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<article article-type="brief-report" xmlns:xlink="http://www.w3.org/1999/xlink">
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>microPublication Biology</journal-title>
      </journal-title-group>
      <issn pub-type="epub">2578-9430</issn>
      <publisher>
        <publisher-name>Caltech Library</publisher-name>
      </publisher>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.17912/micropub.biology.000953</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>new finding</subject>
        </subj-group>
        <subj-group subj-group-type="subject">
          <subject>methods</subject>
        </subj-group>
        <subj-group subj-group-type="subject">
          <subject>genetic screens</subject>
        </subj-group>
        <subj-group subj-group-type="species">
          <subject>bombyx mori</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>A method for screening the suppressor genes of siRNA and piRNA pathways using cultured silkworm cells</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author" equal-contrib="yes">
          <name>
            <surname>Sugiyama</surname>
            <given-names>Haruka</given-names>
          </name>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Investigation" vocab-term-identifier="https://credit.niso.org/contributor-roles/investigation">Investigation</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Writing - review &amp; editing" vocab-term-identifier="https://credit.niso.org/contributor-roles/Writing-review-editing">Writing - review &amp; editing</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Formal analysis" vocab-term-identifier="https://credit.niso.org/contributor-roles/formal-analysis">Formal analysis</role>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author" equal-contrib="yes">
          <name>
            <surname>Katsuma</surname>
            <given-names>Susumu</given-names>
          </name>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Conceptualization" vocab-term-identifier="https://credit.niso.org/contributor-roles/onceptualization">Conceptualization</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Formal analysis" vocab-term-identifier="https://credit.niso.org/contributor-roles/formal-analysis">Formal analysis</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Funding acquisition" vocab-term-identifier="https://credit.niso.org/contributor-roles/funding-acquisition">Funding acquisition</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Investigation" vocab-term-identifier="https://credit.niso.org/contributor-roles/investigation">Investigation</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Methodology" vocab-term-identifier="https://credit.niso.org/contributor-roles/methodology">Methodology</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Supervision" vocab-term-identifier="https://credit.niso.org/contributor-roles/supervision">Supervision</role>
          <role vocab="credit" vocab-identifier="https://credit.niso.org/" vocab-term="Writing - original draft" vocab-term-identifier="https://credit.niso.org/contributor-roles/writing-original-draft">Writing - original draft</role>
          <xref ref-type="aff" rid="aff1">1</xref>
          <xref ref-type="corresp" rid="cor1">§</xref>
        </contrib>
        <aff id="aff1">
          <label>1</label>
          Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
        </aff>
      </contrib-group>
      <contrib-group>
        <contrib contrib-type="reviewer">
          <anonymous/>
        </contrib>
      </contrib-group>
      <author-notes>
        <corresp id="cor1">
          <label>§</label>
          Correspondence to: Susumu Katsuma (
          <email>skatsuma@g.ecc.u-tokyo.ac.jp</email>
          )
        </corresp>
        <fn fn-type="coi-statement">
          <p>The authors declare that there are no conflicts of interest present.</p>
        </fn>
      </author-notes>
      <pub-date date-type="pub" publication-format="electronic">
        <day>15</day>
        <month>9</month>
        <year>2023</year>
      </pub-date>
      <pub-date date-type="collection" publication-format="electronic">
        <year>2023</year>
      </pub-date>
      <volume>2023</volume>
      <elocation-id>10.17912/micropub.biology.000953</elocation-id>
      <history>
        <date date-type="received">
          <day>14</day>
          <month>8</month>
          <year>2023</year>
        </date>
        <date date-type="rev-recd">
          <day>30</day>
          <month>8</month>
          <year>2023</year>
        </date>
        <date date-type="accepted">
          <day>29</day>
          <month>8</month>
          <year>2023</year>
        </date>
      </history>
      <permissions>
        <copyright-statement>Copyright: © 2023 by the authors</copyright-statement>
        <copyright-year>2023</copyright-year>
        <license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/">
          <license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
        </license>
      </permissions>
      <abstract>
        <p>
          The BmN-4 cell line originates from the ovaries of silkworm, 
          <italic>Bombyx mori</italic>
          , and possesses endogenous small interfering RNA (siRNA) and PIWI-interacting RNA (piRNA) pathways. BmN-4 cells are latently infected with 
          <italic>Bombyx mori latent virus</italic>
           (BmLV), an RNA virus whose replication is strictly controlled by both siRNA and piRNA pathways. Knockdown or knockout of the core factors of these two small RNA pathways increases BmLV RNA amount, which in turn inhibits cell growth. Here, we used the known RNAi suppressor CrPV-1A to assess whether the BmN-4 cell line can be used for screening the suppressors of siRNA and piRNA pathways.
        </p>
      </abstract>
      <funding-group>
        <funding-statement>This work was supported by JSPS KAKENHI 17H06431.</funding-statement>
      </funding-group>
    </article-meta>
  </front>
  <body>
    <fig position="anchor" id="f1">
      <label>
        Figure 1. 
