{ "abstract": "In Arabidopsis, BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-INTERACTING RECEPTOR-LIKE KINASE 1 (BIR1) is a negative regulator of plant immunity and cell death. BIR1 was earlier described as a target of epigenetic and post-transcriptional degradation. During virus infections, degradome analysis of BIR1 transcripts mapped predominant mRNA cleavage sites at the 5’-untranslated leader region (site A) and the protein-coding sequence (sites B and C). Here, we identified another virus-associated cleavage site (D) within the BIR1 coding region and investigated the contribution of site-directed mRNA cleavage to BIR1 regulation. Mutations at B, C, and D sites enhanced mRNA stability by impairing transcript cleavage, resulting in increased BIR1 mRNA and protein accumulation. This regulation is disrupted in RNA silencing mutants, supporting a model of cis-directed small interfering RNA (siRNA)-mediated degradation. We next demonstrate that virus infection reduces BIR1 translation in Arabidopsis. Furthermore, our data reveal a repressive role for the 5’-leader in regulating BIR1 translation, potentially mediated by upstream open reading frames (uORFs) and a virus-responsive long non-coding RNA (lncRNA) derived from the natural antisense At4g39838 locus. Together, these findings reveal a multilayered regulatory mechanism that integrates sRNA-mediated cleavage with translational control, with broader implications for the fine-tuning of stress-responsive gene expression during infection. Author summary: Plants must tightly control immune responses to ensure effective defense while avoiding immune-associated self-damage. In Arabidopsis thaliana, the receptor-like kinase BIR1 functions as a negative regulator of multiple immune resistance pathways. Previous reports have shown that misregulation of BIR1 leads to cell-death-like phenotypes, underscoring the need for precise control of its expression. However, the mechanisms governing BIR1 expression have remained largely unexplored. Here, we show that BIR1 transcripts are subject to post-transcriptional gene silencing and, through mutational analysis, identify the precise cleavage sites involved. In addition, we demonstrate that virus infection compromises BIR1 translation efficiency and reveal a previously uncharacterized translational control mechanism mediated by the BIR1 5’- leader, involving the combined action of multiple upstream open reading frames and a virus-responsive long non-coding RNA derived from the antisense At4g39838 locus. These findings reveal an unexpected and sophisticated regulatory architecture controlling BIR1 expression, with potential relevance for the broader BIR receptor family and plant immune signaling networks.", "abstract_shown": true, "affiliations": [ "Centro de Investigaciones Biológicas Margarita Salas. Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain", "Doctorado en Biotecnología y Recursos Genéticos de Plantas y Microorganismos Asociados, Universidad Politécnica de Madrid, Madrid, Spain", "Department of Plant Molecular Genetics. Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin, Madrid, Spain", "State Key Laboratory of Hybrid Rice, Hubei Provincial Research Center for Basic Biological Sciences, Hubei Hongshan Laboratory, RNA Institute, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei, China", "Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Boulevard Louis Pasteur, Málaga, Spain" ], "article_type": "Research Article", "arxiv": null, "author_total": 9, "authors": [ { "affs": [ 0 ], "name": "Irene Guzmán-Benito" }, { "affs": [ 1 ], "name": "Carmen Robinson" }, { "affs": [ 2 ], "name": "Livia Donaire" }, { "affs": [ 3 ], "name": "Lourdes Fernández-Calvino" }, { "affs": [ 4 ], "name": "José Manuel Franco-Zorrilla" }, { "name": "Ruixia Niu" }, { "name": "Guoyong Xu" }, { "name": "Catharina Merchante" }, { "name": "César Llave" } ], "bibtex": "https://research.draconitic.com/paper/9ypvqce6ykvng.bib", "cited_by": 0, "doi": "10.1371/journal.ppat.1014571", "fulltext_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014571", "id": "9ypvqce6ykvng", "issns": [ "1553-7374" ], "landing_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014571", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1110|Plant Virus Research Studies" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/Messenger RNA" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/Non-coding RNA/Long non-coding RNA" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/Non-coding RNA/Small interfering RNA" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/RNA interference" ], [ "plos", "/Biology and life sciences/Genetics/Epigenetics/RNA interference" ], [ "plos", "/Biology and life sciences/Genetics/Gene expression/Gene regulation/Small interfering RNA" ], [ "plos", "/Biology and life sciences/Genetics/Gene expression/Protein translation" ], [ "plos", "/Biology and life sciences/Genetics/Gene expression/RNA interference" ], [ "plos", "/Biology and life sciences/Genetics/Genetic interference/RNA interference" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Plants/Brassica/Arabidopsis thaliana" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Plants/Flowering plants/Nicotiana" ], [ "plos", "/Biology and life sciences/Plant science/Plant anatomy/Leaves" ], [ "plos", "/Research and analysis methods/Animal studies/Experimental organism systems/Model organisms/Arabidopsis thaliana" ], [ "plos", "/Research and analysis methods/Animal studies/Experimental organism systems/Plant and algal models/Arabidopsis thaliana" ], [ "plos", "/Research and analysis methods/Model organisms/Arabidopsis thaliana" ] ], "openalex": "W7213293341", "pdf_url": "https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1014571&type=printable", "pmcid": null, "pmid": null, "published": "2026-09-15", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/9ypvqce6ykvng.ris", "sources": [ { "first_seen": "2026-10-30T12:17:49Z", "native_id": "10.1371/journal.ppat.1014571", "source": "plos", "url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014571" } ], "subjects": [ { "field": "biochemistry", "origin": "plos:gene expression", "subfield": "molecular-biology" }, { "field": "biology", "origin": "plos:genetics", "subfield": "genetics-genomics" } ], "title": "Dual regulation of the receptor-like kinase BIR1 involves site-directed transcript cleavage and 5’-leader-mediated translational control", "title_text": "Dual regulation of the receptor-like kinase BIR1 involves site-directed transcript cleavage and 5’-leader-mediated translational control", "type": "peer-reviewed", "updated_at": "2026-10-30T12:17:49Z", "url": "https://research.draconitic.com/paper/9ypvqce6ykvng", "venue": "PLOS Pathogens", "versions": [] }