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Background <p>The development and functioning of root nodules in legumes are regulated by a cascade of gene expression events involving early and late nodulins. Early nodulins participate in infection and cortical cell division, whereas late nodulins support mature nodule function. Previously, a unique late nodulin gene, <i>LjPLP-IV</i> (<i>Lotus japonicus</i> phosphatidylinositol transfer protein-like protein IV), was identified. This gene contains a bidirectional promoter (BiP) within its tenth intron that drives the expression of both an antisense RNA and another late nodulin transcript. However, the antisense transcript remained largely unexplored.</p> Methods and Results <p>In this study, we characterized a novel long non-coding RNA, <i>LjPLR</i> (<i>L. japonicus</i> PLP-IV lncRNA), through strand-specific transcriptome analysis of <i>L. japonicus</i> nodules. Sequence alignment revealed that <i>LjPLR</i> is highly complementary to the sense strand of <i>LjPLP-IV</i>, with its first exon aligning precisely at the tenth exon–intron boundary of the <i>LjPLP-IV</i> gene. These results strongly suggest that <i>LjPLR</i> corresponds to the previously reported antisense RNA transcribed from the BiP. Real-time PCR analysis further demonstrated an inverse temporal expression pattern between <i>LjPLR</i> and <i>LjPLP-IV</i> during nodule development.</p> Conclusion <p>Together with <i>in silico </i><i>target prediction</i> analyses, our findings indicate that <i>LjPLP-IV</i> is the sole putative target of <i>LjPLR</i>. We therefore hypothesize that <i>LjPLR</i> likely regulates <i>LjPLP-IV</i>, a gene implicated in rhizobial infection of root cortical cells in <i>L. japonicus</i>. Collectively, these results provide novel insight into the regulatory landscape underlying symbiotic nitrogen fixation in <i>L. japonicus</i>.</p>

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An intronic bidirectional promoter–driven lncRNA (LjPLR) putatively modulates a late nodulin gene during nodulation in Lotus japonicus

  • 期刊论文

  • 发表日期：

    2026年3月19日

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  • Aniruddho Das,
  • Troyee Das,
  • Zhumur Ghosh,
  • Anirban Siddhanta

摘要

Background

The development and functioning of root nodules in legumes are regulated by a cascade of gene expression events involving early and late nodulins. Early nodulins participate in infection and cortical cell division, whereas late nodulins support mature nodule function. Previously, a unique late nodulin gene, LjPLP-IV (Lotus japonicus phosphatidylinositol transfer protein-like protein IV), was identified. This gene contains a bidirectional promoter (BiP) within its tenth intron that drives the expression of both an antisense RNA and another late nodulin transcript. However, the antisense transcript remained largely unexplored.

Methods and Results

In this study, we characterized a novel long non-coding RNA, LjPLR (L. japonicus PLP-IV lncRNA), through strand-specific transcriptome analysis of L. japonicus nodules. Sequence alignment revealed that LjPLR is highly complementary to the sense strand of LjPLP-IV, with its first exon aligning precisely at the tenth exon–intron boundary of the LjPLP-IV gene. These results strongly suggest that LjPLR corresponds to the previously reported antisense RNA transcribed from the BiP. Real-time PCR analysis further demonstrated an inverse temporal expression pattern between LjPLR and LjPLP-IV during nodule development.

Conclusion

Together with in silico target prediction analyses, our findings indicate that LjPLP-IV is the sole putative target of LjPLR. We therefore hypothesize that LjPLR likely regulates LjPLP-IV, a gene implicated in rhizobial infection of root cortical cells in L. japonicus. Collectively, these results provide novel insight into the regulatory landscape underlying symbiotic nitrogen fixation in L. japonicus.