The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope

Abstract

The sequence space accessible to evolving proteins can be enhanced by cellular chaperones that assist biophysically defective clients in navigating complex folding landscapes. It is also possible, at least in theory, for proteostasis mechanisms that promote strict quality control to greatly constrain accessible protein sequence space. Unfortunately, most efforts to understand how proteostasis mechanisms influence evolution rely on artificial inhibition or genetic knockdown of specific chaperones. The few experiments that perturb quality control pathways also generally modulate the levels of only individual quality control factors. Here, we use chemical genetic strategies to tune proteostasis networks via natural stress response pathways that regulate the levels of entire suites of chaperones and quality control mechanisms. Specifically, we upregulate the unfolded protein response (UPR) to test the hypothesis that the host endoplasmic reticulum (ER) proteostasis network shapes the sequence space accessible to human immunodeficiency virus-1 (HIV-1) envelope (Env) protein. Elucidating factors that enhance or constrain Env sequence space is critical because Env evolves extremely rapidly, yielding HIV strains with antibody- and drug-escape mutations. We find that UPR-mediated upregulation of ER proteostasis factors, particularly those controlled by the IRE1-XBP1s UPR arm, globally reduces Env mutational tolerance. Conserved, functionally important Env regions exhibit the largest decreases in mutational tolerance upon XBP1s induction. Our data indicate that this phenomenon likely reflects strict quality control endowed by XBP1s-mediated remodeling of the ER proteostasis environment. Intriguingly, and in contrast, specific regions of Env, including regions targeted by broadly neutralizing antibodies, display enhanced mutational tolerance when XBP1s is induced, hinting at a role for host proteostasis network hijacking in potentiating antibody escape. These observations reveal a key function for proteostasis networks in decreasing instead of expanding the sequence space accessible to client proteins, while also demonstrating that the host ER proteostasis network profoundly shapes the mutational tolerance of Env in ways that could have important consequences for HIV adaptation.

Viral Evolution Shaped by Host Proteostasis Networks

“…The extent to which a viral protein can successfully fold thus determines the sequence space accessible to any given viral protein (shaded area of the graph). client proteins (64)(65)(66)(67)(68). Lindquist and others (69-74) pioneered the idea that the Hsp90 chaperone can affect cognate client protein evolution.…”

The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure

“…Emerging studies since the 2010s began to show that host proteostasis networks can shape the evolution of viral proteins (13,(37)(38)(39)(40)(41)(42). Nevertheless, while it is evident that host proteostasis factors, particularly chaperones, can define the fitness of viral protein variants, the molecular mechanism has been largely left unclear (16).…”

Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance

“…Further, future studies should utilize newer technologies to examine protein space at a larger scale. For example, the use of deep mutational scanning has revealed substitutions in SARS-CoV-2 proteins that may be relevant for the design of vaccines and therapeutics [51][52][53], and revealed how host cell chaperones shape the evolution of viral pathogens [54][55][56]. These tools may reveal how epistasis and pleiotropy play out across subspaces that are thousands of nodes in size.…”