SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells

Abstract

Despite the efficacy of vaccines, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 5 million individuals worldwide and continues to spread in countries where the vaccines are not yet widely available or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR), a key host cell pathway widely believed essential for viral replication. We examined the activation status and requirement of the master UPR sensor IRE1α kinase/RNase and its downstream transcription factor effector XBP1s, which is processed through an IRE1α-mediated mRNA splicing event, in human lung-derived cells infected with betacoronaviruses. We found human respiratory coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV), and the murine coronavirus (MHV) all induce ER stress and strongly trigger the kinase and RNase activities of IRE1α as well as XBP1 splicing. In contrast, SARS-CoV-2 only partially activates IRE1α whereby it autophosphorylates, but its RNase fails to splice XBP1. Moreover, IRE1α was dispensable for optimal replication in human cells for all coronaviruses tested. Our findings demonstrate that IRE1α activation status differs upon infection with distinct betacoronaviruses and is not essential for efficient replication of any of them. Our data suggest that SARS-CoV-2 actively inhibits the RNase of autophosphorylated IRE1α through an unknown mechanism, perhaps as a strategy to eliminate detection by the host immune system.

Modulation of Endoplasmic Reticulum Stress Response Pathways by Respiratory Viruses

“…In contrast to RSV and IAV infection, the human CoVs demonstrate a distinct UPR profile. Three human coronaviruses (MERS-CoV, HCoV-OC43 and SARS-CoV-2) replicate efficiently in IRE1 deficient cells, suggesting IRE1 activation is not necessary for CoV replication [163]. Extensive and prolonged induction of IRE1 in CoV infection may in fact favour a pro-apoptotic response rather than beneficial responses such as increased chaperone expression aimed at restoring homeostasis [163].…”

“…Three human coronaviruses (MERS-CoV, HCoV-OC43 and SARS-CoV-2) replicate efficiently in IRE1 deficient cells, suggesting IRE1 activation is not necessary for CoV replication [163]. Extensive and prolonged induction of IRE1 in CoV infection may in fact favour a pro-apoptotic response rather than beneficial responses such as increased chaperone expression aimed at restoring homeostasis [163]. Although SARS-CoV-2 induces IRE1, downstream XBP1 splicing is actually suppressed by the virus, perhaps to limit cytokine signalling that could trigger detection by the host immune system [163].…”

“…Extensive and prolonged induction of IRE1 in CoV infection may in fact favour a pro-apoptotic response rather than beneficial responses such as increased chaperone expression aimed at restoring homeostasis [163]. Although SARS-CoV-2 induces IRE1, downstream XBP1 splicing is actually suppressed by the virus, perhaps to limit cytokine signalling that could trigger detection by the host immune system [163]. SARS-CoV-1 selectively activates PERK rather than IRE1, to promote its replication.…”

Non-canonical activation of IRE1α duringCandida albicansinfection enhances macrophage fungicidal activity

“…IRE1α has broad regulatory roles and consequences for infection and immunity. For example, the IRE1α-XBP1S axis can promote the expression of proinflammatory cytokines 6,22 , modulate metabolic plasticity 24 , and promote ER homeostasis 25 during infection. Additionally, IRE1α can facilitate intra-organelle communication for ER-mitochondria calcium signaling and promotion of reactive oxygen species (ROS) generation 12,13,26 .…”