Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden.
BMC Biol. 2024 Sep 30;22(1):219. doi: 10.1186/s12915-024-02014-9.
Small RNA (sRNAs)- mediated RNA silencing is emerging as a key player in host-microbe interactions. However, its role in fungus-plant interactions relevant to biocontrol of plant diseases is yet to be explored. This study aimed to investigate Dicer (DCL)-mediated endogenous and cross-kingdom gene expression regulation in the biocontrol fungus Clonostachys rosea and wheat roots during interactions.
C. rosea Δdcl2 strain exhibited significantly higher root colonization than the WT, whereas no significant differences were observed for Δdcl1 strains. Dual RNA-seq revealed the upregulation of CAZymes, membrane transporters, and effector coding genes in C. rosea, whereas wheat roots responded with the upregulation of stress-related genes and the downregulation of growth-related genes. The expression of many of these genes was downregulated in wheat during the interaction with DCL deletion strains, underscoring the influence of fungal DCL genes on wheat defense response. sRNA sequencing identified 18 wheat miRNAs responsive to C. rosea, and three were predicted to target the C. rosea polyketide synthase gene pks29. Two of these miRNAs (mir_17532_x1 and mir_12061_x13) were observed to enter C. rosea from wheat roots with fluorescence analyses and to downregulate the expression of pks29, showing plausible cross-kingdom RNA silencing of the C. rosea gene by wheat miRNAs.
We provide insights into the mechanisms underlying the interaction between biocontrol fungi and plant roots. Moreover, the study sheds light on the role of sRNA-mediated gene expression regulation in C. rosea-wheat interactions and provides preliminary evidence of cross-kingdom RNA silencing between plants and biocontrol fungi.
小 RNA（sRNAs）介导的 RNA 沉默在宿主-微生物相互作用中崭露头角，成为关键因素。然而，其在与植物疾病生物防治相关的真菌-植物相互作用中的作用仍有待探索。本研究旨在研究生物防治真菌粉红粘帚霉（Clonostachys rosea）及其与小麦根互作过程中 Dicer（DCL）介导的内源性和跨物种基因表达调控。
与野生型相比，Δdcl2 突变株在根定殖方面表现出显著优势，而 Δdcl1 突变株则无明显差异。双 RNA-seq 揭示了 C. rosea 中 CAZymes、膜转运蛋白和效应编码基因的上调，而小麦根则对与胁迫相关基因的上调和与生长相关基因的下调作出响应。在与 DCL 缺失菌株的相互作用中，许多这些基因在小麦中表达下调，这突显了真菌 DCL 基因对小麦防御反应的影响。sRNA 测序鉴定出 18 个响应 C. rosea 的小麦 miRNA，其中 3 个被预测靶向 C. rosea 的聚酮合酶基因 pks29。通过荧光分析观察到其中两个 miRNA（mir_17532_x1 和 mir_12061_x13）从小麦根进入 C. rosea，并下调 pks29 的表达，表明小麦 miRNA 对 C. rosea 基因进行了跨物种 RNA 沉默。
本研究为生物防治真菌与植物根相互作用的机制提供了新的见解。此外，本研究揭示了 sRNA 介导的基因表达调控在 C. rosea-小麦相互作用中的作用，并为植物和生物防治真菌之间的跨物种 RNA 沉默提供了初步证据。
