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SARS-CoV-2 ORF6 protein targets TRIM25 for proteasomal degradation to diminish K63-linked RIG-I ubiquitination and type-I interferon induction

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Abstract

Evasion and antagonism of host cellular immunity upon SARS-CoV-2 infection provide replication advantage to the virus and contribute to COVID-19 pathogenesis. We explored the ability of different SARS-CoV-2 proteins to antagonize the host’s innate immune system and found that the ORF6 protein mitigated type-I Interferon (IFN) induction and downstream IFN signaling. Our findings also corroborated previous reports that ORF6 blocks the nuclear import of IRF3 and STAT1 to inhibit IFN induction and signaling. Here we show that ORF6 directly interacts with RIG-I and blocks downstream type-I IFN induction and signaling by reducing the levels of K63-linked ubiquitinated RIG-I. This involves ORF6-mediated targeting of E3 ligase TRIM25 for proteasomal degradation, which was also observed during SARS-CoV-2 infection. The type-I IFN antagonistic activity of ORF6 was mapped to its C-terminal cytoplasmic tail, specifically to amino acid residues 52–61. Overall, we provide new insights into how SARS-CoV-2 inhibits type-I IFN induction and signaling through distinct actions of the viral ORF6 protein.

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All primary data associated with this study have been included in the manuscript. Any additional information query can be directed to corresponding author.

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Acknowledgements

We are grateful to Prof. Adolfo Garcia Sastre, Microbiology Department, Icahn School of Medicine, New York, and Prof. Nevan J. Krogan, Cellular Molecular Pharmacology, University of California, San Francisco, for providing plasmids for studying IFN response and SARS-CoV-2 protein expression, respectively. We thank Rajesh Thangavel Yadav for his help with creating the 3D structure model of ORF6.

Funding

We acknowledge research funding to ST Lab and infrastructure support to IISc from the DBT-IISc partnership, DBT-BIRAC, Crypto Relief Fund, L & T Trust, and DST-FIST program to IISc.

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Authors and Affiliations

  1. Emerging Viral Pathogens Laboratory, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India

    Oyahida Khatun, Mansi Sharma, Rohan Narayan & Shashank Tripathi

  2. Microbiology and Cell Biology Department, Biological Sciences Division, Indian Institute of Science, Bengaluru, India

    Oyahida Khatun, Mansi Sharma, Rohan Narayan & Shashank Tripathi

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Conceptualization, funding acquisition, project administration, supervision, resources: ST. Methodology, data curation, formal analysis, validation, visualization: OK, MS, RN, ST. Manuscript writing—review and editing: OK, MS, RN, ST.

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Correspondence to Shashank Tripathi.

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This study was conducted in compliance with institutional biosafety guidelines, (IBSC/IISc/ST/17/2020; IBSC/IISc/ST/18/2021). All experiments involving SARS-CoV-2 virus were performed in Viral BSL3 facility, following the Indian Council of Medical Research and Department of Biotechnology recommendations.

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Khatun, O., Sharma, M., Narayan, R. et al. SARS-CoV-2 ORF6 protein targets TRIM25 for proteasomal degradation to diminish K63-linked RIG-I ubiquitination and type-I interferon induction. Cell. Mol. Life Sci. 80, 364 (2023). https://doi.org/10.1007/s00018-023-05011-3

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