Specificity and Mechanism of Coronavirus, Rotavirus, and Mammalian Two-Histidine Phosphoesterases That Antagonize Antiviral Innate Immunity

  1. Abhishek Asthana
  2. Christina Gaughan
  3. Beihua Dong
  4. Susan R. Weiss
  5. Robert H. Silverman

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Viruses often encode accessory proteins that antagonize the host antiviral immune response. Here, we probed the evolutionary relationships and biochemical activities of two-histidine phosphoesterases (2H-PEs) that allow some coronaviruses and rotaviruses to counteract antiviral innate immunity.

Article activity feed

  1. Version published to 10.1128/mbio.01781-21
  2. ScreenIT

    SciScore for 10.1101/2021.06.16.448777: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Recombinant DNA
    SentencesResources
    cDNA cloning and plasmids: Human PDE12 cDNA was PCR amplified (using DNASU cDNA clone HsCD00296464 in vector pDONR221, GenBank: NM_177966.5) with forward primer 5’- TTCAAgaattcATGTGGAGGCTCCCAGGCGC-3’ (with an EcoRI restriction site) and the reverse primer 5’- TTCAAgtcgacTCATTTCCATTTTAAATCACATACAAGTGCTATGTGATC-3’ (with a SalI restriction site).
    pDONR221
    suggested: RRID:Addgene_63743)
    PDE12E351A pGEX 6P-1 mutant (34) plasmid was constructed by MegaPrimer method (50) using mutagenic reverse primer 5’- GCGCGGTCAACCgCCTGCAAACAG-3’.
    pGEX 6P-1
    suggested: None
    The cDNAs were PCR amplified and cloned into plasmid pMAL-C5X at the XmnI (blunt cloned) and NcoI (sticky end) restriction site.
    pMAL-C5X
    suggested: RRID:Addgene_66999)
    Protein expression and purification: Proteins were expressed from pGEX-6P-1 or pMAL constructs in E. coli strain BL21(DE3)/pLysS
    pGEX-6P-1
    suggested: None
    pMAL
    suggested: RRID:Addgene_161783)
    Software and Algorithms
    SentencesResources
    The mass spectrometer was coupled to the outlet of HPLC system that consisted of an UHPLC system (Vanquish, Thermos Fisher Scientific, USA)
    Thermos Fisher Scientific
    suggested: None
    The Xcalibur software was used for data processing.
    Xcalibur
    suggested: (Thermo Xcalibur, RRID:SCR_014593)
    Bioinformatic Analysis: The PDE domain sequences from different 2’,5’-PEs were used for creating a multiple sequence alignment using MAFFT version 7 (54) employing iterative refinement method E-INS-I (https://mafft.cbrc.jp/alignment/server/).
    Bioinformatic
    suggested: (QFAB Bioinformatics, RRID:SCR_012513)
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The MAFFT sequence alignment result was downloaded in clustal format and visualized using Jalview 2.11.1.3 software.
    Jalview
    suggested: (Jalview, RRID:SCR_006459)

    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: 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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.06.16.448777v1 on bioRxiv