When the heat is on, HYL1 steps in: Regulating miRNA biogenesis for plant thermotolerance

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Changes in environmental temperature are a major source of stress for plants. Plants have evolved various adaptive strategies that combat heat stress (HS) and mitigate potential negative effects on development and productivity. One such strategy involves microRNAs (miRNAs), small single-stranded RNAs, typically 21 nucleotides long, that play key regulatory roles, primarily through post-transcriptional gene silencing. In this process, miRNAs, once loaded into a protein complex, recognize target transcripts, leading to their cleavage and subsequent degradation (Huntzinger and Izaurralde 2011).

While specific miRNAs have been linked to HS responses, Yiming Cao, Jiaxin Zhang, and colleagues (Cao et al. 2025) set out to explore the broader, global role of miRNAs in plant adaptation to HS, using Arabidopsis (A. thaliana) as a model organism. Their findings reveal that most miRNAs are upregulated under HS, leading to the downregulation of their target genes. However, an intriguing observation emerged: pri-miRNA (hairpin-folded primary miRNA transcript) levels did not follow the same pattern.

MicroRNA synthesis is a multi-step process. In the nucleus, the core microprocessor complex comprising DICER-LIKE1 (DCL1), SERRATE (SE), and HYPONASTIC LEAVES 1 (HYL1) recognizes pri-miRNAs and processes them into mature miRNAs (Mencia et al. 2023). The observed discrepancy between pri-miRNA and mature miRNA levels suggests that HS may influence the global miRNA biogenesis pathway rather than just individual miRNAs.

A closer look at the miRNA biogenesis pathway revealed a surprising finding: although overall HYL1 levels decreased under HS, its nuclear localization increased. The routing of HYL1 to the nucleus led to greater binding to pri-miRNAs in HS-treated plants, which could explain the higher miRNA accumulation due to increased microprocessor activity. Furthermore, mutants with defects in the microprocessor displayed greater sensitivity to HS than wild-type plants, underscoring the crucial role of miRNA biogenesis in HS responses.

It was previously shown that nuclear localization of HYL1 is orchestrated by its phosphorylation state (Gonzalo et al. 2024). This led the authors to investigate whether HS could affect HYL1 phosphorylation, thereby triggering increased miRNA biogenesis. Analysis of mutant plants carrying a nonphosphorylated version of HYL1 revealed reduced nuclear localization, lower miRNA induction, and increased sensitivity to HS, further supporting the central role of HYL1 phosphorylation in the HS response.

HYL1 phosphorylation is regulated by the dynamic balance between the phosphatase CPL1 and the kinase MPK3 (Gonzalo et al. 2024). In their study, Cao et al. (2025) examined the interaction between CPL1 and MPK3, determining that the 2 proteins physically interact. Additionally, they found that MPK3 phosphorylates CPL1, regulating its stability. Interestingly, mutants lacking CPL1 exhibited increased MPK3 kinase activity, suggesting a reciprocal regulatory mechanism between these 2 proteins (Figure). Moreover, when analyzing mutant plants lacking MPK3, they observed increased nuclear accumulation of HYL1, higher miRNA abundance, and enhanced tolerance to HS. Overall, the work by Cao et al. provides valuable insights into the role of miRNA biogenesis in HS adaptation, shedding light on the regulation of HYL1 and its contribution to plant stress responses.

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