The Host Cell's ER Proteostasis Network Shapes HIV Envelope Mutational Tolerance

Buffering of deleterious mutations by molecular chaperones and degradation of misfolding or aggregation-prone proteins by quality control systems are both major factors that can impact the mutational tolerance of an evolving protein. The impacts of the proteostasis network on protein mutational tolerance are not limited to just endogenous clients. Host proteostasis components can also shape the mutational tolerance of rapidly evolving pathogen proteins, ultimately defining the accessible mutational landscape. Here, we test the hypothesis that the composition of the host cell's endoplasmic reticulum (ER) proteostasis network shapes the mutational tolerance of human immunodeficiency virus 1 (HIV) envelope (Env), a membrane glycoprotein that folds and matures in the host cell's secretory pathway. We apply chemical genetic methods to activate the IRE1-XBP1s and/or the ATF6 transcriptional arms of the unfolded protein response independent of ER stress. We then quantitatively assess the impact of the resulting altered host cell ER proteostasis environments on the relative enrichment of all Env single amino acid substitutions using deep mutational scanning. We find that upregulation of host ER proteostasis factors, particularly those controlled by the IRE1-XBP1s transcriptional arm of the UPR, globally reduces the mutational tolerance of HIV Env. The effects of ATF6 activation are less global, but still significant at particular Env sites. The impact of the XBP1s-induced ER proteostasis environment is disparate for diverse structural elements of Env. Highly conserved, functionally important Env regions generally exhibit the largest decreases in mutational tolerance upon XBP1s activation. In contrast, specific regions of Env, including regions targeted by broadly neutralizing antibodies, display greatly enhanced mutational tolerance when XBP1s is activated, hinting at a role for host ER proteostasis network hijacking in potentiating adaptive immune system escape. Altogether, these data reveal a new set of host factors that specifically shape the mutational space accessible to HIV Env and, more generally, provide compelling evidence that UPR-regulated proteostasis mechanisms play critical roles in membrane protein evolution.