Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125, Torino, Italy.
Institute for Sustainable Plant Protection - CNR Torino, Strada delle Cacce 73, 10131, Torino, Italy.
BMC Genomics. 2019 Mar 4;20(1):169. doi: 10.1186/s12864-019-5561-0.
Small RNAs (sRNAs) are short non-coding RNA molecules (20-30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA interference (RNAi). Recent studies have highlighted that they are also involved in cross-kingdom communication: sRNAs can move across the contact surfaces from "donor" to "receiver" organisms and, once in the host cells of the receiver, they can target specific mRNAs, leading to a modulation of host metabolic pathways and defense responses. Very little is known about RNAi mechanism and sRNAs occurrence in Arbuscular Mycorrhizal Fungi (AMF), an important component of the plant root microbiota that provide several benefits to host plants, such as improved mineral uptake and tolerance to biotic and abiotic stress.
Taking advantage of the available genomic resources for the AMF Rhizophagus irregularis we described its putative RNAi machinery, which is characterized by a single Dicer-like (DCL) gene and an unusual expansion of Argonaute-like (AGO-like) and RNA-dependent RNA polymerase (RdRp) gene families. In silico investigations of previously published transcriptomic data and experimental assays carried out in this work provided evidence of gene expression for most of the identified sequences. Focusing on the symbiosis between R. irregularis and the model plant Medicago truncatula, we characterized the fungal sRNA population, highlighting the occurrence of an active sRNA-generating pathway and the presence of microRNA-like sequences. In silico analyses, supported by host plant degradome data, revealed that several fungal sRNAs have the potential to target M. truncatula transcripts, including some specific mRNA already shown to be modulated in roots upon AMF colonization.
The identification of RNAi-related genes, together with the characterization of the sRNAs population, suggest that R. irregularis is equipped with a functional sRNA-generating pathway. Moreover, the in silico analysis predicted 237 plant transcripts as putative targets of specific fungal sRNAs suggesting that cross-kingdom post-transcriptional gene silencing may occur during AMF colonization.
小 RNA（sRNA）是一类短的非编码 RNA 分子（20-30nt），通过 RNA 干扰（RNAi）机制，在许多真核生物中调节转录或转录后水平的基因表达。最近的研究表明，它们也参与了跨界交流：sRNA 可以通过“供体”到“受体”生物体的接触表面移动，一旦进入受体生物的宿主细胞，它们就可以靶向特定的 mRNA，导致宿主代谢途径和防御反应的调节。关于 RNAi 机制和丛枝菌根真菌（AMF）中 sRNA 的发生，人们知之甚少。AMF 是植物根微生物组的一个重要组成部分，为宿主植物提供了多种益处，例如改善矿物质吸收和对生物和非生物胁迫的耐受。
利用 AMF 泡囊丛枝菌 Rhizophagus irregularis 的可用基因组资源，我们描述了其假定的 RNAi 机制，该机制的特征是单个 Dicer-like（DCL）基因和 Argonaute-like（AGO-like）和 RNA 依赖性 RNA 聚合酶（RdRp）基因家族的不寻常扩张。对先前发表的转录组数据的计算机分析和本工作中进行的实验研究提供了大多数鉴定序列的基因表达证据。关注 R. irregularis 与模式植物 Medicago truncatula 之间的共生关系，我们描述了真菌 sRNA 群体，突出了活性 sRNA 生成途径的发生和 microRNA 样序列的存在。计算机分析，得到宿主植物降解组数据的支持，揭示了一些真菌 sRNA 可能靶向 M. truncatula 转录物，包括一些已经在 AMF 定植后根中被证明被调节的特定 mRNA。
RNAi 相关基因的鉴定，以及 sRNA 群体的特征，表明 R. irregularis 具有功能齐全的 sRNA 生成途径。此外，计算机分析预测了 237 个植物转录物作为特定真菌 sRNA 的潜在靶标，表明在 AMF 定植过程中可能发生跨界转录后基因沉默。
