagy and metabolism. As dysregulation of ER-mitochondria contacts is also a characteristic of neurodegenerative and metabolic disorders, our work has implications beyond HCMV infection.