Dual regulation of the receptor-like kinase BIR1 involves site-directed transcript cleavage and 5-leader-mediated translational control

In Arabidopsis, receptor-like kinase 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 silencing. Degradome analysis 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 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. Cleavage events are highly localized, occurring at a limited number of sites that involve only a few siRNAs. 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 long non-coding RNA (lncRNA) derived from the natural antisense At4g39838 locus. This lncRNA is complementary to a TCA-rich repeat region encompassing cleavage site A, which may serve as a putative binding site. 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.