        <bold>A screening method of the suppressors of small RNA pathways using cultured silkworm cells</bold>
      </label>
      <caption>
        <p>(A) An experimental flow.</p>
        <p>
          (B) RT-qPCR results for the BmLV 
          <italic>cp</italic>
           and 
          <italic>rdrp</italic>
           genes. BmN-4 cells were transfected with a plasmid expressing GFP- or CrPV-1A, cultured in zeocin-containing medium, and then subjected to RT-qPCR of two BmLV genes. The 
          <italic>cp</italic>
           and 
          <italic>rdrp</italic>
           mRNA levels were normalized to that of 
          <italic>B. mori</italic>
          <italic>rp49</italic>
          . The data are shown as means ± standard deviation of three independent experiments. 
          <italic>p</italic>
          -values were calculated via one sample 
          <italic>t</italic>
           test (two-tailed).
        </p>
        <p>(C) Fluorescence microscopy of BmN-4 cells stably expressing GFP or CrPV-1A. The scale bar represents 100 μm.</p>
      </caption>
      <graphic xlink:href="25789430-2023-micropub.biology.000953"/>
    </fig>
    <sec>
      <title>Description</title>
      <p>
        Cultured cell lines are an important biological resource for producing recombinant proteins and evaluating gene function. The silkworm 
        <italic>Bombyx mori </italic>
        cell line BmN-4 is a well-known ovary-derived cell line 
        <xref ref-type="bibr" rid="R1">(Grace, 1967)</xref>
         that has been routinely used for protein production by a baculovirus expression system 
        <xref ref-type="bibr" rid="R9">(Maeda et al. 1985)</xref>
        . In 2009, our group identified PIWI proteins and PIWI-interacting RNAs (piRNAs) that were endogenously expressed in BmN-4 cells. This was the first discovery of a cultured cell line that expressed PIWI/piRNA complexes 
        <xref ref-type="bibr" rid="R7">(Kawaoka et al. 2009)</xref>
        . Many groundbreaking studies involving piRNA factors used this piRNA-producing cell line 
        <xref ref-type="bibr" rid="R7">(Kawaoka et al. 2011; Izumi et al. 2020; Matsumoto et al. 2016)</xref>
        , and it has become a valuable resource for small RNA research 
        <xref ref-type="bibr" rid="R12">(Tsukioka et al. 2006; Kawaoka et al. 2009)</xref>
        .
      </p>
      <p>
        <italic>Bombyx mori latent virus</italic>
         (formerly known as 
        <italic>Bombyx mori macula-like virus</italic>
        , BmMLV) is a positive, single-stranded insect RNA virus that is closely related to plant maculaviruses. BmLV was first discovered in BmN-4 cells, and has been found to infect almost all 
        <italic>B. mori</italic>
        -derived cultured cell lines 
        <xref ref-type="bibr" rid="R4">(Katsuma et al. 2005)</xref>
        . Surprisingly, BmLV accumulates to extremely high levels (approximately 15% of total mRNA) in BmN-4 cells 
        <xref ref-type="bibr" rid="R4">(Katsuma et al. 2018)</xref>
        . Knockdown or knockout of the core biogenesis genes for either small interfering RNA (siRNA) and piRNA revealed that disruption of these small RNA pathways results in increased BmLV accumulation and inhibition of BmN-4 cell growth 
        <xref ref-type="bibr" rid="R4">(Katsuma et al. 2018; Katsuma et al. 2021)</xref>
        . These findings show that the siRNA and piRNA pathways function cooperatively to silence BmLV RNA and that both pathways are required for the normal growth of BmLV-infected silkworm cells.
      </p>
      <p>
        In this study, we tested whether BmN-4 cells can be used to assess the suppressor activity of foreign genes by measuring the expression levels of BmLV genes and observing the degree of inhibition of cell growth. We selected the cricket paralysis virus 1A protein (CrPV-1A) gene as the suppressor gene. CrPV-1A has been found to inhibit Ago2-dependent RNAi via blocking the initial target searching by Ago2-RISC 
        <xref ref-type="bibr" rid="R13">(Watanabe et al. 2017; Nayak et al. 2018)</xref>
        .
