Human coronavirus 3CL protease manipulates host protein STIM1 to facilitate immune evasion, 2025, Lee et al.

[SNT Gatchaman]

Human coronavirus 3CL protease manipulates host protein STIM1 to facilitate immune evasion

Spoiler: Authors

Lee, Yoon Young; Lee, Ah Reum; Seo, Seongkyung; Park, Uni; Kim, Taehun; Lee, Sang Kwon; Jeong, Hyeongsun; Jeong, Su Ji; Kweon, Yeong Cheon; Eun Park, Go; Kim, Min Ji; Kim, Byung-Gyu; Kwon, Taejoon; Cho, Nam-Hyuk; Moo Kwon, Hyug; Myung, Kyungjae; Lee, Sang Min; Park, Chan Young

Coronaviruses rely on intricate interactions with host proteins to create an environment conducive to their replication and survival. The 3CL protease of coronavirus acts as a key mediator, serving a dual role in cleaving viral polyproteins to produce essential components for replication and targeting host proteins to disrupt regulatory pathways and suppress immune defenses. However, the mechanisms by which 3CL protease manipulates host proteins remain poorly understood.

Here, we identify STIM1, a substrate of the 3CL protease, as a dual immune suppressor. Cleavage at the Q496 residue generates two stable products, N-terminal (NT) and C-terminal (CT) fragments, which acquire de novo immunomodulatory functions. NT suppresses MAVS aggregation and MAVS-TRAF2-TBK1 signalosome formation, while CT attenuates IKKα-induced p65 phosphorylation and nuclear translocation by interacting with HSP70.

Collectively, these dual modules simultaneously lead to the suppression of IFN-β production and the weakening of antiviral defenses. These findings reveal a distinct function of STIM1 and delineate a strategy employed by coronaviruses to modulate host immunity, offering insights into viral pathogenesis and potential avenues for therapeutic intervention.

SIGNIFICANCE
Coronaviruses, including SARS-CoV-2, rely on viral proteases to coordinate their replication and evade host defense systems. We identify that the coronavirus main protease (3CLpro/Mpro) cleaves the host protein STIM1. Two cleaved STIM1 fragments inhibit antiviral signaling and dampen interferon responses, thereby weakening host innate immunity. These findings uncover a previously unrecognized mechanism by which coronaviruses subvert immune regulation, suggesting therapeutic opportunities to counteract SARS-CoV-2 and related viral infections.

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[SNT Gatchaman]

Coronaviruses possess a positive-sense single-stranded RNA genome, which can be directly translated into proteins upon entry into the host cell. The genome comprises multiple open reading frames (ORFs), with ORF1a and ORF1b encoding two large polyproteins, pp1a and pp1ab. These polyproteins are processed by viral proteases into nonstructural proteins (NSPs) that are essential for viral replication and transcription.

Among these, NSP3 (papain-like protease, PLpro) and NSP5 (main protease, 3CLpro) play critical roles in processing viral polyproteins into functional units. Notably, 3CLpro, a canonical cysteine protease, cleaves the ORF1ab polyprotein at 11 distinct sites to generate 12 NSPs (NSP5 to NSP16), which are necessary for assembling the viral replication machinery. In addition to processing viral proteins, 3CLpro can also cleave host proteins to suppress antiviral responses and facilitate an environment conducive to viral replication and survival.

Stromal interaction molecule 1 (STIM1) is an ER-resident Ca2+ sensor that plays a key role in coordinating cellular Ca2+ signaling. Upon depletion of ER Ca2+ stores, STIM1 is activated and subsequently interacts with the Orai1 Ca channel, triggering Ca2+ influx from the extracellular space.

Beyond its role as a Ca2+ signaling regulator, STIM1 has been implicated in various processes associated with viral infection, including modulation of immune responses (e.g., interferon (IFN) production and T cell activation) and alterations in calcium homeostasis to support viral replication. Several viruses exploit these processes by hijacking STIM1 to enhance their survival and propagation..

Likewise, increased STIM1 expression has been detected in the serum of patients infected with Influenza A virus (IAV), where it plays a role in regulating IAV-induced inflammation. Building on these findings, recent research has revealed the pivotal role of STIM1 in coronavirus infections. Notably, the SARS-CoV-2 spike protein interacts with the ACE2–STIM1 complex, triggering Ca2+ release from the ER, a key step for viral envelope fusion with the host cell membrane.

Loss of STIM1 has been shown to confer strong resistance to SARS-CoV-2 infection, underscoring its importance in viral pathogenesis. Additionally, STIM1 inhibits STING activation—a recently found regulator of IFN response after SARS-CoV-2 infection—by preventing its translocation to the ER-Golgi intermediate compartment, thereby suppressing the type I IFN response.

Here, we identified that STIM1 is cleaved by the coronavirus 3CLpro, acquiring dual immune-suppressing functions. This cleavage, occurring specifically at the residue Q496, generates two stable fragments, NT and CT, with distinct subcellular localizations: STIM1 NT localizes to the ER, while STIM1 CT is distributed in the cytosol and nucleus. These fragments acquire proviral functions that modulate the host innate immune response, with both ultimately suppressing IFN-β production by disrupting MAVS- and p65-mediated pathways.