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The Role of Autophagy and ER Stress in Viral Infection

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The regulation of ER stress and autophagy during viral infection is an important factor in the balance of virus and host survival. In this series, we look at pathways that are regulated through cellular responses to virus, as well as in response to virally encoded proteins. Infection of the coronaviruses SARS-CoV and SARS-CoV-2 causes severe lung injury with extensive damages to alveolar and bronchial epithelial cells, and produces extra-pulmonary damage.

To learn more about the role of different types of cell death in viral infection, specifically SARS-CoV-2, check out this post.

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The replication of coronavirus relies heavily on the endoplasmic reticulum (ER), which is required for the processing of transmembrane viral proteins. As such, viral infection can cause ER stress and induce the unfolded protein response (UPR). The UPR is largely controlled by the activities of three pathways: PERK, IRE1a, and ATF-6. Activation of these pathways is regulated by the ER chaperone protein BiP that binds to misfolded proteins aiding in repair. Accumulation of BiP and misfolded protein leads to dissociation and activation of PERK and ATF-6. PERK activity, which can be monitored by phosphorylation at Thr980, leads to phosphorylation of eIF2a at Ser51, which represses the translation of most mRNAs, but is capable of inducing a key transcription factor, ATF-4. Coronaviruses can induce the activation of the transcription factor ATF-6. ATF-6 is also disassociated from BiP during ER stress, and then translocates to the Golgi where it is activated by proteases. Accumulation of misfolded proteins by BiP can directly activate IRE1a. This leads to alternative splicing of the XBP1 mRNA that converts XBP1 from an unspliced form to the spliced form XPB-1s, that is a potent transcriptional activator of stress response genes. These pathways lead to transcription of additional stress regulatory genes like CHOP and GADD34, which together trigger programs that regulate cell responses including cell death and autophagy.

Autophagy is catabolic process for the degradation of cellular components, including protein aggregates, damaged organelles, and bacterial and viral pathogens. The process involves the engulfment of these components into a double membrane structure, the autophagosome, which fuses to the lysosome for degradation. Autophagy has emerged as a critical process in the control of viral infection and immunity. The precise role for autophagy in coronavirus infection is still unclear, but it seems likely that autophagy may play both pro-viral and anti-viral roles. The anti-malarial drugs chloroquine and hydroxychloroquine inhibit autophagic flux by interfering with autophagosome-lysosome fusion. In addition, these drugs prevent endosomal acidification that can prevent SARS-CoV cellular entry. RNA viruses have been reported to subvert autophagy to favor their own replication and release, but in many cases autophagy is stimulated through the UPR process described above. The process of autophagy is generally monitored through accumulation of LC3 stained autophagosomes. Autophagy is associated with conversion of LC3-I to LC3-II in which LC3 is lipidated and incorporated into the autophagosome membrane, serving as receptors for the vast variety of targeted complexes for degradation. Autophagy can be controlled by the antagonistic activities of energy sensing enzymes AMPK and mTORC1. The kinases have opposing actions on the autophagy kinase ULK1, which is activated by AMPK and inhibited by mTORC1. ULK1 is phosphorylated by AMPK at Ser555 and Ser317 and at Ser757 by mTORC1. ULK1 phosphorylates a number of autophagy proteins [including Atg13(Ser355), Atg14(Ser29), Beclin-1(Ser15), Beclin-1(Ser30)] that promote autophagosome formation and maturation. mTORC1 also inhibits the transcription factor TFEB via phosphorylation at Ser211 and Ser122, and is involved in the regulation of lysosomal biogenesis. Lysosomal damage induced by SARS 3a activates TFEB. Several studies suggest that mTORC1 inhibition, which can promote autophagy, can have anti-viral activity on respiratory coronaviruses.

The response to infection can include activation of pathways of ER stress and autophagy that can play a critical role in viral virulence and damage to host tissues. These pathways have a high degree of crosstalk, but the emergence of new regents to tease apart these pathways should enable a much better understanding. The role for emerging therapeutics that regulate these responses is an area of intense interest.


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Gary Kasof, PhD
Gary Kasof, PhD
Dr. Gary Kasof is a Senior Research Fellow working on antibody development and has been at Cell Signaling Technology for over 17 years. He has contributed to the release of nearly 1000 antibodies in several research areas, most notable in cell death and autophagy. Prior to CST he received his PhD from Columbia University in 1995, and has worked at Rutgers University and AstraZeneca.

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