      </p>
      <p>
        First, we cloned 
        <italic>CrPV-1A</italic>
         into the vector, pIZ/His-V5-g3, so that the cloned gene would be expressed under the control of the 
        <italic>B. mori hsp90</italic>
         promoter 
        <xref ref-type="bibr" rid="R2">(Hirota et al., 2021)</xref>
        . Next, pIZ/His-V5-g3-CrPV-1A or pIZ/His-V5-g3-GFP (i.e., control vector) was transfected into BmN-4 cells and treated with zeocin from 3 days after transfection (
        <xref ref-type="fig" rid="f1">Fig. 1A</xref>
        ). Selection was conducted for 9 days, after which cells were photographed and then collected for RNA isolation (
        <xref ref-type="fig" rid="f1">Fig. 1A</xref>
        ). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments revealed that CrPV-1A expression increased the mRNA levels of two BmLV genes, 
        <italic>coat protein</italic>
         (
        <italic>cp</italic>
        ) and 
        <italic>RNA-dependent RNA polymerase</italic>
         (
        <italic>rdrp</italic>
        ) (
        <xref ref-type="fig" rid="f1">Fig. 1B</xref>
        ), suggesting that CrPV-1A may block one or both of the siRNA and piRNA pathways. In addition, CrPV-1A expression also strongly inhibited the cell growth of BmN-4 cells (
        <xref ref-type="fig" rid="f1">Fig. 1C</xref>
        ). Taken together, these results demonstrate that BmN-4 cells can be used for a simple screening system to identify novel putative suppressors of the siRNA and/or piRNA pathways.
      </p>
    </sec>
    <sec>
      <title>Methods</title>
      <p>
        <bold>Cell line</bold>
      </p>
      <p>
        BmN-4 cells (provided by Chisa Yasunaga-Aoki, Kyushu University, and maintained in our laboratory) 
        <xref ref-type="bibr" rid="R9">(Maeda et al. 1985)</xref>
         were cultured at 27°C in IPL-41 medium (Applichem) supplemented with 10% fetal bovine serum.
      </p>
      <p>
        <bold>Plasmid construction</bold>
      </p>
      <p>
        A CrPV-1A fragment was amplified from pCold II-CrPV-1A (provided by Yukihide Tomari) 
        <xref ref-type="bibr" rid="R13">(Watanabe et al. 2017)</xref>
        . This fragment was then cloned into the vector pIZ/V5-His-g3 
        <xref ref-type="bibr" rid="R2">(Hirota et al., 2021)</xref>
         using the In-Fusion HD Cloning Kit (Clontech). pIZ/V5-His-g3-GFP 
        <xref ref-type="bibr" rid="R2">(Hirota et al., 2021)</xref>
         was used as a control.
      </p>
      <p>
        <bold>Transfection and generation of stably transfected BmN-4 cells</bold>
      </p>
      <p>
        BmN-4 cells (2 × 10
        <sup>5</sup>
         cells per 35 mm dish) were transfected with 1 µg of pIZ/V5-His-g3-GFP or pIZ/V5-His-g3-GFP-CrPV-1A using FuGENE HD (Promega). Three days after transfection, zeocin (InvivoGen, final concentration of 500 µg/mL) was added to the medium 
        <xref ref-type="bibr" rid="R7">(Kawaoka et al. 2009)</xref>
        . Nine days after drug selection, cells were observed using a FLoid
        <sup>TM</sup>
         cell imaging station (Life Technologies). Thereafter they were collected for RNA extraction.
      </p>
      <p>
        <bold>RT-qPCR</bold>
      </p>
      <p>
        Total RNA was isolated using TRI Reagent® (Sigma-Aldrich) and then subjected to reverse transcription with avian myeloblastosis virus reverse transcriptase and an oligo-dT primer (TaKaRa). RT-qPCR was performed using a KAPA SYBR FAST qPCR kit (Kapa Biosystems) and the specific primers. The expression values were calculated using the 2
        <sup>−ΔΔCt</sup>
         method.
      </p>
    </sec>
    <sec>
      <title>Reagents</title>
      <p>PCR primers for CrPV-1A</p>
      <p>CrPV1A-f: TACCGAGCTCGGATCatgtcttttcaacaaacaaacaacaacgc</p>
      <p>CrPV1A-r: GCCACTGTGCTGGATctagaaggctctgcattcatcattac</p>
      <p>
        qPCR primers for BmLV 
        <italic>cp</italic>
      </p>
      <p>coat-2F: TCCTCTCGCATTACTATTGG</p>
      <p>coat-2R: ATGGAGCCTCTGATGACAAC</p>
      <p>
        qPCR primers for BmLV 
        <italic>rdrp</italic>
      </p>
      <p>rdrp-2F: TCTCTCATGAAATCAGCACC</p>
      <p>rdrp-2R: TCACGATATGGTTTGAGATG</p>
      <p>
        qPCR primers for 
        <italic>B. mori rp49</italic>
      </p>
      <p>rp49-F: CCCAACATTGGTTACGGTTC</p>
      <p>rp49-R: GCTCTTTCCACGATCAGCTT</p>
    </sec>
  </body>
  <back>
    <ack>
      <sec>
        <title>Acknowledgments</title>
        <p>We thank H. Hikida and N. Matsuda-Imai for technical assistance, C. Yasunaga-Aoki for providing BmN-4 cells, and Y. Tomari for providing pCold II-CrPV-1A.</p>
      </sec>
    </ack>
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