Mapping the host protein interactome of non-coding regions in SARS-CoV-2 genome

  1. Liuyiqi Jiang
  2. Mu Xiao
  3. Qing-Qing Liao
  4. Luqian Zheng
  5. Chunyan Li
  6. Yuemei Liu
  7. Bing Yang
  8. Aiming Ren
  9. Chao Jiang
  10. Xin-Hua Feng

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Abstract

A deep understanding of SARS-CoV-2-host interactions is crucial to the development of effective therapeutics. The role of non-coding regions of viral RNA (ncrRNAs) has not been scrutinized. We developed a method using MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS) to systematically map the interactome of SARS-CoV-2 ncrRNA in different human cell lines. Integration of the results defined the core and cell-type-specific ncrRNA-host protein interactomes. The majority of ncrRNA-binding proteins were involved in RNA biogenesis, protein translation, viral infection, and stress response. The 5′ UTR interactome is enriched with proteins in the snRNP family and is a target for the regulation of viral replication and transcription. The 3′ UTR interactome is enriched with proteins involved in the cytoplasmic RNP granule (stress granule) and translation regulation. We show that the ORF10 is likely to be a part of 3′ UTR. Intriguingly, the interactions between negative-sense ncrRNAs and host proteins, such as translation initiation factors and antiviral factors, suggest a pathological role of negative-sense ncrRNAs. Moreover, the cell-type-specific interactions between ncrRNAs and mitochondria may explain the differences of cell lines in viral susceptibility. Our study unveils a comprehensive landscape of the functional SARS-CoV-2 ncrRNA-host protein interactome, providing a new perspective on virus-host interactions and the design of future therapeutics.

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  1. ScreenIT

    SciScore for 10.1101/2021.06.19.449092: (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

    Experimental Models: Cell Lines
    SentencesResources
    Finally, 638 and 449 proteins were detected in Calu-3 and Huh7 cells, respectively.
    Calu-3
    suggested: KCLB Cat# 30055, RRID:CVCL_0609)
    Huh7
    suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336)
    RIP experiment: HEK 293T cells were transfected with plasmids co-expressing individual RNA binding protein, MS2, 5‘UTR and 3’ UTR.
    HEK 293T
    suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
    Recombinant DNA
    SentencesResources
    RNA purification and preparation: The DNA sequence of each NRC (NRC1-12) was cloned into pUT7 vector bearing the T7 RNA polymerase promoter82 and was amplified by PCR with pfu DNA polymerase, which was used as the templates for transcription.
    pUT7
    suggested: None
    Software and Algorithms
    SentencesResources
    Mass spectrometry data were searched by MaxQuant (Version 1.6.10.43).
    MaxQuant
    suggested: (MaxQuant, RRID:SCR_014485)
    Protein domain enrichment analysis was carried out using the STRING web interface (https://string-db.org/)87.
    STRING
    suggested: (STRING, RRID:SCR_005223)
    Cytoscape software (version 3.8.2)29 was applied to visualize the network.
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Limitations of the study: MAMS method is an in vitro binding assay. The rationale was to limit the impact of viral proteins associated with infection experiments, but the expression of host proteins could change during infection. Some interactions may be missing as the proteins may not be present without prolonged infection. We also did not validate all ncrRNA-protein interaction in vivo and in all cell lines. In addition, we revealed several potential therapeutic targets, but future investigations of these targets are needed to verify.

    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.

    About SciScore

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  2. Version published to 10.1101/2021.06.19.449092v1 on bioRxiv