SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression

  1. Najla Arshad
  2. Maudry Laurent-Rolle
  3. Wesam S. Ahmed
  4. Jack Chun-Chieh Hsu
  5. Susan M. Mitchell
  6. Joanna Pawlak
  7. Debrup Sengupta
  8. Kabir H. Biswas
  9. Peter Cresswell

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Abstract

Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small-protein β 2 -microglobulin (β 2 m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells, these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8 + T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that down-regulate MHC-I expression to avoid CD8 + T cell recognition. Here, we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, down-regulate MHC-I expression using distinct mechanisms. First, ORF3a, a viroporin, reduces the global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of β 2 m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a specific mechanism that allows immune evasion by SARS-CoV-2.

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  1. Version published to 10.1073/pnas.2208525120
  2. ScreenIT

    SciScore for 10.1101/2022.05.17.492198: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    The antihuman tapasin antibodies PaSta1(46) and the anti-HLA-A2 antibody BB7.2(47) have been reported previously.
    antihuman tapasin
    suggested: None
    anti-HLA-A2
    suggested: None
    Mouse anti-human EGFR antibody conjugated to Alexa Fluor® 647(352917)
    anti-human EGFR
    suggested: (BioLegend Cat# 352918, RRID:AB_2650984)
    , mouse anti-human CD47 antibody conjugated to APC (323123) and anti-HA Alexa Fluor® 488 anti-HA.
    anti-human CD47
    suggested: (BioLegend Cat# 323123, RRID:AB_2716202)
    anti-HA
    suggested: None
    Machamer(8), and antibodies to ORF7a (GTX632602) and ORF8 (GTX135591) were purchased from GeneTex.
    GTX135591
    suggested: (GeneTex Cat# GTX135591, RRID:AB_2887502)
    We used a mouse monoclonal antibody to GM130 (BDB610822, from BD Sciences) and a rabbit polyclonal antibody to GM130 (11308 from Proteintech) for Golgi staining.
    GM130
    suggested: None
    The HLA-ABC antibody (clone YTH862.2) was purchased from Novus for immunoprecipitation and immunofluorescence imaging of MHC-I heavy chains.
    HLA-ABC
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Lentiviral particles were generated in HEK293T cells transfected with the packaging vector pCL-Ampho (Imgenex) and the construct of interest using Transit®-Lenti (Mirus) in Opti-MEM (Invitrogen), followed by two rounds of transduction of the recipient cell line with 8 μg/ml Polybrene (Millipore)
    HEK293T
    suggested: RRID:CVCL_HA71)
    Cell culture: VeroE6, HeLaM and HEK293T cells and derivatives were grown in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal calf serum (HyClone) and 1% penicillin/streptomycin (Invitrogen)
    HeLaM
    suggested: None
    Inducible cell lines: HeLaM cells expressing inducible ORF7a (HeLaM-iORF7a) or HEK293T-hAce2 cells expressing inducible proteins (HEK293T-hAce2+iORF7a or HEK293T-hAce2+iORF7a-ARA) were generated by lentiviral transduction of the plasmid encoding the protein of interest followed by puromycin selection (2 ug/ml).
    HEK293T-hAce2
    suggested: RRID:CVCL_A7UK)
    HEK293T-hAce2 cell line and its variants were again transduced with a plasmid encoding the fusion protein of HA-tagged ubiquitin and LMP2A derived peptide (HA-Ub-pLMP2A) to generate HEK293T-hAce2+ipLMP2A, HEK293T-hAce2+iORF7a+ipLMP2A, HEK293T-hAce2+iORF7a-ARA+ipLMP2A.
    HEK293T-hAce2+ipLMP2A
    suggested: None
    HEK293T-hAce2+iORF7a+ipLMP2A
    suggested: None
    Viral titers were determined by plaque assay on Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Metabolic labeling and immunoprecipitation: HeLaM-iORF7a cells were incubated in cysteine- and methionine-free Dulbecco’s modified Eagle’s medium supplemented with 5% dialyzed fetal bovine serum (Invitrogen), 1% Glutamax, 1% penicillin/streptomycin for 1 h, followed by labeling with [35S]methionine/cysteine (PerkinElmer Life Sciences) in the same medium for 15 min.
    HeLaM-iORF7a
    suggested: None
    Recombinant DNA
    SentencesResources
    pCAGGS vector encoding untagged viral proteins ORF3a, ORF7a, ORF8 and ORF7a-ARA were generated by Gibson assembly by PCR amplification from their respective HA-tagged constructs in pCAGGS(43).
    pCAGGS
    suggested: RRID:Addgene_127347)
    pCAGGS(43
    suggested: None
    Plasmid pTRIPZ-puro-ORF7a-WT or ARA was generated by Gibson assembly by the PCR amplification of the genes of interest from their respective pcAGGS constructs and pTRIPZ-puro vector backbone digested with AgeI and EcoRI according to the manufacturer’s instructions.
    pTRIPZ-puro-ORF7a-WT
    suggested: None
    pTRIPZ-puro
    suggested: None
    pTRIPZ-puro-HA-Ub was generated by Gibson assembly by PCR amplification of HA-tagged ubiquitin gene from the plasmid HA-Ubiquitin which was a gift from Edward Yeh (Addgene plasmid # 18712) and pTRIPZ-puro digested with AgeI and XhoI.
    pTRIPZ-puro-HA-Ub
    suggested: None
    HA-Ubiquitin
    suggested: RRID:Addgene_18712)
    This plasmid was digested with EcoRI, and was used along with single stranded DNA primers encoding pLMP2A with 20 bp overlap with the vector in a Gibson assembly reaction according to the manufacturer’s instructions to generate pTRIPZ-puro-HA-Ub-pLMP2A.
    pLMP2A
    suggested: None
    pTRIPZ-puro-HA-Ub-pLMP2A
    suggested: None
    Lentiviral particles were generated in HEK293T cells transfected with the packaging vector pCL-Ampho (Imgenex) and the construct of interest using Transit®-Lenti (Mirus) in Opti-MEM (Invitrogen), followed by two rounds of transduction of the recipient cell line with 8 μg/ml Polybrene (Millipore)
    pCL-Ampho
    suggested: None
    Cell lines generated: HEK293T cells expressing human Ace2 (HEK293T-hAce2) were generated by lentiviral transduction of cells with pLEX307-ACE2-blast, the vector encoding human ACE2, followed by selection with balsticidin (10 ug/ml).
    pLEX307-ACE2-blast
    suggested: RRID:Addgene_158449)
    Software and Algorithms
    SentencesResources
    Cells were washed three times with FACS buffer after incubation with primary and secondary antibody, and analyzed using FACSCalibur (BD Biosciences) and FlowJo software (Tree Star).
    FACSCalibur
    suggested: None
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Colocalization of ORF7a with GRP94 and GM130, respectively, were analyzed by Colocalization Threshold function of Fiji.
    Fiji
    suggested: (Fiji, RRID:SCR_002285)
    Analysis of interaction energy (vdW and electrostatic) throughout the 100 ns simulation was performed using “NAMD Energy” analysis tool available as part of VMD (68).
    Energy”
    suggested: None
    Binding free energy changes (ΔG) were estimated through molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method (70) using CaFE 1.0 tool (71) combined with VMD (68) over the course of entire 100 ns MD simulation runs.
    CaFE
    suggested: (CAFE, RRID:SCR_005983)
    All structures were visualized in PyMOL and images were created in PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2022.05.17.492198v1 on bioRxiv